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Guidelines for the Choice of Sequences for Molecular Plant Taxonomy

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Molecular Plant Taxonomy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1115))

Abstract

This chapter presents an overview of the major plant DNA sequences and molecular methods available for plant taxonomy. Guidelines are provided for the choice of sequences and methods to be used, based on the DNA compartment (nuclear, chloroplastic, mitochondrial), evolutionary mechanisms, and the level of taxonomic differentiation of the plants under survey.

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References

  1. Gregory T (2001) Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol Rev 76:65–101

    Article  CAS  PubMed  Google Scholar 

  2. Thomas C (1971) The genetic organization of chromosomes. Annu Rev Genet 5:237–256

    Article  CAS  PubMed  Google Scholar 

  3. Schmidt T, Heslop-Harrison JS (1998) Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci 3:195–199

    Article  Google Scholar 

  4. Hamby RK, Zimmer EA (1992) Ribosomal RNA as a phylogenetic tool in plant systematics. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematics of plants. Chapman & Hall, New York

    Google Scholar 

  5. Schaal BA, Learn GH (1988) Ribosomal DNA variations between and among plant populations. Ann Mo Bot Gard 75:1207–1216

    Article  Google Scholar 

  6. Hillis DM, Dixon MT (1991) Ribosomal DNA : molecular evolution and phylogenetic inference. Q Rev Biol 66:411–453

    Article  CAS  PubMed  Google Scholar 

  7. Alvarez IA, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol 29:417–434

    Article  CAS  PubMed  Google Scholar 

  8. Poczai P, Hyvönen J (2010) Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects. Mol Biol Rep 37:1897–1912

    Article  CAS  PubMed  Google Scholar 

  9. Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445

    Article  CAS  PubMed  Google Scholar 

  10. SanMiguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann Bot 82:37–44

    Article  CAS  Google Scholar 

  11. Ray DA (2007) SINEs of progress: mobile element applications to molecular ecology. Mol Ecol 16:19–33

    Article  CAS  PubMed  Google Scholar 

  12. Deragon JM, Zhang X (2006) Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers. Syst Biol 55:949–956

    Article  PubMed  Google Scholar 

  13. Schmidt T (1999) LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes. Plant Mol Biol 40:903–910

    Article  CAS  PubMed  Google Scholar 

  14. Feliner GN, Rosselló JA (2007) Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet Evol 44:911–919

    Article  Google Scholar 

  15. Zimmer EA, Wen J (2013) Using nuclear gene data for plant phylogenetics: progress and prospects. Mol Phylogenet Evol 66:539–550

    Article  PubMed  Google Scholar 

  16. Small RL, Cronn RC, Wendel JF (2004) Use of nuclear genes for phylogeny reconstruction in plants. Aust Syst Bot 17:145–170

    Article  CAS  Google Scholar 

  17. Schlötterer C (2004) The evolution of molecular markers – just a matter of fashion? Nat Rev Genet 5:63–69

    Article  PubMed  Google Scholar 

  18. Hudson ME (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Resour 8:3–17

    Article  CAS  PubMed  Google Scholar 

  19. Grover CE, Salmon A, Wendel JF (2012) Targeted sequence capture as a powerful tool for evolutionary analysis. Am J Bot 99:312–319

    Article  PubMed  Google Scholar 

  20. Timme RE, Bachvaroff TR, Delwiche CF (2012) Broad phylogenomic sampling and the sister lineage of land plants. PLoS One 7:1–8

    Article  Google Scholar 

  21. Syvänen AC (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2:930–942

    Article  PubMed  Google Scholar 

  22. Jaccoud D, Peng K, Feinstein D, Killian A (2001) Diversity arrays: a solid state technology for sequence information independant genotyping. Nucleic Acids Res 29:1–7

    Article  Google Scholar 

  23. James KE, Schneider H, Ansell SW, Evers M, Robba L, Uszynski G, Pedersen N, Newton AE, Russell SJ, Vogel JC, Kilian A (2008) Diversity arrays technology (DArT) for pan-genomic evolutionary studies of non-model organisms. PLoS One 3:1–11

    Article  Google Scholar 

  24. Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel H (eds) Evolving genes and proteins. Academic, New York, pp 97–166

    Google Scholar 

  25. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB (2002) Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu Rev Ecol Syst 33:707–740

    Article  Google Scholar 

  26. Kimura M, Ohta T (1974) On some principles governing molecular evolution*(population genetics/mutational pressure/negative selection/random drift). Proc Natl Acad Sci USA 71:2848–2852

    Article  CAS  PubMed  Google Scholar 

  27. Saliba-Colombani V, Causse M, Gervais L, Philouze J (2000) Efficiency of RFLP, RAPD, and AFLP markers for the construction of an intraspecific map of the tomato genome. Genome 43:29–40

    Article  CAS  PubMed  Google Scholar 

  28. Qi X, Stam P, Lindhout P (1998) Use of locus-specific AFLP markers to construct a high-density molecular map in barley. Theor Appl Genet 96:376–384

    Article  CAS  Google Scholar 

  29. Saal B, Wricke G (2002) Clustering of amplified fragment length polymorphism markers in a linkage map of rye. Plant Breed 121:117–123

    Article  CAS  Google Scholar 

  30. Young WP, Schuppet JM, Keim P (1999) DNA methylation and AFLP marker distribution in the soybean genome. Theor Appl Genet 99:785–792

    Article  CAS  Google Scholar 

  31. Shriver MO, Jin L, Chakraborty R, Boerwinkle E (1993) VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics 134:983–993

    CAS  PubMed  Google Scholar 

  32. Bhargava A, Fuentes FF (2010) Mutational dynamics of microsatellites. Mol Biotechnol 44:250–266

    Article  CAS  PubMed  Google Scholar 

  33. Buschiazzo E, Gemmell NJ (2006) The rise, fall and renaissance of microsatellites in eukaryotic genomes. BioEssays 28:1040–1050

    Article  CAS  PubMed  Google Scholar 

  34. Jeffreys AJ, Wilson V, Thein SL (1985) Individual-specific fingerprints of human DNA. Nature 316:76–79

    Article  CAS  PubMed  Google Scholar 

  35. Jobling MA, Gill P (2004) Encoded evidence: DNA in forensic analysis. Nat Rev Genet 5:739–752

    Article  CAS  PubMed  Google Scholar 

  36. Dover G (1982) Molecular drive: a cohesive mode of species evolution. Nature 299:111–117

    Article  CAS  PubMed  Google Scholar 

  37. Dover G (1994) Concerted evolution, molecular drive and natural selection. Curr Biol 4:1165–1166

    Article  CAS  PubMed  Google Scholar 

  38. Plohl M, Luchetti A, Meštrović N, Mantovani B (2008) Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 409:72–82

    Article  CAS  PubMed  Google Scholar 

  39. Nei M, Rooney AP (2005) Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39:121–152

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  40. Ganley ARD, Kobayashi T (2007) Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Res 17:184–191

    Article  CAS  PubMed  Google Scholar 

  41. Hollingsworth ML, Clark A, Forrest LL, Richardson J, Pennington RT, Long DG, Cowan RO, Chase MW, Gaudeul M, Hollingsworth PM (2009) Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Mol Ecol Resour 9:439–457

    Article  CAS  PubMed  Google Scholar 

  42. Wolfe KH, Li W-H, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. PNAS 84:9054–9058

    Article  CAS  PubMed  Google Scholar 

  43. Kress WJ, Wurdack KJ, Zimmer EA, Weig LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. PNAS 102:8369–8374

    Article  CAS  PubMed  Google Scholar 

  44. Capy P, Anxolabehere D, Langin T (1994) The strange phylogenies of transposable elements: are horizontal transfers the only explanation. Trends Genet 7–12

    Google Scholar 

  45. Syvanen M (1994) Horizontal gene transfer: evidence and possible consequences. Annu Rev Genet 28:237–261

    Article  CAS  PubMed  Google Scholar 

  46. McCauley DE, Sunby AK, Bailey MF, Welch ME (2007) Inheritance of chloroplast DNA is not strictly maternal in Silene vulgaris (Caryophyllaceae): evidence from experimental crosses and natural populations. Am J Bot 94:1333–1337

    Article  CAS  PubMed  Google Scholar 

  47. Bensch S, Akesson M (2005) Ten years of AFLP in ecology and evolution: why so few animals? Mol Ecol 14

    Google Scholar 

  48. Mariette S, Corre VL, Austerlitz F, Kremer A (2002) Sampling within the genome for measuring within population diversity: trade-offs between markers. Mol Ecol 11:1145–1156

    Article  CAS  PubMed  Google Scholar 

  49. Morin PA, Luikart G, Wayne RK, The SNP workshop group (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216

    Article  Google Scholar 

  50. Flavell R, Bennett M, Smith J, Smith D (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 12:257–259

    Article  CAS  PubMed  Google Scholar 

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Besse, P. (2014). Guidelines for the Choice of Sequences for Molecular Plant Taxonomy. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 1115. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-767-9_2

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  • DOI: https://doi.org/10.1007/978-1-62703-767-9_2

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-766-2

  • Online ISBN: 978-1-62703-767-9

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