Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding
By Wenpan Dong, Jing Liu, Jing Yu, Ling Wang, Shiliang Zhou. PLoS ONE, 2012
648 citations recorded by the source corpus.
Background At present, plant molecular systematics and DNA barcoding techniques rely heavily on the use of chloroplast gene sequences. Because of the relatively low evolutionary rates of chloroplast genes, there are very few choices suitable for molecular studies on angiosperms at low taxonomic levels, and for DNA barcoding of species. Methodology/Principal Findings We scanned the entire chloroplast genomes of 12 genera to search for highly variable regions. The sequence data of 9 genera were from GenBank and 3 genera were of our own. We identified nearly 5% of the most variable loci from all variable loci in the chloroplast genomes of each genus, and then selected 23 loci that were present in at least three genera. The 23 loci included 4 coding regions, 2 introns, and 17 intergenic spacers. Of the 23 loci, the most variable (in order from highest variability to lowest) were intergenic regions ycf1-a, trnK, rpl32-trnL, and trnH-psbA, followed by trnSUGA-trnGUCC, petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnSUGA-trnGUCC, trnT-psbD, and trnW-psaJ, showed very high nucleotide diversity per site (π values) across three genera. Other loci may have strong potential for resolving phylogenetic and species identification problems at the species level. The loci accD-psaI, rbcL-accD, rpl32-trnL, rps16-trnQ, and ycf1 are absent from some genera. To amplify and sequence the highly variable loci identified in this study, we designed primers from their conserved flanking regions. We tested the applicability of the primers to amplify target sequences in eight species representing basal angiosperms, monocots, eudicots, rosids, and asterids, and confirmed that the primers amplified the desired sequences of these species. Significance/Conclusions Chloroplast genome sequences contain regions that are highly variable. Such regions are the first consideration when screening the suitable loci to resolve closely related species or genera in phylogenetic analyses, and for DNA barcoding.
Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/d6cbf4e042cca83f5ab93591f0df7947c75a1875
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Citations in the corpus
- DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing (2018, background): “Molecular studies related to phylogeny are largely dependent on chloroplast genome sequence data due to their simple and stable genetic nature, making them ideal markers in the evaluation of plant phylogeny [112,113].”
- Plant DNA barcoding: from gene to genome (2015, background): “Molecular evolution of cp-genome sequences also shows both lineage-specific and nonrandom spatial patterns of substitution (Gruenheit et al., 2008; Zhong et al., 2011; Dong et al., 2012; Ahmed et al., 2013).”