Guidelines for the Choice of Sequences for Molecular Plant Taxonomy

  • Pascale Besse
Part of the Methods in Molecular Biology book series (MIMB, volume 1115)


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.

Key words

Nuclear DNA Chloroplast DNA Mitochondrial DNA Repeated DNA Low-copy DNA Evolution Molecular plant taxonomy 


  1. 1.
    Gregory T (2001) Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol Rev 76:65–101PubMedCrossRefGoogle Scholar
  2. 2.
    Thomas C (1971) The genetic organization of chromosomes. Annu Rev Genet 5:237–256PubMedCrossRefGoogle Scholar
  3. 3.
    Schmidt T, Heslop-Harrison JS (1998) Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci 3:195–199CrossRefGoogle Scholar
  4. 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 YorkGoogle Scholar
  5. 5.
    Schaal BA, Learn GH (1988) Ribosomal DNA variations between and among plant populations. Ann Mo Bot Gard 75:1207–1216CrossRefGoogle Scholar
  6. 6.
    Hillis DM, Dixon MT (1991) Ribosomal DNA : molecular evolution and phylogenetic inference. Q Rev Biol 66:411–453PubMedCrossRefGoogle Scholar
  7. 7.
    Alvarez IA, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol 29:417–434PubMedCrossRefGoogle Scholar
  8. 8.
    Poczai P, Hyvönen J (2010) Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects. Mol Biol Rep 37:1897–1912PubMedCrossRefGoogle Scholar
  9. 9.
    Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445PubMedCrossRefGoogle Scholar
  10. 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 82:37–44CrossRefGoogle Scholar
  11. 11.
    Ray DA (2007) SINEs of progress: mobile element applications to molecular ecology. Mol Ecol 16:19–33PubMedCrossRefGoogle Scholar
  12. 12.
    Deragon JM, Zhang X (2006) Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers. Syst Biol 55:949–956PubMedCrossRefGoogle Scholar
  13. 13.
    Schmidt T (1999) LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes. Plant Mol Biol 40:903–910PubMedCrossRefGoogle Scholar
  14. 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 44:911–919CrossRefGoogle Scholar
  15. 15.
    Zimmer EA, Wen J (2013) Using nuclear gene data for plant phylogenetics: progress and prospects. Mol Phylogenet Evol 66:539–550PubMedCrossRefGoogle Scholar
  16. 16.
    Small RL, Cronn RC, Wendel JF (2004) Use of nuclear genes for phylogeny reconstruction in plants. Aust Syst Bot 17:145–170CrossRefGoogle Scholar
  17. 17.
    Schlötterer C (2004) The evolution of molecular markers – just a matter of fashion? Nat Rev Genet 5:63–69PubMedCrossRefGoogle Scholar
  18. 18.
    Hudson ME (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Resour 8:3–17PubMedCrossRefGoogle Scholar
  19. 19.
    Grover CE, Salmon A, Wendel JF (2012) Targeted sequence capture as a powerful tool for evolutionary analysis. Am J Bot 99:312–319PubMedCrossRefGoogle Scholar
  20. 20.
    Timme RE, Bachvaroff TR, Delwiche CF (2012) Broad phylogenomic sampling and the sister lineage of land plants. PLoS One 7:1–8CrossRefGoogle Scholar
  21. 21.
    Syvänen AC (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2:930–942PubMedCrossRefGoogle Scholar
  22. 22.
    Jaccoud D, Peng K, Feinstein D, Killian A (2001) Diversity arrays: a solid state technology for sequence information independant genotyping. Nucleic Acids Res 29:1–7CrossRefGoogle Scholar
  23. 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 3:1–11CrossRefGoogle Scholar
  24. 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 97–166Google Scholar
  25. 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 33:707–740CrossRefGoogle Scholar
  26. 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 71:2848–2852PubMedCrossRefGoogle Scholar
  27. 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 43:29–40PubMedCrossRefGoogle Scholar
  28. 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 96:376–384CrossRefGoogle Scholar
  29. 29.
    Saal B, Wricke G (2002) Clustering of amplified fragment length polymorphism markers in a linkage map of rye. Plant Breed 121:117–123CrossRefGoogle Scholar
  30. 30.
    Young WP, Schuppet JM, Keim P (1999) DNA methylation and AFLP marker distribution in the soybean genome. Theor Appl Genet 99:785–792CrossRefGoogle Scholar
  31. 31.
    Shriver MO, Jin L, Chakraborty R, Boerwinkle E (1993) VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics 134:983–993PubMedGoogle Scholar
  32. 32.
    Bhargava A, Fuentes FF (2010) Mutational dynamics of microsatellites. Mol Biotechnol 44:250–266PubMedCrossRefGoogle Scholar
  33. 33.
    Buschiazzo E, Gemmell NJ (2006) The rise, fall and renaissance of microsatellites in eukaryotic genomes. BioEssays 28:1040–1050PubMedCrossRefGoogle Scholar
  34. 34.
    Jeffreys AJ, Wilson V, Thein SL (1985) Individual-specific fingerprints of human DNA. Nature 316:76–79PubMedCrossRefGoogle Scholar
  35. 35.
    Jobling MA, Gill P (2004) Encoded evidence: DNA in forensic analysis. Nat Rev Genet 5:739–752PubMedCrossRefGoogle Scholar
  36. 36.
    Dover G (1982) Molecular drive: a cohesive mode of species evolution. Nature 299:111–117PubMedCrossRefGoogle Scholar
  37. 37.
    Dover G (1994) Concerted evolution, molecular drive and natural selection. Curr Biol 4:1165–1166PubMedCrossRefGoogle Scholar
  38. 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 409:72–82PubMedCrossRefGoogle Scholar
  39. 39.
    Nei M, Rooney AP (2005) Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39:121–152PubMedCentralPubMedCrossRefGoogle Scholar
  40. 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 17:184–191PubMedCrossRefGoogle Scholar
  41. 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 9:439–457PubMedCrossRefGoogle Scholar
  42. 42.
    Wolfe KH, Li W-H, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. PNAS 84:9054–9058PubMedCrossRefGoogle Scholar
  43. 43.
    Kress WJ, Wurdack KJ, Zimmer EA, Weig LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. PNAS 102:8369–8374PubMedCrossRefGoogle Scholar
  44. 44.
    Capy P, Anxolabehere D, Langin T (1994) The strange phylogenies of transposable elements: are horizontal transfers the only explanation. Trends Genet 7–12Google Scholar
  45. 45.
    Syvanen M (1994) Horizontal gene transfer: evidence and possible consequences. Annu Rev Genet 28:237–261PubMedCrossRefGoogle Scholar
  46. 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 94:1333–1337PubMedCrossRefGoogle Scholar
  47. 47.
    Bensch S, Akesson M (2005) Ten years of AFLP in ecology and evolution: why so few animals? Mol Ecol 14Google Scholar
  48. 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 11:1145–1156PubMedCrossRefGoogle Scholar
  49. 49.
    Morin PA, Luikart G, Wayne RK, The SNP workshop group (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216CrossRefGoogle Scholar
  50. 50.
    Flavell R, Bennett M, Smith J, Smith D (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 12:257–259PubMedCrossRefGoogle Scholar

Copyright information

© Springer New York 2014

Authors and Affiliations

  • Pascale Besse
    • 1
  1. 1.UMR C53 PVBMT Université de la Réunion – Cirad, Université de la RéunionIle de la RéunionFrance

Personalised recommendations