Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.

<h4>Background</h4>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 a...

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Autores principales:	Wenpan Dong, Jing Liu, Jing Yu, Ling Wang, Shiliang Zhou
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/616003854d6f4889a60f83bf1af7eac6
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spelling	oai:doaj.org-article:616003854d6f4889a60f83bf1af7eac62021-11-18T07:22:24ZHighly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.1932-620310.1371/journal.pone.0035071https://doaj.org/article/616003854d6f4889a60f83bf1af7eac62012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22511980/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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 trnS(UGA)-trnG(UCC), petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnS(UGA)-trnG(UCC), 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.<h4>Significance/conclusions</h4>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.Wenpan DongJing LiuJing YuLing WangShiliang ZhouPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 4, p e35071 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wenpan Dong Jing Liu Jing Yu Ling Wang Shiliang Zhou Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.
description	<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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 trnS(UGA)-trnG(UCC), petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnS(UGA)-trnG(UCC), 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.<h4>Significance/conclusions</h4>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.
format	article
author	Wenpan Dong Jing Liu Jing Yu Ling Wang Shiliang Zhou
author_facet	Wenpan Dong Jing Liu Jing Yu Ling Wang Shiliang Zhou
author_sort	Wenpan Dong
title	Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.
title_short	Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.
title_full	Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.
title_fullStr	Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.
title_full_unstemmed	Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.
title_sort	highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for dna barcoding.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/616003854d6f4889a60f83bf1af7eac6
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_version_	1718423536238854144

Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.

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