Underutilised and Neglected Crops: Next Generation Sequencing Approaches for Crop Improvement and Better Food Security



This review illustrates how NGS-derived information can be used to tailor genomic tools for different needs and applications to non-model crop improvement, and how such developments should assist in a better understanding of regulatory pathways and traits responsible for adaptation and domestication. Current over-reliance on a few major staple crops in agriculture has inherent agronomic, ecological and economic risks, is probably unsustainable in the long term, and the risks to crop and world food security is an urgent issue which needs to be addressed at both the scientific and social levels.


Crop improvement Food security Next generation sequencing (NGS) Underutilised (neglected) crops 


  1. Aflitos SA, Schijlen E, Finkers R, Smit S, Wang J, Zhang G et al (2014) Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J 80:136–148PubMedGoogle Scholar
  2. Ahmad P, Ashraf M, Younis M, Hu X, Kumar A, Akram NA, Al-Quariny F (2012) Role of transgenic plants in agriculture and biopharming. Biotechnol Adv 30:524–540PubMedGoogle Scholar
  3. Aker JC (2011) Dial “a” for agriculture: a review of information and communication technologies for agricultural extension in developing countries. Tufts University, Economics Department and Fletcher School, Medford, p 37Google Scholar
  4. Akula S, Miriyala R, Thota H, Rao A, Gedela S (2009) Techniques for integrating‐omics data. Bioinformation 3(6):284PubMedPubMedCentralGoogle Scholar
  5. Albers CA, Lunter G, Mccarthur DG, McVean G, Ouwehand WH, Durbin R (2010) Dindel: accurate indel calls from short-read data. Genome Res.  https://doi.org/10.1101/gr.112326.110
  6. Albert M (2013) Peptides as triggers of plant defence. J Exp Bot 64:5269–5279PubMedGoogle Scholar
  7. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  8. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedPubMedCentralGoogle Scholar
  9. Anderson CL, Strope CL, Moriyama EN (2011) Assessing multiple sequence alignments using visual tools. In: Mahdavi MA (ed) Bioinformatic—trends and methodologies. InTech Publications. http://www.intechopen.com/books/bioinformatics
  10. Andrew RL et al (2012) Adaptation with gene flow across the landscape in a dune sunflower. Mol Ecol 21:2078–2091PubMedGoogle Scholar
  11. Andrews SJ, Rothnagel JA (2014) Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet 15:193–204PubMedGoogle Scholar
  12. Angres B (2005) Cell microarrays. Expert Rev Mol Diagn 5:769–779PubMedGoogle Scholar
  13. Aparicio G, Götz S, Conesa A, Segrelles D, Blanque GJM, Hernandez V, Robles M, Talon M (2006) Blast2go goes grid: developing a grid-enabled prototypefor functional genomics analysis. Stud Health Technol Inform 120:194–204PubMedGoogle Scholar
  14. Araki M, Ishii T (2015) Towards social acceptance of plant breeding by genome editing. Trends Plant Sci 20:145–149PubMedGoogle Scholar
  15. Arita M (2009) A pitfall of wiki solution for biological databases. Brief Bioinform 10:295–296PubMedGoogle Scholar
  16. Arnold B, Corbett-Detig RB, Hartl D, Bomblies K (2013) RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Mol Ecol 22:3179–3190PubMedGoogle Scholar
  17. Ashburner M et al (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25:25–29PubMedPubMedCentralGoogle Scholar
  18. Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2PubMedPubMedCentralGoogle Scholar
  19. Baggerman G, Liu F, Wets G, Schoofs L (2005) Bioinformatic analysis of peptide precursor proteins. Ann N Y Acad Sci 1040:59–65PubMedGoogle Scholar
  20. Baginsky S (2009) Plant proteomics: concepts, applications, and novel strategies for data interpretation. Mass Spectrom Rev 28:93–120PubMedGoogle Scholar
  21. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376PubMedPubMedCentralGoogle Scholar
  22. Barabaschi D, Tondellia A, Desiderioa F, Volanteb A, Vaccinoc P, Valèb G, Cattivelli L (2016) Next generation breeding. Plant Sci 242:3–13PubMedGoogle Scholar
  23. Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K et al (2009) Comparison of the transcriptomes of American chestnut Castaneadentata and Chinese chestnut Castanea mollissima in response to the chestnut blight infection. BMC Plant Biol 9:51PubMedPubMedCentralGoogle Scholar
  24. Barchi B, Morris GP, Borevitz JO (2011) Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol 12:232–239Google Scholar
  25. Barrett JC, Kawasaki ES (2003) Microarrays: the use of oligonucleotides and cDNA for the analysis of gene expression. DDT 8:134–141PubMedGoogle Scholar
  26. Barsky A, Gardy JL, Hancock RE, Munzner T (2007) Cerebral: a cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics 23:1040–1042PubMedGoogle Scholar
  27. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297PubMedPubMedCentralGoogle Scholar
  28. Benson DA et al (2006) GenBank. Nucleic Acids Res 34:D16–D20PubMedGoogle Scholar
  29. Benson DA, Karsch-Mizrach I, Lipman DJ, Ostell J, Wheeler DL (2008) Genbank. Nucleic Acids Res 36:D25–D30PubMedGoogle Scholar
  30. Beranova-Giorgianni S (2003) Proteome analysis by two-dimensional gel electrophoresis and mass spectrometry: strengths and limitations. Trends Anal Chem 22:273–281Google Scholar
  31. Berezin C, Glaser F, Rosenberg J, Paz I, Pupko T, Fariselli P, Casadio R, Ben-Tal N (2003) ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 20:1322–1324Google Scholar
  32. Berkman PJ, Lai K, Lorenc MT, Edwards D (2012) Next generation sequencing applications for wheat crop improvement. Am J Bot 99:365–371PubMedGoogle Scholar
  33. Bernatsky R, Tanksley S (1986) Towards a saturated linkagemap in tomato based on isozymes and random cDNA sequences. Genetics 112:887–898Google Scholar
  34. Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR (2007) Mapping the chromosomal targets of STAT1 by sequence tag analysis of genomic enrichment (STAGE). Genome Res 17:910–916PubMedPubMedCentralGoogle Scholar
  35. Bianco A, Cestaro DJ, Sargent E, Banchi S, Derdak M, Di Guardo S, Salvi J, Jansen R, Viola I, Gut F, Laurens D, Chagné R, Velasco E et al (2014) Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh). PLoS One 9:e110377PubMedPubMedCentralGoogle Scholar
  36. Biselli C, Urso S, Tacconi G, Steuernagel B, Schulte D, Gianinetti A, Bagnaresi P, Stein N, Cattivelli L, Valè G (2013) Haplotype variability andidentification of new functional alleles at the Rdg2a leaf stripe resistance gene locus. Theor Appl Genet 126:1575–1586PubMedGoogle Scholar
  37. Blaalid R, Carlsen T, Kumar S, Halvorsen R, Ugland KI, Fontana G, Kauserud HV (2012) Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing. Mol Ecol 21:1897–1908PubMedGoogle Scholar
  38. Bohmann K, Evans A, Gilbert MT, Carvalho GR, Creer S et al (2014) Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol Evol 29:358–367PubMedGoogle Scholar
  39. Boonen K, Landuyt B, Baggerman G, Husson SJ, Huybrechts J, Schoofs L (2008) Peptidomics: the integrated approach of MS, hyphenated techniques and bioinformatics for neuropeptide analysis. J Sep Sci 31:427–445PubMedGoogle Scholar
  40. Bossdorf O, Richards CL, Pigliucci M (2008) Epigenetics for ecologists. Ecol Lett 11:106–115PubMedGoogle Scholar
  41. Botstein D, White RL, Skolnick M, Davis RW (1980) Constructionof a genetic linkage map in man using restrictionfragment length polymorphism. Am J Hum Genet 32:314–331PubMedPubMedCentralGoogle Scholar
  42. Brautigam A, Shrestha RP, Whitten D, Wilkerson CG, Carr KM, Froehlich JE et al (2008) Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes. J Biotechnol 136:44–53PubMedGoogle Scholar
  43. Brazas MD et al (2010) Providing web servers and training in bioinformatics: 2010 update on the bioinformatics links directory. Nucleic Acids Res 38:W3–W6PubMedPubMedCentralGoogle Scholar
  44. Broadhurst LM (2013) A genetic analysis of scattered yellow box trees (Eucalyptusmelliodora a. Cunn. Ex Schauer, Myrtaceae) and their restored cohorts. Biol Conserv 161:48–57Google Scholar
  45. Broadhurst LM et al (2006) Sourcing seed for Acacia acinacea, a key revegetation species in south eastern Australia. Conserv Genet 7:49–63Google Scholar
  46. Broadhurst LM et al (2008) Seed supply for broadscale restoration: maximizing evolutionary potential. Evol Appl 1:587–597PubMedPubMedCentralGoogle Scholar
  47. Brown ME, Funk CC (2008) Food security under climate change. Science 319:580–581PubMedGoogle Scholar
  48. Brumlop S, Finckh MR (2011) Applications and potentials of marker assisted selection (MAS) in plant breeding. Bundesamtfür-Naturschutz (BfN), Bonn, GermanyGoogle Scholar
  49. Buggs RJA (2013) The consequences of polyploidy and hybridisation for transcriptome dynamics. Unravelling gene expression of complex crop genomes. Heredity 110:97–98PubMedGoogle Scholar
  50. Buggs RJA, Renny-Byfield M, Chester IE, Jordon-Thaden LF, Viccini S, Chamala AR, Leitch R et al (2012) Next generation sequencing and genome evolution in allopolyploids. Am J Bot 99:372–382PubMedGoogle Scholar
  51. Bundock PC, Eliott FG, Ablett G, Benson AD, Casu RE, Aitken KS et al (2009) Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol J 7:347–354PubMedGoogle Scholar
  52. Burke M, Lobell D, Guarino L (2009) Shifts in African crop climates by 2050, and the implications for crop improvement and genetic resources conservation. Glob Environ Chang 19:317–325Google Scholar
  53. Burton PR, Clayton DG, Cardon LR, Craddock N, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI, Ouwehand WH, Samani NJ et al (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls. Nature 44:661–678Google Scholar
  54. Bus A, Hecht J, Huettel B, Reinhardt R, Stich B (2012) High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. BMC Genomics 13:281PubMedPubMedCentralGoogle Scholar
  55. Bussell JD et al (2006) Rapid genetic delineation of local provenance seed-collection zones for effective rehabilitation of an urban bushland remnant. Austral Ecol 31:164–175Google Scholar
  56. Cai L, Friedman N, Xie S (2006) Stochastic protein expression in individual cells at thesingle molecule level. Nature 440:358–362PubMedGoogle Scholar
  57. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421PubMedPubMedCentralGoogle Scholar
  58. Cannon SB, McKain MR, Harkess A, Nelson MN et al (2014) Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes. Mol Biol Evol 32:193–210PubMedPubMedCentralGoogle Scholar
  59. Cao J et al (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43:956–963PubMedGoogle Scholar
  60. Cao K, Zheng Z, Wang L, Liu X, Zhu G (2014) Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops. Genome Biol 15:415PubMedPubMedCentralGoogle Scholar
  61. Carrière SM, Rodary E, Méral P, Serpantié G, Boisvert V, Kuli CA, Lestrelin G, Lhoutellier L, Moizo B, Smektala G et al (2013) Rio+20, biodiversity marginalized. Conserv Lett 6:6–11Google Scholar
  62. de Carvalho JF, Poulain J, Da Silva C, Wincker P, Michon-Coudouel S et al (2013) Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartinaalterniflora (Poaceae). Heredity 110:181–193Google Scholar
  63. Ceol A et al (2010) MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 38:D532–D539PubMedGoogle Scholar
  64. Cericola F, Portis E, Lanteri S, Toppino L, Barchi L, Acciarri N, Pulcini L, Sala T, Rotino GL (2014) Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant. BMC Genomics 15:896PubMedPubMedCentralGoogle Scholar
  65. Chan EY (2009) Next-generation sequencing methods: impact of sequencing accuracy on SNP discovery. Methods Mol Biol 578:95–111PubMedGoogle Scholar
  66. Chen W, Gao Y, Xie W, Gong L, Lu K, Wang W, Li Y, Liu X, Zhang H, Dong H, Zhang W, Zhang L, Yu S, Wang G, Lian X, Luo J (2014a) Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nat Genet 46:714–721PubMedGoogle Scholar
  67. Chen H, Xie W, He H, Yu H, Chen W, Li J, Yu R, Yao Y, Zhang W, He Y, Tang X, Zhou F, Wang W, Deng X, Zhang Q (2014b) A high-density SNP genotyping array for rice biology and molecular breeding. Mol Plant 7:541–553PubMedGoogle Scholar
  68. Chiu RWK, Sun H, Akolekar R, Clouser C, Lee C, McKernan K, Zhou D et al (2010) Maternal plasma DNA analysis with massively parallel sequencing byligation for non-invasive prenatal diagnosis of trisomy 21. Clin Chem 56:459–463PubMedGoogle Scholar
  69. Chivenge P, Mabhaudhi T, Modi AT, Mafongoya P (2015) The potential role of neglected and underutilised crop species as future crops under water scarce conditions in sub-Saharan Africa. Int J Environ Res Public Health 12:5685–5711PubMedPubMedCentralGoogle Scholar
  70. Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5:823–826PubMedPubMedCentralGoogle Scholar
  71. Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué L, Corey A, Filichkina T, Johnson EA, Patrick M, Hayes PM (2011) Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley. BMC Genomics 12:4PubMedPubMedCentralGoogle Scholar
  72. Clark KR, Gorley RN (2001) Primer version 5.2.7 user manual/tutorial. Plymouth Marine Laboratory, PRIMER-E Ltd., Plymouth, UKGoogle Scholar
  73. Collins LJ, Biggs PJ, Voelckel C, Joly S (2008) An approach totranscriptome analysis of non-model organisms using shortreadsequences. Genome Inform 21:3–14PubMedGoogle Scholar
  74. Comadran J, Kilian B, Russell J, Ramsay L, Stein N, Ganal M, Shaw P, Bayer M, Thomas W, Marshall D, Hedley P, Tondelli A, Pecchioni N, Francia E, Korzun V, Walther A, Waugh R (2012) Natural variation in a homolog of Antirrhinum centroradıalıs contributed to spring growth habit and environmental adaptation in cultivated barley. Nat Genet 44:1388–1392PubMedGoogle Scholar
  75. Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA et al (2004) Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. Plant J 37:778–786PubMedGoogle Scholar
  76. Conn R, Loomis RS, Cassman KG (2011) Targeted enrichment strategies for next generation plant biology. Am J Bot 99:291–311Google Scholar
  77. Connor DJ, Loomis RS, Cassman KG (2011) Crop ecology-productivity and management in agricultural systems, 2nd edn. Cambridge University Press, Cambridge, p 562Google Scholar
  78. Conte MG, Gaillard S, Lanau N, Rouard M, Perin C (2008) GreenPhylDB: a database for plant comparative genomics. Nucleic Acids Res 3:D991–D998Google Scholar
  79. Costa LM et al (2014) Central cell-derived peptides regulate early embryo patterning in flowering plants. Science 344:168–172PubMedGoogle Scholar
  80. Craft JA, Gilbert JA, Temperton B, Dempsey KE, Ashelford K, Tiwari B et al (2010) Pyrosequencing of Mytilusgalloprovincialis galloprovincialiscDNAs: tissue-specific expression patterns. PLoS One 5:e8875PubMedPubMedCentralGoogle Scholar
  81. Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg LA, Bouffard P et al (2010) Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol 8:e1000475.  https://doi.org/10.1371/journal.pbio.1000475 CrossRefPubMedPubMedCentralGoogle Scholar
  82. Dang L, Van Damme EJM (2015) Toxic proteins in plants. Phytochemistry 117:51–64PubMedGoogle Scholar
  83. Dardel F, Kepes F (2006) Sequence comparison. In: Bioinformatics: genomics and post-genomics. John Wiley and Sons, USA, pp 25–50Google Scholar
  84. Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM (2009) Shedding light on an extremophile lifestyle through transcriptomics. New Phytol 183:764–775PubMedGoogle Scholar
  85. Datta S, Datta S, Kim S, Chakraborty S, Gill RS (2010) Statistical analyses of nextgeneration sequence data: a partial overview. J Proteomics Bioinform 3:183–190PubMedPubMedCentralGoogle Scholar
  86. Davey JW, Hohenloh PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510PubMedGoogle Scholar
  87. Davey JW, Cezard TE, Fuentes-Utrilla P, Eland C, Gharbi K, Blaxter ML (2013) Special features of RAD sequencing data: implications for genotyping. Mol Ecol 22:3151–3164PubMedGoogle Scholar
  88. Davidson RM, Gowda M, Moghe G, Lin H, Vaillancourt B et al (2012) Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant J 71:492–502PubMedGoogle Scholar
  89. De Filippis LF (2013) Bioinformatic tools in crop improvement. In: Hakeem KR, Ahmad PA, Ozturk MA (eds) Crop improvement—new approaches and modern techniques, Springer, Dordrecht, pp 49–122Google Scholar
  90. De Filippis LF, Magel E (2012) Identification of biochemical differences between the sapwood and transition zone in Robinia pseudoacacia L. by differential display of proteins. Z Holzforschung 66:543–549Google Scholar
  91. De Wit P, Pespeni MH, Ladner JT, Barshis DJ, Seneca F et al (2012) The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis. Mol Ecol Resour 12:1058–1067PubMedGoogle Scholar
  92. Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008) Substantial biases in ultrashortread data sets from high-throughput DNA sequencing. Nucleic Acids Res 36:e105PubMedPubMedCentralGoogle Scholar
  93. Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press, CambridgeGoogle Scholar
  94. Durbin R, Eddy S, Krogh A, Mitchison G (2004) Biological sequence analysis. CambridgeUniversity Press, CambridgeGoogle Scholar
  95. Ebert AW (2014) Potential of underutilised traditional vegetables and legume crops to contribute to food and nutritional security, income and more sustainable production systems. Sustainability 6:319–335Google Scholar
  96. Edgar RC (2009) Optimising substitution matrix choice and gap parameters for sequence alignment. BMC Bioinformarics 10:396Google Scholar
  97. Edgar RC (2010) Quality measures for protein benchmarks. Nucleic Acids Res 38:2145–2153PubMedPubMedCentralGoogle Scholar
  98. Edgar RC, Sjolander K (2004) COACH: profile–profile alignment of protein families using hidden Markov models. Bioinformatics 20:1309–1318PubMedGoogle Scholar
  99. Egan AN, Schlueter J, Spooner DM (2012) Applications of next-generation sequencingin plant biology. Am J Bot 99:175–185PubMedGoogle Scholar
  100. Ekblom R, Galindo J (2011) Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 107:1–15PubMedGoogle Scholar
  101. Ekins R, Chu F, Biggart E (1989) Development of microspot multi-analyte ratiometric immunoassay using dual fluorescent-labelled antibodies. Anal Chim Acta 227:73–96Google Scholar
  102. ElHefnawi M, Mysara M (2011) In-silico approaches for RNAi post-transcriptional gene regulation: optimizing siRNA design and selection tools. In: Mahdavi MA (ed) Bioinformatic-trends and methodologies. InTech Publications. http://www.intechopen.com/books/bioinformatics Google Scholar
  103. Ellegren H (2008) Sequencing goes 454 and takes large-scale genomics in the wild. Mol Ecol 17:1629–1631PubMedGoogle Scholar
  104. Etter PD, Preston JL, Bassham S et al (2011) Local de novo assembly of RAD paired-end contigs using short sequencing reads. PLoS One 6:e18561PubMedPubMedCentralGoogle Scholar
  105. Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P et al (2014) Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet 46:1089–1096PubMedGoogle Scholar
  106. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194PubMedPubMedCentralGoogle Scholar
  107. Farsani SF, Mahdavi MA (2011) Quantification of gene expression based on microarray. In: Mahdavi MA (ed) Bioinformatic-trends and methodologies. InTech Publications. http://www.intechopen.com/books/bioinformatics
  108. Feder ME, Mitchell-Olds T (2003) Evolutionary and ecologicalfunctional genomics. Nat Rev Genet 4:649–655Google Scholar
  109. Feng DF, Doolittle RF (1987) Progressive sequence alignment as prerequisite to correctphylogenetic trees. J Mol Evol 25:351–360PubMedGoogle Scholar
  110. Ferdinandez YS et al (2005) Detecting genetic changes over two generations of seed increase in an awned slender wheatgrass population using AFLP markers. Crop Sci 45:1064–1068Google Scholar
  111. Fernandez A, Drozdzecki A, Hoogewijs K, Nguyen A, Beeckman T, Madder A, Hilson P (2013) Transcriptionaland functional classification of the GOLVEN/ROOT GROWTHFACTOR/CLE-like signaling peptides reveals their role in lateral root and hair formation. Plant Physiol 161:954–970PubMedGoogle Scholar
  112. Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biol Lett 4:423–425PubMedPubMedCentralGoogle Scholar
  113. Fierst JL (2011) A history of phenotypic plasticity accelerates adaptation to a new environment. J Evol Biol 24:1992–2001PubMedGoogle Scholar
  114. De Filippis LF (2017) Plant bioinformatics: next geneation sequencing approaches. In: Hakeem KR, Malik A, Ozturk MA, Sukan FV (eds) Plant bioinformatics: decoding the phyta. Springer, Dordrecht, pp 1–40Google Scholar
  115. Fischer RA, Edmeades GO (2010) Breeding and cereal yield progress. Crop Sci 50:S-85–S-98Google Scholar
  116. Fitch WM (1970a) Distinguishing homologous from analogous proteins. Syst Zool 19:99–113PubMedGoogle Scholar
  117. Fitch WM (1970b) An improved method for determining codon variability in a gene and its application to the rate of fixation of the mutations in evolution. Biochem Genet 4:579–593PubMedGoogle Scholar
  118. Fodor SPA, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251:767–773PubMedGoogle Scholar
  119. Foley JA, Ramankutty N, Brauman KA (2011) Solutions for a cultivated planet. Nature 478:337–342PubMedGoogle Scholar
  120. Food and Agriculture Organisation (FAO) (2010a) The first report on the state of the world’s plant genetic resourcesfor food and agriculture. Food and Agriculture Organization, Rome, ItalyGoogle Scholar
  121. Food and Agriculture Organisation (FAO) (2010b) The state of food insecurity in the world—addressing food insecurity in protracted crises. Food and Agriculture Organization, Rome, ItalyGoogle Scholar
  122. Food and Agriculture Organisation (FAO) (2012a) The second report on the state of the world’s plant genetic resourcesfor food and agriculture. Food and Agriculture Organization, Rome, ItalyGoogle Scholar
  123. Food and Agriculture Organisation (FAO) (2012b) Statistics at FAO—The Food and Agriculture Organization of the United Nations, Rome Italy, http://www.fao.org/statistics/en/
  124. Food and Agriculture Organisation FAO (2013) Food outlook-biannual report on global food markets. Food and Agriculture Organization, Rome, Italy, p 140. http://www.fao.org/3/a-i4136e.pdf Google Scholar
  125. Ford-Lloyd BV, Schmidt M, Armstrong SJ, Barazani O, Engels J, Hadas R, Hammer K, Kell SP, Kang D, Khoshbakht K, Li Y, Long C, Lu B-R, Ma K, Nguyen VT, Qiu L et al (2011) Crop wild relatives-undervalued, underutilized and under threat? Bioscience 61:559–565Google Scholar
  126. Frison EA, Cherfas J, Hodgkin T (2011) Agricultural biodiversity is essential for a sustainable improvement in food and nutrition security. Sustainability 3:238–253Google Scholar
  127. Frith MC, Wan R, Horton P (2010) Incorporating sequence quality data intoalignment improves DNA read mapping. Nucleic Acids Res 38:e100PubMedPubMedCentralGoogle Scholar
  128. Gasc C, Peyretaillade E, Peyret P (2016) Sequence capture by hybridisation to explore modern and ancient genomic diversity in model and non-model organisms. Nucleic Acids Res 1.  https://doi.org/10.1093/nar/gkw309
  129. Gepts P (2004) Crop domestication as a longterm selection experiment. Plant Breed Rev 24:1–44Google Scholar
  130. Ghahremani A, Mahdavi MA (2011) Optimal sequence alignment and its relationship with phylogeny. In: Mahdavi MA (ed) Bioinformatic-trends and methodologies. InTech Publications. http://www.intechopen.com/books/bioinformatics Google Scholar
  131. Gilad Y, Pritchard JK, Thornton K (2009) Characterizing naturalvariation using next-generation sequencing technologies. Trends Genet 25:463–471PubMedPubMedCentralGoogle Scholar
  132. Giles J (2005) Internet encyclopaedias go head to head. Nature 438:900–901PubMedGoogle Scholar
  133. Giles J (2007) Key biology databases go wiki. Nature 445:691PubMedGoogle Scholar
  134. Gilks WR, Audit B, De Angeli D, Tsoka S, Ouzounis CA (2002) Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics 18:1641–1649PubMedGoogle Scholar
  135. Gill N, Buti M, Kane N, Bellec A, Helmstetter N et al (2014) Sequence-based analysis of structural organization and composition of the cultivated sunflower (Helianthus annuus L.) Genome Biol 3:295–319Google Scholar
  136. Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ et al (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One 9:e90346PubMedPubMedCentralGoogle Scholar
  137. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W et al (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27:182PubMedPubMedCentralGoogle Scholar
  138. Godfray HCJ, Beddington JR, Crute IR, Haddad L, Lawrence D, Muir JF, Pretty J, Robinson S, Thomas SM, Toulmin C (2010) Food security: the challenge of feeding 9 billion people. Science 327:812–818PubMedPubMedCentralGoogle Scholar
  139. Goodswen SJ, Kadarmideen HN (2011) SNP pattern: a genetic tool to derive haplotype blocks and measure genomic diversity in populations using SNP genotypes. In: Mahdavi MA (ed) Bioinformatic-trends and methodologies. InTech Publications. http://www.intechopen.com/books/bioinformatics
  140. Goodswen SJ, Gondro C, Watson-Haigh NS, Kadarmideen HN (2010) FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP database. BMC Bioinformatics 11:2–15Google Scholar
  141. Goyal RK, Mattoo AK (2014) Multitasking antimicrobial peptides in plant development and host defense against biotic/ abiotic stress. Plant Sci 228:135–149PubMedGoogle Scholar
  142. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652PubMedPubMedCentralGoogle Scholar
  143. Greene LH et al (2007) The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 35:D291–D297PubMedGoogle Scholar
  144. Gribskov M, Homyak M, Edenfield J, Eisenberg D (1988) Profile scanning for three dimensional structural patterns in protein sequences. Comput Appl Biosci 4:61–66PubMedGoogle Scholar
  145. Griffin PC, Robin C, Hoffmann AA (2011) A next-generation sequencing methods of overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biol 9:19PubMedPubMedCentralGoogle Scholar
  146. Grover CE, Salmon A, Wendel JE (2012) Targeted sequence capture as a powerful tool for evolutionary analysis. Am J Bot 9:312–319Google Scholar
  147. Guggisberg A, Lai Z, Huang J, Rieseberg LH (2013) Transcriptome divergence between introduced and native populations of Canada thistle Cirsium arvense. New Phytol 199:595–608PubMedGoogle Scholar
  148. Guillén G, Díaz-Camino C, Loyola-Torres CA, Aparicio-Fabre R, Hernández-López A, Díaz-Sánchez M, Sanchez F (2013) Detailed analysis of putative genes encoding small proteins in legume genomes. Front Plant Sci 4:208PubMedPubMedCentralGoogle Scholar
  149. Guo W, Huang Y, He Z, Yan Y, Zhou R et al (2013) Development and characterization of microsatellite loci for smooth cordgrass Spartina alterniflora (Poaceae). Appl Plant Sci 1.  https://doi.org/10.3732/apps.1200211 Google Scholar
  150. Guo P, Yoshimura A, Ishikawa N, Yamaguchi T, Guo Y, Tsukaya H (2015) Comparative analysis of the RTFL peptide family on the control of plant organogenesis. J Plant Res 128:497–510PubMedPubMedCentralGoogle Scholar
  151. Gupta PK (2008) Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 26:602–611PubMedGoogle Scholar
  152. Gupta K, Sengupta A, Saha J, Gupta B (2014) The attributes of RNA interference in relation to plant abiotic stress tolerance. Gene Technol 3:1. ISSN 2329-6682 GNTGoogle Scholar
  153. Guttikonda SK, Marri P, Mammadov J, Ye L, Soe K, Richey K, Cruse J, Zuang M, Gao Z, Evans C, Rounsley S, Kumpatia SP (2016) Molecular charecterisation of transgenic events using next generation sequencing approach. PLoS One 11:e0149515.  https://doi.org/10.1371/journal.pone.0149515 CrossRefPubMedPubMedCentralGoogle Scholar
  154. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD et al (2013) De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512PubMedPubMedCentralGoogle Scholar
  155. Hanada K et al (2013) Small open reading frames associated with morphogenesis are hidden in plant genomes. Proc Natl Acad Sci U S A 110:2395–2400PubMedPubMedCentralGoogle Scholar
  156. Hayden EC (2009) Genome sequencing: the third generation. Nature 457:768–769Google Scholar
  157. Hayden EC (2014) The $1000 genome. Nature 507:294–295PubMedGoogle Scholar
  158. He R, Kim MJ, Nelson W, Balbuena TS, Kim R et al (2012) Next-generation sequencing-based transcriptomic and proteomic analysis of the common reed Phragmites australis (Poaceae) reveals genes involved in invasiveness and rhizome specificity. Am J Bot 99:232–247PubMedGoogle Scholar
  159. He J, Zhao X, Laroche A, Lu Z-X, Liu HK, Li Z (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 5:484PubMedPubMedCentralGoogle Scholar
  160. Hebert PD, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc Roy Soc 270:313–321Google Scholar
  161. Hedrick PW (2004) Recent developments in conservation genetics. For Ecol Manag 197:3–19Google Scholar
  162. Heffner EL, Jannink J-L, Iwata H, Souza E, Sorrells ME (2011) Genomic selection accuracy for grain quality traits in biparental wheat populations. Crop Sci 51:2597–2606Google Scholar
  163. Hegde PS, White IR, Debouck C (2003) Interplay of transcriptomics and proteomics. Curr Opin Biotechnol 14:647–651PubMedGoogle Scholar
  164. Henikoff JG, Greene EA, Pietrokovski S, Henikoff S (2000) Increased coverage of protein families with the blocks database servers. Nucleic Acids Res 28:228–230PubMedPubMedCentralGoogle Scholar
  165. Henry RJ (2012) Next-generation sequencing for understanding and accelerating crop domestication. Brief Funct Genomics 11:51–56PubMedGoogle Scholar
  166. Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948PubMedGoogle Scholar
  167. Hirsch JM, Foerster JM, Johnson RS, Sekhon G, Muttoni B, Vaillancourta F, Penagaricano E, Lindquist MA, Pedraza K et al (2014) Insight into the maize pan-genome and pan-transcriptome. Plant Cell 26:121–135PubMedPubMedCentralGoogle Scholar
  168. Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW et al (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet 39:1522–1527PubMedGoogle Scholar
  169. Hoeglund J (2009) Evolutionary conservation genetics. Oxford University Press, Oxford, UKGoogle Scholar
  170. Holderegger R et al (2008) Land ahead: using genome scans to identify molecular markers of adaptive relevance. Plant Ecol Divers 1:273–283Google Scholar
  171. Huang YL, Fang XT, Lu L, Yan YB, Chen SF et al (2012) Transcriptome analysis of an invasive weed Mikania micrantha. Biol Plantarum 56:111–116Google Scholar
  172. Huang X-C, Xi X-Q, Conran JG, Li J (2015) Application of DNA barcodes in Asian tropical trees-a case study from Xishuangbanna nature reserve, Sothwest China. PLoS One 10:e0129295PubMedPubMedCentralGoogle Scholar
  173. Huey RB, Gilchrist GW, Hendry AP (2005) Using invasive species to study evolution: case studies with Drosophila and salmon. In: Sax DF, Stachowicz JJ, Gaines SD (eds) Species invasions: insights into ecology, evolution, and biogeography. Sinauer Associates Inc., Sunderland, MA, pp 139–164Google Scholar
  174. Hufford KM et al (2012) Inbreeding and outbreeding depression in Stylidium hispidum: implications for mixing seed sources for ecological restoration. Ecol Evol 2:2262–2273PubMedPubMedCentralGoogle Scholar
  175. Hurd PJ, Nelson CJ (2009) Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct Genomic Proteomic 8:174–183PubMedGoogle Scholar
  176. Husemann P, Stoye J (2010) Phylogenetic comparative assembly. Algorithms Mol Biol 5:3.  https://doi.org/10.1186/1748-7188-5-3 CrossRefPubMedPubMedCentralGoogle Scholar
  177. Husson SJ, Landuyt B, Nys T, Baggerman G, Boonen K, Clynen E, Lindemans M, Janssen T, Schoofs L (2009) Comparative peptidomics of Caenorhabditis elegans versus C. briggsae by LC-MALDI-TOF MS. Peptides 30:449–457PubMedGoogle Scholar
  178. Husson SJ, Clynen E, Boonen K, Janssen T, Lindemans M, Baggerman G, Schoofs L (2010) Approaches to identify endogenous peptides in the soil nematode Caenorhabditis elegans. Methods Mol Biol 615:29–47PubMedGoogle Scholar
  179. Ilut DC, Coate JE, Luciano AK, Owens TG, May GD, Farmer A, Doyle JJ (2012) A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species. Am J Bot 9:383–396Google Scholar
  180. Imelfort M, Duran C, Batley J, Edwards D (2009) Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnol J 7:312–317PubMedGoogle Scholar
  181. Ingvardsen CR, Schejbel B, Lubberstedt T (2008) Functional markers in resistance breeding. In: Luttge U, Beyschlag W, Murata J (eds) Progress in botany. Springer, BerlinGoogle Scholar
  182. Isakov O, Shomron N (2011) Deep sequencing data analysis: challenges and solutions. In: Mahdavi MA (ed) Bioinformatic-trends and methodologies. InTech Publications. http://www.intechopen.com/books/bioinformatics Google Scholar
  183. Isakov O, Modai S, Shomron N (2011) Pathogen detection using short-RNA deep sequencing subtraction and assembly. Bioinformatics 27:2027–2030PubMedPubMedCentralGoogle Scholar
  184. Jackson AL, Linsley PS (2010) Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nat Rev Drug Discov 9:57–67PubMedGoogle Scholar
  185. Jackson SA, Iwata A, Lee S-H, Schmutz J, Shoemaker R (2011) Sequencing crop genomes: approaches and applications. New Pytol 191:915–926Google Scholar
  186. Jacobs DF et al (2013) A conceptual framework for restoration of threatened plants: the effective model of American chestnut (Castanea dentata) reintroduction. New Phytol 197:378–393PubMedGoogle Scholar
  187. Jacobsen S-E, Sørensen M, Pedersen SM, Weiner J (2013) Feeding the world: genetically modified crops versus agrobiodiversity. Agron Sustain Dev 33:651–662Google Scholar
  188. Jacobsen S-E, Sorensen M, Pedersen SM, Weiner J (2015) Using our agrobiodiversity: plant-based solutions to feed the world. Agron Sustain Dev 35:1217–1235Google Scholar
  189. Jain SM, Gupta SD (eds) (2013) Biotechnology of neglected and underutilized crops. Springer, Berlin, GermanyGoogle Scholar
  190. Jia M-A, Li YQ, Lei L, Di D, Miao HQ, Fan Z (2012) Alteration of gene expression profile in maize infected with a double-stranded RNA fijivirus associated with symptom development. Mol Plant Pathol 13:251–262PubMedGoogle Scholar
  191. Jia G, Huang X, Zhi H, Zhao Y, Zhao Q et al (2013) A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet 45:957–961PubMedGoogle Scholar
  192. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) Ncbi blast: a better web interface. Nucleic Acids Res 36:W5–W9PubMedPubMedCentralGoogle Scholar
  193. Jonassen I, Collins JF, Higgins DG (1995) Finding flexible patterns in unaligned protein sequences. Protein Sci 4:1587–1595PubMedPubMedCentralGoogle Scholar
  194. Jorgensen RA, Dorantes-Acosta AE (2012) Conserved peptide upstream open reading frames are associated with regulatory genes in angiosperms. Front Plant Sci 3:191PubMedPubMedCentralGoogle Scholar
  195. Juma C (2011) The new harvest—agricultural innovations in Africa. Oxford University Press, Inc., Oxford, p 296Google Scholar
  196. Kahane R, Hodgkin T, Jaenicke H, Hoogendoorn C, Hermann M, Keatinge JDH, Hughes JDA, Padulosi S, Looney N (2013) Agrobiodiversity for food security, health and income. Agron Sustain Dev 33:671–693Google Scholar
  197. Kane N, Sveinsson S, Dempewolf H, Yang JY, Zhang DZ, Engels MM, Cronk Q (2012) Ultra-barcoding in cacao (Theobroma spp; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA. Am J Bot 99:320–329PubMedGoogle Scholar
  198. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M et al (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 3:D480–D484Google Scholar
  199. Kang C, Zhang J, Wang Y, Liu N, Liu J, Zeng H, Jiang T, You Y, Pu P (2011) Data mining identifies core signalings and miRNA regulatory module. In: Mahdavi MA (ed) Bioinformatic-trends and methodologies. InTech Publications. http://www.intechopen.com/books/bioinformatics
  200. Karakach TK, Flight RM, Douglas S (2010) An introduction to DNA microarrays for gene expression analysis. Chemom Intell Lab Syst 104:28–52Google Scholar
  201. Karasavvas KA et al (2004) Bioinformatics integration and agent technology. J Biomed Inform 37:205–219PubMedGoogle Scholar
  202. Kawabe A, Miyashita NT (2003) Patterns of codon usage bias in three dicot and four monocot plant species. Genes Genet Syst 78:343–352PubMedGoogle Scholar
  203. Keatinge JDH, Easdown W, Yang R-Y, Chadha M, Shanmugasundaram S (2011a) Overcoming chronic malnutrition in a future warming world: the key importance of mungbean and vegetable soybean. Euphytica 180:129–141Google Scholar
  204. Keatinge JDH, Yang R-Y, Hughes JDA, Easdown WJ, Holmer R (2011b) The importance of vegetables in ensuring both food and nutritional security in attainment of the millennium development goals. Food Sci 3:491–501Google Scholar
  205. Keatinge JDH, Ledesma DR, Keatinge FJD, Hughes JDA (2013) Projecting annual air temperature changes to 2025 and beyond: implications for vegetable horticulture worldwide. J Agric Sci.  https://doi.org/10.1017/S0021859612000913
  206. Kelly RP, Port JA, Yamahara KM, Crowder LB (2014) Using environmental DNA to census marine fishes in a large mesocosm. PLoS One 9:e86175PubMedPubMedCentralGoogle Scholar
  207. Kemena C, Notredame C (2009) Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics 25:2455–2465PubMedPubMedCentralGoogle Scholar
  208. Khan F, Azman R, Chai HH, Mayes S, Lu C (2016) Genomic and transcriptomic approaches towards the genetic improvement of an underutilised crop: the case of Bambara groundnut. African Crop Sci J 24:429–458Google Scholar
  209. Kim MY, Lee S, Van K et al (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycinesoja Sieb. And Zucc.) genome. Proc Natl Acad Sci U S A 107:22032–22037PubMedPubMedCentralGoogle Scholar
  210. Kim S-I, Tai TH et al (2014) Identification of novel rice low phytic acid mutations via TILLING by sequencing. Mol Breed 34:1717–1729Google Scholar
  211. Kircher M, Kelso J (2010) High-throughput DNA sequencing concepts and limitations. BioEssays 32:524–536PubMedGoogle Scholar
  212. Kirk H, Dorn S, Mazzi D (2013) Molecular genetics and genomics generate new insights into invertebrate pest invasions. Evol Appl 6:842–856PubMedPubMedCentralGoogle Scholar
  213. Kislyuk AO, Katz LS, Agrawal S, Hagen MS, Conley AB, Jayaraman P, Nelakuditi V, Humphrey JC, Sammons SA, Govil D et al (2010) A computationalgenomics pipeline for prokaryotic sequencing projects. Bioinformatics 26:1819–1826PubMedPubMedCentralGoogle Scholar
  214. Koboldt DC, Ding L, Mardis ER, Wilson RK (2010) Challenges of sequencing human genomes. Brief Bioinform 11:484–498PubMedPubMedCentralGoogle Scholar
  215. Kolari I-L, Laitinan P, Turunen MP, Yla-Herttuala S (2015) Novel nuclear biology of small non-coding RNAs. Gene Technol 4:2Google Scholar
  216. Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410PubMedGoogle Scholar
  217. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705PubMedGoogle Scholar
  218. Krauss SL, He TH (2006) Rapid genetic identification of local provenance seed collection zones for ecological restoration and biodiversity conservation. J Nat Conserv 14:190–199Google Scholar
  219. Krauss SL et al (2013) An ecological genetic delineation of local seed-source provenance for ecological restoration. Ecol Evol 3:2138–2149PubMedPubMedCentralGoogle Scholar
  220. Kroc M, Koczyk G, Swiecicki W, Kilian A, Nelson MN (2014) New evidence of ancestral polyploidy in the Genistoid legume Lupinus angustifolius L (narrow-leafed lupin). Theor Appl Genet 127:1237–1249PubMedGoogle Scholar
  221. Ku C, Chung W-C, Chen L-L, Kuo C-H (2013) The complete plastid genome sequence of Madagascar periwinkle Catharanthus roseus L. G .Don: plastid genome evolution, molecular marker identification, and phylogenetic implications in asterids. PLoS One 8:e68518PubMedPubMedCentralGoogle Scholar
  222. Kvam VM, Liu P, Si Y (2012) A comparison of statistical methodsfor detecting differentially expressed genes from RNA-seq data. Am J Bot 99:248–256PubMedGoogle Scholar
  223. Lambirth KC, Whaley AM, Blakley IC, Schlueter JA, Bost KL, Loraine AE, Piller KJ (2016) A comparison of transgenic and wild type soybean seeds: analysis of transcriptomeprofiles using RNA-Seq. BMC Biotechnol 15:89Google Scholar
  224. Langlet (1971) Two hundred years geneecology. Taxon 20:653–721Google Scholar
  225. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948PubMedGoogle Scholar
  226. Lauressergues D, Couzigou J-M, Clemente HS, Martinez Y, Dunand C, Bécard G, Combier J-P (2015) Primary transcripts of microRNAs encode regulatory peptides. Nature 520:90–93PubMedGoogle Scholar
  227. Lee RM, Thimmapuram J, Thinglum KA, Gong G, Hernandez AG, Wright CL et al (2009) Sampling the waterhemp (Amaranthus tuberculatus) genome using pyrosequencing technology. Weed Sci 57:463–469Google Scholar
  228. Lee JS, Kuroha T, Hnilova M, Khatayevich D, Kanaoka MM, McAbee JM, Sarikaya M, Tamerler C, Torii KU (2012) Direct interaction of ligand-receptor pairs specifying stomatal patterning. Genes Dev 26:126–136PubMedPubMedCentralGoogle Scholar
  229. Lee YW, Gould BA, Stinchcombe JR (2014) Identifying the genes underlying quantitative traits: a rationale for the QTN programme. AoB Plants 6. plu004PubMedPubMedCentralGoogle Scholar
  230. Lerat E, Ochman H (2005) Recognizing the pseudogenes in bacterial genomes. Nucleic Acids Res 33:3125–3132PubMedPubMedCentralGoogle Scholar
  231. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD et al (2008) DNA sequencing of acytogenetically normal acute myeloid leukaemia genome. Nature 456:66–72PubMedPubMedCentralGoogle Scholar
  232. Li A (2006) Facing the challenges of data integreation in biosciences. Eng Lett 13. EL-13Google Scholar
  233. Li H (2011) Improving SNP discovery by base alignment quality. Bioinformatics 27:1157–1158PubMedPubMedCentralGoogle Scholar
  234. Li H et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079PubMedPubMedCentralGoogle Scholar
  235. Li L, Shig M, Ching W-K, Mamitsuka H (2010) Annotating gene functions with integrative spectral clustering on microarray expressions and sequences. Genome Inform 22:95–120PubMedGoogle Scholar
  236. Li S-L, Vasemägi A, Matos-Máravi P, Ramula S (2013) Development and testing of microsatellite loci for the invasive herb Lupinus polyphyllus through 454 pyrosequencing. Mol Ecol Resour 13:760–762PubMedGoogle Scholar
  237. Lin BB (2011) Resilience in agriculture through crop diversification: adaptive management for environmental change. Bioscience 61:183–193Google Scholar
  238. Lipshutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nat Genet Suppl 21:20–24Google Scholar
  239. Liu F, Schoofs L, Baggerman G, Wets G, Lindemans M (2011) A pattern search method for discovering conserved motifs in bioactive peptide families. In: Mahdavi MA (ed) Bioinformatic-trends and methodologies. InTech Publications. http://www.intechopen.com/books/bioinformatics Google Scholar
  240. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol:251364.  https://doi.org/10.1155/2012/251364
  241. Liu H, Bayer M, Druka A, Russell JR, Hackett CA, Poland J, Ramsay L, Hedley PE, Waugh R (2014) An evaluation of genotyping by sequencing (GBS) to map the Breviaristatumae (ari-e) locus in cultivated barley. BMC Genomics 15:104PubMedPubMedCentralGoogle Scholar
  242. Liu H et al (2015) Development of genome-wide insertion and deletion polymorphism markers from next-generation sequencing data. Rice 8:27PubMedCentralGoogle Scholar
  243. Llaca V (2012) Sequencing technologies and their use in plant biotechnology and breeding. In: Munshi A (ed) DNA sequencing—methods and applications. InTech, Rijeka, Croatia. ISBN: 978-953-51-0564-0Google Scholar
  244. Lobell DB, Burke MB, Tebaldi C, Mastrandrea MD, Falcon WP, Naylor RL (2008) Prioritizing climate change adaptation needs for food security in 2030. Science 319:607–610PubMedGoogle Scholar
  245. López Herráez D, Bauchet M, Tang K, Theunert C, Pugach I et al (2009) Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. PLoS One 4:e7888PubMedPubMedCentralGoogle Scholar
  246. Mahon AR, Nathan LR, Jerde CL (2014) Meta-genomic surveillance of invasive species in the bait trade. Conserv Genet Res 6:563–567Google Scholar
  247. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A et al (2010) Target-enrichment strategies for next generationsequencing. Nat Methods 7:111–118PubMedGoogle Scholar
  248. Manos PS, Doyle JJ, Nixon KC (1999) Phylogeny, biogeography, and processes of molecular differentiation in Qurcus subgenus (Fagaceae). Mol Phylogenet Evol 12:333–349PubMedGoogle Scholar
  249. Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141PubMedGoogle Scholar
  250. Mardis ER (2010) The $1,000 genome, the $100,000 analysis? Genome Med 2:84PubMedPubMedCentralGoogle Scholar
  251. Mardis ER (2011) A decade’s perspective on DNA sequencing technology. Nature 470:198–203PubMedGoogle Scholar
  252. Marescaux J, Van Doninck K (2013) Using DNA barcoding to differentiate invasive Dreissena species (Mollusca, Bivalvia). ZooKeys 365:235–244Google Scholar
  253. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z (2005) Genome sequencing inmicrofabricated high-density picolitre reactors. Nature 437:376–380PubMedPubMedCentralGoogle Scholar
  254. Mariman EC (2009) 2DE-proteomics meta-data indicate the existence of distinct cellular stress-responsive mechanisms. Expert Rev Proteomics 6:337–339PubMedGoogle Scholar
  255. Marmiroli N, Maestri E (2014) Plant peptides in defense and signaling. Peptides 56:30–44PubMedGoogle Scholar
  256. Mayes S, Massawe FJ, Alderson PG, Roberts JA, Azam-Ali SN, Hermann M (2012) The potential for underutilized crops to improve security of food production. J Exp Bot 63:1075–1079PubMedPubMedCentralGoogle Scholar
  257. McCouch SR, McNally KL, Wang W, Hamilton RS (2012) Genomics of gene banks: a case study in rice. Am J Bot 99:407–423PubMedGoogle Scholar
  258. McElroy K, Thomas T, Luciani F (2014) Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions. Microb Inform Exp 4:1PubMedPubMedCentralGoogle Scholar
  259. McKain MR, Wickett ZNY, Yyampalayam SA, McCombie WR, Chase MW, Pires JC et al (2012) Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). Am J Bot 99:397–406PubMedGoogle Scholar
  260. McKay JR, Latta RG (2002) Adaptive divergence population: markers, QTLs and traits. Trends Ecol Evol 17:285–291Google Scholar
  261. McKay JK et al (2005) ‘How local is local?’ A review of practical and conceptual issues in the genetics of restoration. Restor Ecol 13:432–440Google Scholar
  262. McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Pearson TA, Manolio TA (2008) How to interpret a genome-wide association study. JAMA 299:1335–1344Google Scholar
  263. McLean R et al (2007) The effect of web 2.0 on the future of medical practice and education: Darwinian evolution or folksonomic revolution? Med J Aust 187:174–177PubMedGoogle Scholar
  264. Medvedev P, Stanciu M, Brudno M (2009) Computational methods for discoveringstructural variation with next-generation sequencing. Nat Methods 6:S13–S20PubMedGoogle Scholar
  265. Mejlhede N, Kyjovska Z, Backes G, Burhenne K, Rasmussen SK, Jahoor A (2006) EcoTILLING for the identification of allelic variation in the powdery mildew resistance genes Mlo and Mla in barley. Plant Breed 125:461–467Google Scholar
  266. Memon AR (2012) Transcriptomics and proteomics analysis of root nodules of modern legume plants. In: Asharaf M, MSA A, Ozturk M, Aksoy A (eds) Crop production for agricultural improvement. Springer Science – Business Media, BerlinGoogle Scholar
  267. Menschaert G, Vandekerckhove TT, Baggerman G, Schoofs L, Luyten W, Van Criekinge W (2010) Peptidomics coming of age: a review of contributionsfrom a bioinformatics angle. J Proteome Res 9:2051–2061PubMedGoogle Scholar
  268. Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46PubMedGoogle Scholar
  269. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A (2003) Gendb–an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31:2187–2195PubMedPubMedCentralGoogle Scholar
  270. Meyer RS, DuVal AE, Jensen HR (2012) Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops. New Phytol 196:29–48PubMedGoogle Scholar
  271. Michael TP, Jackson S (2013) The first 5 plant genomes. Plant Genome 6:1–7.  https://doi.org/10.3835/plantgenome2013.03.0001 CrossRefGoogle Scholar
  272. Miller AC, Woeste KE, Anagnostakis SL, Jacobs DF (2014) Exploration of a rare population of Chinese chestnut in North America: stand dynamics, health and genetic relationships. AoB Plants 6. plu065PubMedPubMedCentralGoogle Scholar
  273. Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE (2006) An initial map of insertion and deletion (INDEL) variationin the human genome. Genome Res 16:1182–1190PubMedPubMedCentralGoogle Scholar
  274. Mizrachi E, Hefer CA, Ranik M, Joubert F, Myburg AA (2010) De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq. BMC Genomics 11:681–692PubMedPubMedCentralGoogle Scholar
  275. Mochida K, Shinozaki K (2010) Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol 51:497–523PubMedPubMedCentralGoogle Scholar
  276. Molina C, Rotter B, Horres R, Udupa S, Besser B, Bellarmino L et al (2008) SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics 9:553PubMedPubMedCentralGoogle Scholar
  277. Molina J, Sikora M, Garud N et al (2011) Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci U S A 108:8351–8356PubMedPubMedCentralGoogle Scholar
  278. Montalvo AM, Ellstrand NC (2001) Transplantation of the subshrub Lotus scoparius: testing the home-site advantage hypothesis. Conserv Biol 14(1034–1045):28Google Scholar
  279. Mosner E et al (2012) Floodplain willows in fragmented river landscapes: understanding spatio-temporal genetic patterns as a basis for restoration plantings. Biol Conserv 153:211–218Google Scholar
  280. Mullaney JM, Mills RE, Pittard WS, Devine SE (2010) Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet 19:R2–R131Google Scholar
  281. Myles J-M, Chia B, Hurwitz C, Simon G, Zhong Y, Buckler E, Ware D (2010) Rapid genomic characterization of the genus vitis. PLoS One 5:e8219PubMedPubMedCentralGoogle Scholar
  282. Nawrot R, Barylski J, Nowicki G, Broniarczyk J, Buchwald W, Gozdzicka-Józefiak A (2014) Plant antimicrobial peptides. Folia Microbiol (Praha) 59:181–196Google Scholar
  283. Newton AC, Johnson SN, Gregory PJ (2011) Implications of climate change for diseases, crop yields and food security. Euphytica 179:3–18Google Scholar
  284. Nicolai M, Pisani C, Bouchet J-P et al (2012) Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum). Genet Mol Res 11:2295–2300PubMedGoogle Scholar
  285. Nothnagel M, Herrmann A, Wolf A, Schreiber S, Platzer M, Siebert R, Krawczak M et al (2011) Technology-specific error signatures in the 1000 genomes project data. Hum Genet.  https://doi.org/10.1007/s00439-011-0971-3
  286. Novaes E, Drost DR, Farmerie WG, Pappas GJP Jr, Grattapaglia D, Sederoff RR et al (2009) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9:312Google Scholar
  287. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A et al (2008) Genes mirror geography within Europe. Nature 456:98PubMedPubMedCentralGoogle Scholar
  288. Novy A, Flory SL, Honig JA, Bonos S, Hartman JM (2012) Characterization of polymorphic microsatellites for the invasive grass Microstegium vimineum (Poaceae). Am J Bot 99:e56–e58PubMedGoogle Scholar
  289. Ochatt S, Jain SM (2007) Breeding of neglected and under-utilized crops, spices and herbs. Science Publishers Inc., Enfield, NHGoogle Scholar
  290. Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME (2007) Microarray-based genomic selection for high throughput resequencing. Nat Methods 4:907–909PubMedGoogle Scholar
  291. Oshlack A, Robinson MD, Young MD (2010) From RNA-seq reads to differential expression results. Genome Biol 11:220–229PubMedPubMedCentralGoogle Scholar
  292. Padulosi S, Heywood V, Hunter D, Jarvis A (2011) Underutilized species and climate change: current status and outlook. In: Yadav SS, Redden RJ, Hatfield JL, Lotze-Campen H, Hall AE (eds) Crop adaptation to climate change, 1st edn. John Wiley & Sons, Oxford, pp 507–521Google Scholar
  293. Paran I, Michelmore RW (1993) Development of reliable PCRbasedmarkers linked to downy mildew resistance genes inlettuce. Theor Appl Genet 85:985–993PubMedGoogle Scholar
  294. Parkinson H et al (2011) ArrayExpress update-an archive of microarray and highthroughput sequencing-based functional genomics experiments. Nucleic Acids Res 39:D1002–D1004PubMedGoogle Scholar
  295. Paszkiewicz K, Studholme DJ (2010) De novo assembly of short sequence reads. Brief Bioinform:457–472PubMedGoogle Scholar
  296. Pearson WR (1998) Empirical statistical estimates for sequence similarity searches. J Mol Biol 276:71–84PubMedGoogle Scholar
  297. Pearson WR (2000) Flexible sequence similarity searching with FASTA3 program package. Methods Mol Biol 132:185–219PubMedGoogle Scholar
  298. Peng Y, Lai Z, Lane T, Nageswara-Rao M, Okada M et al (2014) De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms. Plant Physiol 166:1241–1254PubMedPubMedCentralGoogle Scholar
  299. Perdew GH, Vanden Heuvel JP, Peters JM (2006) Regulation of gene expression: molecular mechanisms. Humana Press, pp 11–30Google Scholar
  300. Pfender WF, Saha MC, Johnson EA, Slabaugh MB (2011) Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet 122:1467–1480PubMedGoogle Scholar
  301. Piaggio AJ, Engeman RM, Hopken MW, Humphrey JS, Keacher KL et al (2014) Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA. Mol Ecol Resour 14:374–380PubMedGoogle Scholar
  302. Pimentel D, Marklein A, Toth MA, Karpoff MN, Paul GS, McCormack R, Kyriazis J, Krueger T (2009) Food versus biofuels: environmental and economic costs. Hum Ecol 37:1–12Google Scholar
  303. Pinet F (2009) Identifying patients at risk of progressive left ventricular dysfunction. Heart Metab 42:10–14Google Scholar
  304. Pingali P, Raney T (2005) From the green revolution to the gene revolution: how will the poor fare? ESA Working Paper No. 05–09. Food and Agriculture Organization (FAO), United NationsGoogle Scholar
  305. Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012a) Developmentof high-density genetic maps for barley and wheat using a noveltwo-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253PubMedPubMedCentralGoogle Scholar
  306. Poland JA, Endelman J, Dawson J et al (2012b) Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome 5:103–113Google Scholar
  307. Pop M, Salzberg SL (2008) Bioinformatics challenges of new sequencing technology. Trends Genet 24:142–149PubMedPubMedCentralGoogle Scholar
  308. Poptsova MS, Gogarten JP (2010) Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology 156:1909–1917PubMedGoogle Scholar
  309. Porter JR, Challinor A, Ewert F, Falloon P, Fischer T, Gregory P, Van IMK, Olesen JE, Moore KJ, Rosenzweig C, Smith P (2010) Food security: focus on agriculture. Science 328:172–173PubMedGoogle Scholar
  310. Powell W, Machray G, Provan J (1996) Polymorphism revealedby simple sequence repeats. Trends Plant Sci 1:215–222Google Scholar
  311. Prigent J, Panigai L, Lamourette P, Sauvaire D, Devilliers K, Plaisance M, Volland H, Creminon C, Simon S (2011) Neutralising antibodies against ricin toxin. PLoS One 6(5):e20166PubMedPubMedCentralGoogle Scholar
  312. Primmer CR (2009) From conservation genetics to conservation genomics. Ann N Y Acad Sci 1162:357–368PubMedGoogle Scholar
  313. Pruitt KD et al (2009) NCBI reference sequences: current status, policy and newinitiatives. Nucleic Acids Res 37:D32–D36PubMedGoogle Scholar
  314. Pu P, Zhang Z, Kang C, Jiang R, Jia Z, Wang G, Jiang H (2009) Downregulation of Wnt2and beta-catenin by siRNA suppresses malignant glioma cell growth. Cancer Gene Ther 16:351–361PubMedGoogle Scholar
  315. Qi J, Liu X, Shen D et al (2013) A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat Genet 45:1510–1515PubMedGoogle Scholar
  316. Rai A, Saito K, Yamazaki M (2017) Integrated omics analysis of specialized metabolism in medicinal plants. Plant J 90:764–787PubMedGoogle Scholar
  317. Ray S, Satya PN (2014) Next tgeneration sequencing technologies fornext generation plant breeding. Front Plant Sci 5:367PubMedPubMedCentralGoogle Scholar
  318. Renaut J, Lutts S, Hoffmann L, Hausman J-F (2004) Responses of poplar tochilling temperatures: proteomic and physiological aspects. Plant Biol 6:81–90PubMedGoogle Scholar
  319. Renaut S, Grassa CJ, Moyers BT, Kane NC, Rieseberg LH (2012) The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq. Biology 1:575–596PubMedPubMedCentralGoogle Scholar
  320. Ribaut J-M, de Vicente MC, Delannay X (2010) Molecular breeding in developing countries: challenges and perspectives. Curr Opin Plant Biol 13:213–218PubMedGoogle Scholar
  321. Ritchie AL, Krauss SL (2012) A genetic assessment of ecological restoration success in Banksiaattenuata. Restor Ecol 20:441–449Google Scholar
  322. Roda F, Ambrose L, Walter GM, Liu HL, Schaul A, Lowe A, Pelser PB, Prentis P, Rieseberg LH, Ortiz-Barrientos D (2013) Genomic evidence for the parallel evolution of coastal forms in the Seneciolautus complex. Mol Ecol 22:2941–2952PubMedGoogle Scholar
  323. Rojas W, Soto J, Pinto M, Jager M, Padulosi S (2010) Granos andinos: avances, logros y experiencias desarrolladas en quinua, cañahua y amaranto en Bolivia. Bioversity International, Rome, p 191Google Scholar
  324. Rose JCK, Bashir S, Giovannoni JJ, Jahn MM, Saravanan RS (2004) Tackling the plant proteome: practical approaches, hurdles and experimental tools. Plant J 39:715–733PubMedGoogle Scholar
  325. Rose PW et al (2011) The RCSB protein data bank: redesigned web site and web services. Nucleic Acids Res 39:D392–D401PubMedGoogle Scholar
  326. Rudebjer P, van Schagen B, Chakeredza S, Njoroge K, Kamau H, Baena M (2011) Teaching agrobiodiversity: a curriculum guide for higher education. Bioversity International, Rome, p 96Google Scholar
  327. Ruiz-Orera J, Messeguer X, Subirana JA, Alba MM (2014) Long non-coding RNAs as a source of new peptides. elife 3:e03523PubMedPubMedCentralGoogle Scholar
  328. Ryan AB et al (2007) Identification and genetic characterization of smooth cordgrass for coastal wetland restoration. J Aquat Plant Manage 45:90–99Google Scholar
  329. Saintenac C, Jiang D, Wang S, Akhunov E (2013) Sequence-based mapping of the polyploid wheat genome. G3 (Bethesda) 3:1105–1114Google Scholar
  330. Sakk E, Odebode IE (2011) Vector space information retrieval techniques. In: Mahdavi MA (ed) Bioinformatic-trends and methodologies. InTech Publications. http://www.intechopen.com/books/bioinformatics
  331. Salgotra RK, Gupta BB, Stewart CN Jr (2014) From genomics to functional markers in the era of next-generation sequencing. Biotechnol Lett 36:417–426PubMedGoogle Scholar
  332. Salwinski L et al (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res 32:D449–D451PubMedPubMedCentralGoogle Scholar
  333. Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (1977a) Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265:687–695PubMedGoogle Scholar
  334. Sanger F, Nicklen S, Coulson AR (1977b) DNA sequencing withchain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5546PubMedPubMedCentralGoogle Scholar
  335. Sansaloni C et al (2011) Diversity arrays technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus. Proc BMC 5(Suppl 7):54. BioMed Central LtdGoogle Scholar
  336. Savolainen O, Lascoux M, Merila J (2013) Ecological genomics of local adaptation. Nat Rev Genet 14:807–820PubMedGoogle Scholar
  337. Saxena A, Cramer CS (2013) Metabolomics: a potential tool for breeding nutraceutical vegetables. Adv Crop Sci Technol 1:106.  https://doi.org/10.4172/2329.8863.1000106 CrossRefGoogle Scholar
  338. Sayers EW et al (2011) Database resources of the National Center for biotechnology information. Nucleic Acids Res 39:D38–D51PubMedGoogle Scholar
  339. Schadt EE et al (2010a) Computational solutions to large-scale data management and analysis. Nat Rev Genet 11:647–657PubMedPubMedCentralGoogle Scholar
  340. Schadt EE, Turner S, Kasarskis A (2010b) A window into third-generation sequencing. Hum Mol Genet 19(R2):R227–R240PubMedGoogle Scholar
  341. Schaub MC, Lucchinetti E, Zaugg M (2009) Genomics, transcriptomics, and proteomics of the ischemic heart. Heart Metab 42:4–9Google Scholar
  342. Schmidhuber J, Tubiello F (2007) Global food security under climate change. PNAS 104:19703–19708PubMedPubMedCentralGoogle Scholar
  343. Schmutz J, Steven B, Cannon Schlueter J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183PubMedGoogle Scholar
  344. Schmutz J et al (2014) A reference genome for common bean and genome-wide analysis of dual domestication. Nat Genet 46:1754–1760Google Scholar
  345. Schnable PS (2013) Next generation phenotyping and breeding. http://schnablelab.plantgenomics.iastate.edu/docs/resources/media/Schnable-UMN-3-25-13.pdf
  346. Schnable PS, Springer NM (2013) Progress toward understanding heterosis incrop plants. Annu Rev Plant Biol 64:71–88PubMedGoogle Scholar
  347. Schoofs L, Baggerman G (2003) Peptidomics in Drosophila melanogaster. Brief Funct Genomic Proteomic 2:114–120PubMedGoogle Scholar
  348. Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21:1794–1805PubMedGoogle Scholar
  349. Shokralla S, Gibson JF, Nikbakht H, Janzen DH, Hallwachs W et al (2014) Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Mol Ecol Resour 14:892–901PubMedPubMedCentralGoogle Scholar
  350. Sim S-C, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, Hamilton JP, Buell CR, Causse M, Wijeratne S, Francis DM (2012) Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One 7:e40563PubMedPubMedCentralGoogle Scholar
  351. Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D et al (2009) Short-read sequencing technologies for transcription alanalyses. Annu Rev Plant Biol 60:305–333PubMedGoogle Scholar
  352. Slate J, Gratten J, Beraldi D, Stapley J, Hale M, Pemberton J (2009) Gene mapping in the wild with SNPs: guidelines andfuture directions. Genetica 136:97–107PubMedGoogle Scholar
  353. Sleator RD (2010) An overview of the current status of eukaryote gene prediction strategies. Gene 461:1–4PubMedGoogle Scholar
  354. Smith FI, Eyzaguirre P (2007) African leafy vegetables: their role in the World Health Organization’s global fruit and vegetables initiative. Afr J Food Agric Nutr Dev 7:1–17Google Scholar
  355. Smith CD, Zimin A, Holt C, Abouheif E, Benton R et al (2011) Draft genome of the globally widespread and invasive argentine ant Linepithema humile. Proc Nat Acad Sci U S A 108:5673–5678Google Scholar
  356. Song J, Braun G, Bevis E, Doncaster K (2006) A simple protocol for proteinextraction of recalcitrant fruit tissues suitable for 2-D electrophoresis and MSanalysis. Electrophoresis 27:3144–3151PubMedGoogle Scholar
  357. Stamp P, Messmer R, Walter A (2012) Competitive underutilized crops will depend on the state of funding of breeding programmes: an opinion on the example of Europe. Plant Breed 131:461–464Google Scholar
  358. Stapley J, Reger J, Feulner PGD, Smadja C, Galindo J, Ekblom R et al (2010) Adaptation genomics: the next generation. Trends Ecol Evol 25:705–712PubMedGoogle Scholar
  359. Steele PR, Hertweck KL, Mayfield D, McKain MR, Leebens-Mack JH, Pires JC (2012) Quality and quantity of data recovered from massively parallel sequencing: examples in Asparagales and Poaceae. Am J Bot 99:330–348PubMedGoogle Scholar
  360. Stein LD (2003) Integrating biological databases. Nat Rev Genet 4:337–345PubMedGoogle Scholar
  361. Stein LD (2010) The case for cloud computing in genome informatics. Genome Biol 11:207PubMedPubMedCentralGoogle Scholar
  362. Stinchcombe JR, Hoekstra HE (2007) Combining populationgenomics and quantitative genetics: finding thegenes underlying ecologically important traits. Heredity 100:158–170PubMedGoogle Scholar
  363. Stingemore JA, Nevill PG, Gardener MG, Krauss SL (2013) Development of microsatellite markers for two Australian Persoonia (Proteaceae) species using two different techniques. Appl Plant Sci 1:1300023Google Scholar
  364. Straub SC, Parks M, Weitemeir K, Fishbein M, Cronn RC, Liston A (2012) Navigating the tip of the genetic iceberg: next generation sequencing for plant systematic. Am J Bot 99:349–364PubMedGoogle Scholar
  365. Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B (2005) DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics 6:66PubMedPubMedCentralGoogle Scholar
  366. Tabata R, Sawa S (2014) Maturation processes and structures of small secreted peptides in plants. Front Plant Sci 5:311PubMedPubMedCentralGoogle Scholar
  367. Tagu D, Colbourne JK, Nègre N (2014) Genomic data integration for ecological and evolutionary traits in non-model organisms. BMC Genomics 15:490PubMedPubMedCentralGoogle Scholar
  368. Takahashi T, Nagata N, Sota T (2014) Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock. Mol Phylogenet Evol 80:137–144PubMedGoogle Scholar
  369. Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066PubMedGoogle Scholar
  370. Tavormina P, De Coninck B, Nikonorova N, De Met I, Cammue BP (2015) The plant peptidome: an expanding repertoire of structural features and biological functions. Plant Cell 27:2095–2118PubMedPubMedCentralGoogle Scholar
  371. Taylor WR, Jonassen I (2004) A structural pattern-based method for protein foldrecognition. Proteins 56:222–234PubMedGoogle Scholar
  372. Taylor KH, Kramer RS, Davis JW, Guo J, Duff DJ, Xu D et al (2007) Ultra-deep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454sequencing. Cancer Res 67:8511–8518PubMedGoogle Scholar
  373. Teer JK, Johnston JJ, Anzick SL, Pineda M, Stone G (2013) NISC comparative sequencing program, massively parallell sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting. BMC Genomics 14:253PubMedPubMedCentralGoogle Scholar
  374. Tester M, Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science 327:818–822PubMedGoogle Scholar
  375. Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M et al (2012) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565–2573PubMedGoogle Scholar
  376. Thomson M, Zhao K, Wright M, McNally K, Rey J et al (2011) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Mol Breed 29:1–12Google Scholar
  377. Thottathil GP, Jayasekaran K, Othman AS (2016) Sequencing crop genomes: a gateway to improved agriculture. Trop Life Sci Res 27:93–114PubMedPubMedCentralGoogle Scholar
  378. Tilman D, Balzer C, Hill J, Befort BL (2011) Global food demand and the sustainable intensification of agriculture. Proc Natl Acad Sci U S A 108:20260–20264PubMedPubMedCentralGoogle Scholar
  379. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515PubMedPubMedCentralGoogle Scholar
  380. Travis SE et al (2002) A comparative assessment of genetic diversity among differently-aged populations of Spartina alterniflora on restored versus natural wetlands. Restor Ecol 10:37–42Google Scholar
  381. Trayhuru P (1996) Northern blotting. Proc Nutr Soc 55:583–589Google Scholar
  382. Tsai H, Howell T, Nitcher R, Missirian V, Watson BK, Ngo J, Lieberman M, Fass J, Uauy C, Tran RK, Khan AA, Filkov V, Tai TH, Dubcovsky J, Comai L (2011) Discovery of rare mutations in populations: TILLING by sequencing. Plant Physiol 156:1257–1268PubMedPubMedCentralGoogle Scholar
  383. Tsiridis E, Giannoudis PV (2006) Transcriptomics and proteomics. Advancing theunderstanding of genetic basis of fracture healing. Intern J Care Injury 37S:S13–S19Google Scholar
  384. Turesson G (1922) The genotypical response of plant species to their habitat. Hereditas 3:211–227Google Scholar
  385. Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV (2010) Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet 42:260–263PubMedGoogle Scholar
  386. Unamba CIN, Nag A, Sharma RK (2015) Next generation sequencing technologies: the doorway to the unexplored genomics of non-model plants. Front Plant Sci 6:1074.  https://doi.org/10.3389/fpls.2015.01074 CrossRefPubMedPubMedCentralGoogle Scholar
  387. Uusiku NP, Oelofse A, Duodu KG, Bester MJ, Faber M (2010) Nutritional value of leafy vegetables of sub-Saharan Africa and their potential contribution to human health: a review. J Food Composit Anal 23:499–509Google Scholar
  388. Valentini A, Pompanon F, Taberlet P (2009) DNA barcoding for ecologists. Trends Ecol Evol 24:110–117PubMedGoogle Scholar
  389. Van der Weerden NL, Bleackley MR, Anderson MA (2013) Properties and mechanisms of action of naturally occurring ant-ifungal peptides. Cell Mol Life Sci 70:3545–3570PubMedGoogle Scholar
  390. Vandershuren H, Nyaboga E, Poon JS, Baerenfaller K, Grossmann J, Hirsch-Hoffmann M, Kirchgessner N, Nanni P, Gruissem W (2014) Large-scale proteomics of the cassava storage root and identification of a target gene to reduce postharvest deterioration. Plant Cell 26:1913–1924Google Scholar
  391. Varshney RK, Tuberosa R (eds) (2007) Genomic assisted crop improvement: genomics approaches and platforms. Springer Verlag, NewYork, NYGoogle Scholar
  392. Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530PubMedGoogle Scholar
  393. Varshney RK, Song C, Saxena RK, Azam S, Yu S et al (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol 31:240–246PubMedGoogle Scholar
  394. Varshney RK, Terauchi R, McCouch SR (2014) Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol 12(6):e1001883.  https://doi.org/10.1371/journal.pbio.1001883 CrossRefPubMedPubMedCentralGoogle Scholar
  395. Vaughan DA, Balazs E, Heslop-Harrison JS (2007) From crop domestication to super-domestication. Ann Bot 100:893–901PubMedPubMedCentralGoogle Scholar
  396. Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, Gasic K, Micheletti D et al (2012) Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One 7:e35668PubMedPubMedCentralGoogle Scholar
  397. Vogt G, Etzold T, Argos P (1995) An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. J Mol Biol 249:816–831PubMedGoogle Scholar
  398. Vos P et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedPubMedCentralGoogle Scholar
  399. Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H et al (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 10:347PubMedPubMedCentralGoogle Scholar
  400. Wang JTL, Zaki MJ, Toivonen HTT, Sasha D (eds) (2005) Data Mining in Bioinformatics. Spinger Verlag Press, HeidelbergGoogle Scholar
  401. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63PubMedPubMedCentralGoogle Scholar
  402. Wang N, Thomson M, Bodles WJA, Crawford RMM, Hunt H, Featherstone AW, Pellicer J, Buggs RJA (2013a) Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Mol Ecol 22:3098–3111PubMedGoogle Scholar
  403. Wang XQ, Zhao L, Eaton DAR et al (2013b) Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing. Mol Ecol Resour 13:938–945PubMedGoogle Scholar
  404. Wang JTL et al (2017) Footprints of domestication revealed by RAD-tag resequencing in loquat: SNP data reveals a non-significant domestication bottleneck and a single domestication event. BMC Genomics 18:354.  https://doi.org/10.1186/s12864-017-3738-y CrossRefPubMedPubMedCentralGoogle Scholar
  405. Weinberger K (2007) Are indigenous vegetables underutilised crops? Some evidence from eastern Africa and Southeast Asia. Acta Hortic (752):29–34Google Scholar
  406. Wen ZN, Wang K, Li M, Nie F, Yang Y (2005) Analyzing functional similarity of protein sequences with discrete wavelet transform. Comput Biol Chem 29:220–228PubMedGoogle Scholar
  407. Wendel JF, Weeden NF (1989) Visualization and interpretation of plant isozymes. Plant Biol 5(45):29Google Scholar
  408. van der Werf MJ, Jellema RH, Hankemeier T (2005) Microbial metabolomics: replacing trial-and-error by the unbiased selection and ranking of targets. J Ind Microbiol Biotechnol 32:234–252PubMedGoogle Scholar
  409. Wetterstrand KA (2014) DNA sequencing costs: data from the NHGRI Genome Sequencing Program. http://www.genome.gov/sequencingcosts
  410. Wheat C (2010) Rapidly developing functional genomics inecological model systems via 454 transcriptome sequencing. Genetica 138:433–451PubMedGoogle Scholar
  411. Wheeler N, Sederoff R (2009) Role of genomics in the potential restoration of the American chestnut. Tree Genet Genomes 5:181–187Google Scholar
  412. Williams J, Kubelik A, Livak K et al (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535PubMedPubMedCentralGoogle Scholar
  413. Williams AV, Nevill PG, Krauss SL (2014) Next generation restoration genetics: applications. Trends Plant Sci 19:529–537PubMedGoogle Scholar
  414. Wong KL, Wong RNS, Zhang L, Liu WK, Ng TB, Shaw PC et al (2014) Bioactive proteins and peptides isolated from Chinese medicines with pharmaceutical potential. Chinese Med 9:19Google Scholar
  415. Wu KS, Tanksley SD (1993) Abundance, polymorphism and geneticmapping of microsatellites in rice. Mol Gen Genet 241:225–235PubMedGoogle Scholar
  416. Würschum JC, Reif T, Kraft G, Janssen G, Zhao Y (2013) Genomic selection insugar beet breeding populations. BMC Genet 14:85PubMedPubMedCentralGoogle Scholar
  417. Xiao S (2012) Protecting crops from pathogens: novel approaches to an old problem. Gene Technol 1.  https://doi.org/10.4172/gnt.1000e103
  418. Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407Google Scholar
  419. Xu W, Miranker DP (2003) A metric model of amino acid substitution. Bioinformatics 20:1214–1221Google Scholar
  420. Xu J, Ge X, Dolan MC (2011) Towards high-yield production of pharmaceutical proteins with plant cell suspension cultures. Biotechnol Adv 29:278–299PubMedGoogle Scholar
  421. Yang R-Y, Keding GB (2009) Nutritional contributions of important African indigenous vegetables. In: Shackleton CM, Pasquini M, Drescher AW (eds) African indigenous vegetables in urban agriculture. Earthscan, London, pp 105–143Google Scholar
  422. Yang X et al (2011) Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Res 21:634–641PubMedPubMedCentralGoogle Scholar
  423. Yang H, Tao Y, Zheng Z, Li C, Sweetingham MW, Howieson JG (2012) Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. BMC Genomics 13:318–329PubMedPubMedCentralGoogle Scholar
  424. Yang H, Tao Y, Zheng Z et al (2013a) Rapid development of molecular markers by next-generation sequencing linked to a gene conferring Phomopsis stem blight disease resistance for markerassisted selection in lupin (Lupinus angustifolius L) breeding. Theor Appl Genet 126:511–522PubMedGoogle Scholar
  425. Yang JB, Yang SX, Li HT, Yang J, Li DZ (2013b) Comparative chloroplast genomes of Camellia species. PLoS One 8:e73053PubMedPubMedCentralGoogle Scholar
  426. Yang H, Li C, Lam H-M, Clements J, Yan G, Zhao S (2015a) Sequencing consolidates molecular markers with plant breeding practice. Theor Appl Genet 128:779–795PubMedGoogle Scholar
  427. Yang H, Tao Y, Zheng Z, Li C, Sweetingham MW, Howieson JG (2015b) Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L. BMC Genomics 13:318Google Scholar
  428. Yant Y (2012) Genome-wide mapping of transcription factor bindingreveals developmental process integration and a fresh look at evolutionarydynamics. Am J Bot 9:277–290Google Scholar
  429. Yoder JB, Stanton-Geddes J, Zhou P, Briskine R, Young ND et al (2014) Genomic signature of adaptation to climate in Medicagotruncatula. Genetics 196:1263–1275PubMedPubMedCentralGoogle Scholar
  430. Yoo M-J, Szadkowski E, Wendel JF (2013) Homoeolog expression bias and expression level dominance in allopolyploid cotton. Heredity 110:171–180PubMedPubMedCentralGoogle Scholar
  431. Zalapa JE et al (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99:193–208PubMedGoogle Scholar
  432. Zayed A, Whitfield CW (2008) A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey beeApis mellifera. Proc Nat Acad Sci U S A 105:3421–3426Google Scholar
  433. Zhang Q et al (2007) Strategies for developing green super rice. Proc Natl Acad Sci 104:16402–16409PubMedPubMedCentralGoogle Scholar
  434. Zhang Z et al (2009) Bringing web 2.0 to bioinformatics. Brief Bioinform 10:1–10PubMedGoogle Scholar
  435. Zhang ZH, Lee HK, Mihalek I (2010) Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity. BMC Bioinformatics 11:155PubMedPubMedCentralGoogle Scholar
  436. Zhang Z, Bajic VB, Yu J, Cheung K-H, Townsend JP (2011) Data integration in bioinformatics: current efforts and challenges. In: Mahdavi MA (ed) Bioinformatic-trends and methodologies. InTech Publications. http://www.intechopen.com/books/bioinformatics Google Scholar
  437. Zhang Y, Li L, Yan TL, Liu Q (2014) Complete chloroplast genome sequences of Praxelis (Eupatorium catarium Veldkamp), an important invasive species. Gene 549:58–69PubMedGoogle Scholar
  438. Zhao J, Grant SFA (2010) Advances in whole genome sequencing technology. Mol Cell Biol 17:1549–1560.  https://doi.org/10.1089/cmb.2010.0127 CrossRefGoogle Scholar
  439. Zhou H, Steffenson BJ, Muehlbauer G, Wanyera R, Njau P, Ndeda S (2014) Association mapping of stem rust race TTKSK resistance in US barley breeding germplasm. Theor Appl Genet 127:1293–1304PubMedPubMedCentralGoogle Scholar
  440. Zhou L et al (2015) Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method. Sci Rep 5:9350.  https://doi.org/10.1038/srep09350 CrossRefPubMedPubMedCentralGoogle Scholar
  441. Zimmermann MB, Hurrell R (2002) Improving iron, zinc and vitamin a nutrition through plant biotechnology. Curr Opin Biotechnol 13:142–145PubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.School of Life Sciences, Faculty of ScienceUniversity of Technology Sydney (UTS)SydneyAustralia

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