Advertisement

Comparative Genomics of Pineapple and Other Angiosperm Genomes

  • Pingping Liang
  • Xuequn Chen
  • Xingtan Zhang
  • Haibao Tang
Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 22)

Abstract

The draft pineapple genome is a remarkable resource to breeders and plant biologists. The study of the gene repertoire involved in the crassulacean acid metabolism (CAM) photosynthetic pathway enables researchers to track down genomic and regulatory changes necessary for a shift from C3 metabolism, also shedding light on the evolution of the C4 metabolism. In addition to its unique photosynthetic pathway, pineapple occupies a unique evolutionary position on the monocot tree of life, making it an ideal genome proxy for the Poales clade. The lineage of pineapple, known as the bromeliads, serve as an excellent out-group to the well-studied cereal group while retaining a less complex genome that reflects a close-to-ancestral karyotype. Herein, we take an in-depth look on the genomic comparisons both on the whole-genome level and the local scale. On the whole-genome level, we have compared pineapple against several related monocot, eudicot, and basal angiosperm genomes providing a solid framework to study the patterns of macroscale genome evolution, in order to clarify the nature and dating of recurring genome duplication events. On the local scale, we have identified significant sequence conservation outside the coding regions that have so far remained underexplored yet critical to our understanding of the unique biology and physiology of the pineapple species.

Keywords

Synteny Homology Genome evolution Polyploidy Cyber-infrastructure 

Notes

Acknowledgment

We thank the Fujian provincial government for a Fujian “100 Talent Plan” award to HT. This work was supported by the National Key Research and Development Program of China (2016YFD0100305). Competing interests: the authors declare that they have no competing interests.

References

  1. Amborella Genome P (2013) The Amborella genome and the evolution of flowering plants. Science 342(6165):1241089.  https://doi.org/10.1126/science.1241089CrossRefGoogle Scholar
  2. Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12(7):1021–1029CrossRefGoogle Scholar
  3. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM et al (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14(4):708–715.  https://doi.org/10.1101/Gr.1933104CrossRefPubMedPubMedCentralGoogle Scholar
  4. Blanchette M, Bataille AR, Chen X, Poitras C, Laganière J, Lefèbvre C et al (2006) Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res 16(5):656–668CrossRefGoogle Scholar
  5. Bolouri H, Davidson EH (2002) Modeling DNA sequence-based cis-regulatory gene networks. Dev Biol 246(1):2–13CrossRefGoogle Scholar
  6. Bossolini E, Wicker T, Knobel PA, Keller B (2007) Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation. Plant J 49(4):704–717CrossRefGoogle Scholar
  7. Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G et al (2016) JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol 17:66.  https://doi.org/10.1186/s13059-016-0924-1CrossRefPubMedPubMedCentralGoogle Scholar
  8. Burgess D, Freeling M (2014) The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates. Plant Cell 26(3):946–961CrossRefGoogle Scholar
  9. Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW et al (2015) The genome sequence of the orchid Phalaenopsis equestris. Nat Genet 47(1):65–72.  https://doi.org/10.1038/ng.3149CrossRefPubMedGoogle Scholar
  10. Colinas J, Birnbaum K, Benfey PN (2002) Using cauliflower to find conserved non-coding regions in Arabidopsis. Plant Physiol 129(2):451–454CrossRefGoogle Scholar
  11. D’Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F, Garsmeur O et al (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213–217CrossRefGoogle Scholar
  12. Devos KM, Gale MD (2000) Genome relationships: the grass model in current research. Plant Cell 12(5):637–646CrossRefGoogle Scholar
  13. Duret L, Bucher P (1997) Searching for regulatory elements in human noncoding sequences. Curr Opin Struct Biol 7(3):399–406CrossRefGoogle Scholar
  14. Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD (2006) The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 20(11):1470–1484CrossRefGoogle Scholar
  15. Freeling M, Subramaniam S (2009) Conserved noncoding sequences (CNSs) in higher plants. Curr Opin Plant Biol 12(2):126–132CrossRefGoogle Scholar
  16. Frith MC, Kawaguchi R (2015) Split-alignment of genomes finds orthologies more accurately. Genome Biol 16:106.  https://doi.org/10.1186/S13059-015-0670-9CrossRefPubMedPubMedCentralGoogle Scholar
  17. Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci 93(19):10274–10279CrossRefGoogle Scholar
  18. Givnish TJ, Barfuss MH, Van Ee B, Riina R, Schulte K, Horres R et al (2014) Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae. Mol Phylogenet Evol 71:55–78CrossRefGoogle Scholar
  19. Guo H, Moose SP (2003) Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 15(5):1143–1158CrossRefGoogle Scholar
  20. Haberer G, Mader MT, Kosarev P, Spannagl M, Yang L, Mayer KF (2006) Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea. Plant Physiol 142(4):1589–1602CrossRefGoogle Scholar
  21. Hardison RC (2000) Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet 16(9):369–372CrossRefGoogle Scholar
  22. Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ et al (2013) An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet 45(8):891–898CrossRefGoogle Scholar
  23. Higo K, Ugawa Y, Iwamoto M, Higo H (1998) PLACE: a database of plant cis-acting regulatory DNA elements. Nucleic Acids Res 26(1):358–359.  https://doi.org/10.1093/nar/26.1.358CrossRefPubMedPubMedCentralGoogle Scholar
  24. Hupalo D, Kern AD (2013) Conservation and functional element discovery in 20 angiosperm plant genomes. Mol Biol Evol 30(7):1729–1744CrossRefGoogle Scholar
  25. Inada DC, Bashir A, Lee C, Thomas BC, Ko C, Goff SA et al (2003) Conserved noncoding sequences in the grasses4. Genome Res 13(9):2030–2041CrossRefGoogle Scholar
  26. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467.  https://doi.org/10.1038/nature06148CrossRefPubMedPubMedCentralGoogle Scholar
  27. Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J et al (2012) A genome triplication associated with early diversification of the core eudicots. Genome Biol 13(1):R3.  https://doi.org/10.1186/gb-2012-13-1-r3CrossRefPubMedPubMedCentralGoogle Scholar
  28. Jiao Y, Li J, Tang H, Paterson AH (2014) Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. Plant Cell 26(7):2792–2802.  https://doi.org/10.1105/tpc.114.127597CrossRefPubMedPubMedCentralGoogle Scholar
  29. Kaplinsky NJ, Braun DM, Penterman J, Goff SA, Freeling M (2002) Utility and distribution of conserved noncoding sequences in the grasses. Proc Natl Acad Sci 99(9):6147–6151CrossRefGoogle Scholar
  30. Kellogg EA (2001) Evolutionary history of the grasses. Plant Physiol 125(3):1198–1205CrossRefGoogle Scholar
  31. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D (2003) Evolution’s cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 100(20):11484–11489.  https://doi.org/10.1073/pnas.1932072100CrossRefPubMedPubMedCentralGoogle Scholar
  32. Lee H, Golicz AA, Bayer PE, Jiao Y, Tang H, Paterson AH et al (2016) The genome of a southern hemisphere seagrass species (Zostera muelleri). Plant Physiol 172(1):272–283.  https://doi.org/10.1104/pp.16.00868CrossRefPubMedPubMedCentralGoogle Scholar
  33. Li X, Tan L, Wang L, Hu S, Sun C (2009) Isolation and characterization of conserved non-coding sequences among rice (Oryza sativa L.) paralogous regions. Mol Gen Genomics 281(1):11–18CrossRefGoogle Scholar
  34. Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H et al (2008) Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol 148(4):1772–1781.  https://doi.org/10.1104/pp.108.124867CrossRefPubMedPubMedCentralGoogle Scholar
  35. Magallón S, Gómez-Acevedo S, Sánchez-Reyes LL, Hernández-Hernández T (2015) A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. New Phytol 207(2):437–453CrossRefGoogle Scholar
  36. Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A et al (2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res 17(6):760–774CrossRefGoogle Scholar
  37. Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE et al (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 47(12):1435–1442.  https://doi.org/10.1038/ng.3435CrossRefPubMedPubMedCentralGoogle Scholar
  38. Ming R, Wai CM, Guyot R (2016) Pineapple genome: a reference for monocots and CAM photosynthesis. Trends Genet 32(11):690–696.  https://doi.org/10.1016/j.tig.2016.08.008CrossRefPubMedGoogle Scholar
  39. Panne D, Maniatis T, Harrison SC (2007) An atomic model of the interferon-β enhanceosome. Cell 129(6):1111–1123CrossRefGoogle Scholar
  40. Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A 101(26):9903–9908.  https://doi.org/10.1073/pnas.0307901101CrossRefPubMedPubMedCentralGoogle Scholar
  41. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551–556.  https://doi.org/10.1038/nature07723CrossRefPubMedGoogle Scholar
  42. Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D et al (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492(7429):423–427.  https://doi.org/10.1038/nature11798CrossRefGoogle Scholar
  43. Pennacchio LA, Loots GG, Nobrega MA, Ovcharenko I (2007) Predicting tissue-specific enhancers in the human genome. Genome Res 17(2):201–211CrossRefGoogle Scholar
  44. Priest HD, Filichkin SA, Mockler TC (2009) Cis-regulatory elements in plant cell signaling. Curr Opin Plant Biol 12(5):643–649CrossRefGoogle Scholar
  45. Reineke AR, Bornberg-Bauer E, Gu J (2011) Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes. Nucleic Acids Res 39(14):6029–6043CrossRefGoogle Scholar
  46. Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler KA et al (2007) Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci 104(27):11376–11381CrossRefGoogle Scholar
  47. Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S et al (2012) A map of the cis-regulatory sequences in the mouse genome. Nature 488(7409):116–120CrossRefGoogle Scholar
  48. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K et al (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15(8):1034–1050CrossRefGoogle Scholar
  49. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW et al (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450(7167):219–232CrossRefGoogle Scholar
  50. Strähle U, Rastegar S (2008) Conserved non-coding sequences and transcriptional regulation. Brain Res Bull 75(2):225–230CrossRefGoogle Scholar
  51. Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH (2008) Synteny and collinearity in plant genomes. Science 320(5875):486–488.  https://doi.org/10.1126/science.1153917CrossRefPubMedGoogle Scholar
  52. Tang H, Bowers JE, Wang X, Paterson AH (2010) Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A 107(1):472–477.  https://doi.org/10.1073/pnas.0908007107CrossRefPubMedGoogle Scholar
  53. The Angiosperm Phylogeny G (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 161(2):105–121.  https://doi.org/10.1111/j.1095-8339.2009.00996.xCrossRefGoogle Scholar
  54. Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S et al (2009) FlyBase: enhancing Drosophila gene ontology annotations. Nucleic Acids Res 37(suppl 1):D555–D5D9CrossRefGoogle Scholar
  55. Wang W, Haberer G, Gundlach H, Glasser C, Nussbaumer T, Luo MC et al (2014) The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun 5:3311.  https://doi.org/10.1038/ncomms4311CrossRefPubMedPubMedCentralGoogle Scholar
  56. Wolfe KH, Gouy M, Yang Y-W, Sharp PM, Li W-H (1989) Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci 86(16):6201–6205CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Pingping Liang
    • 1
  • Xuequn Chen
    • 1
  • Xingtan Zhang
    • 1
  • Haibao Tang
    • 1
  1. 1.Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhouChina

Personalised recommendations