Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.

A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technical...

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Autores principales:	Aron J Fazekas, Kevin S Burgess, Prasad R Kesanakurti, Sean W Graham, Steven G Newmaster, Brian C Husband, Diana M Percy, Mehrdad Hajibabaei, Spencer C H Barrett
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/99e0f3c2913f48be98b960ade894af30
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spelling	oai:doaj.org-article:99e0f3c2913f48be98b960ade894af302021-11-25T06:11:22ZMultiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.1932-620310.1371/journal.pone.0002802https://doaj.org/article/99e0f3c2913f48be98b960ade894af302008-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18665273/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s). We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples). The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA) and three non-coding (trnH-psbA, atpF-atpH, and psbK-psbI) loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA) to 59% (trnH-psbA) of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85-100% for plastid loci), with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs). Several loci (matK, psbK-psbI, trnH-psbA) were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69-71%; values that were approached by several two- and three-region combinations). This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the contentious debate on plant barcoding should therefore involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barcoding systems.Aron J FazekasKevin S BurgessPrasad R KesanakurtiSean W GrahamSteven G NewmasterBrian C HusbandDiana M PercyMehrdad HajibabaeiSpencer C H BarrettPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 3, Iss 7, p e2802 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Aron J Fazekas Kevin S Burgess Prasad R Kesanakurti Sean W Graham Steven G Newmaster Brian C Husband Diana M Percy Mehrdad Hajibabaei Spencer C H Barrett Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.
description	A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s). We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples). The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA) and three non-coding (trnH-psbA, atpF-atpH, and psbK-psbI) loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA) to 59% (trnH-psbA) of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85-100% for plastid loci), with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs). Several loci (matK, psbK-psbI, trnH-psbA) were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69-71%; values that were approached by several two- and three-region combinations). This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the contentious debate on plant barcoding should therefore involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barcoding systems.
format	article
author	Aron J Fazekas Kevin S Burgess Prasad R Kesanakurti Sean W Graham Steven G Newmaster Brian C Husband Diana M Percy Mehrdad Hajibabaei Spencer C H Barrett
author_facet	Aron J Fazekas Kevin S Burgess Prasad R Kesanakurti Sean W Graham Steven G Newmaster Brian C Husband Diana M Percy Mehrdad Hajibabaei Spencer C H Barrett
author_sort	Aron J Fazekas
title	Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.
title_short	Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.
title_full	Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.
title_fullStr	Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.
title_full_unstemmed	Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.
title_sort	multiple multilocus dna barcodes from the plastid genome discriminate plant species equally well.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/99e0f3c2913f48be98b960ade894af30
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Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.

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