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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Gregory T (2001) Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol Rev 76:65–101
Thomas C (1971) The genetic organization of chromosomes. Annu Rev Genet 5:237–256
Schmidt T, Heslop-Harrison JS (1998) Genomes, genes and junk: the large-scale organization of plant chromosomes. Trends Plant Sci 3:195–199
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
Schaal BA, Learn GH (1988) Ribosomal DNA variations between and among plant populations. Ann Mo Bot Gard 75:1207–1216
Hillis DM, Dixon MT (1991) Ribosomal DNA : molecular evolution and phylogenetic inference. Q Rev Biol 66:411–453
Alvarez IA, Wendel JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol 29:417–434
Poczai P, Hyvönen J (2010) Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects. Mol Biol Rep 37:1897–1912
Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445
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
Ray DA (2007) SINEs of progress: mobile element applications to molecular ecology. Mol Ecol 16:19–33
Deragon JM, Zhang X (2006) Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers. Syst Biol 55:949–956
Schmidt T (1999) LINEs, SINEs and repetitive DNA: non-LTR retrotransposons in plant genomes. Plant Mol Biol 40:903–910
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
Zimmer EA, Wen J (2013) Using nuclear gene data for plant phylogenetics: progress and prospects. Mol Phylogenet Evol 66:539–550
Small RL, Cronn RC, Wendel JF (2004) Use of nuclear genes for phylogeny reconstruction in plants. Aust Syst Bot 17:145–170
Schlötterer C (2004) The evolution of molecular markers – just a matter of fashion? Nat Rev Genet 5:63–69
Hudson ME (2008) Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Resour 8:3–17
Grover CE, Salmon A, Wendel JF (2012) Targeted sequence capture as a powerful tool for evolutionary analysis. Am J Bot 99:312–319
Timme RE, Bachvaroff TR, Delwiche CF (2012) Broad phylogenomic sampling and the sister lineage of land plants. PLoS One 7:1–8
Syvänen AC (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2:930–942
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
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
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
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
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
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
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
Saal B, Wricke G (2002) Clustering of amplified fragment length polymorphism markers in a linkage map of rye. Plant Breed 121:117–123
Young WP, Schuppet JM, Keim P (1999) DNA methylation and AFLP marker distribution in the soybean genome. Theor Appl Genet 99:785–792
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
Bhargava A, Fuentes FF (2010) Mutational dynamics of microsatellites. Mol Biotechnol 44:250–266
Buschiazzo E, Gemmell NJ (2006) The rise, fall and renaissance of microsatellites in eukaryotic genomes. BioEssays 28:1040–1050
Jeffreys AJ, Wilson V, Thein SL (1985) Individual-specific fingerprints of human DNA. Nature 316:76–79
Jobling MA, Gill P (2004) Encoded evidence: DNA in forensic analysis. Nat Rev Genet 5:739–752
Dover G (1982) Molecular drive: a cohesive mode of species evolution. Nature 299:111–117
Dover G (1994) Concerted evolution, molecular drive and natural selection. Curr Biol 4:1165–1166
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
Nei M, Rooney AP (2005) Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39:121–152
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
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
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
Kress WJ, Wurdack KJ, Zimmer EA, Weig LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. PNAS 102:8369–8374
Capy P, Anxolabehere D, Langin T (1994) The strange phylogenies of transposable elements: are horizontal transfers the only explanation. Trends Genet 7–12
Syvanen M (1994) Horizontal gene transfer: evidence and possible consequences. Annu Rev Genet 28:237–261
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
Bensch S, Akesson M (2005) Ten years of AFLP in ecology and evolution: why so few animals? Mol Ecol 14
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
Morin PA, Luikart G, Wayne RK, The SNP workshop group (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216
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
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer New York
About this protocol
Cite this protocol
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
Download citation
DOI: https://doi.org/10.1007/978-1-62703-767-9_2
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-766-2
Online ISBN: 978-1-62703-767-9
eBook Packages: Springer Protocols