Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.

<h4>Background</h4>DNA barcoding is expected to be an effective identification tool for organisms with heteromorphic generations such as pteridophytes, which possess a morphologically simple gametophyte generation. Although a reference data set including complete coverage of the target l...

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Autores principales:	Atsushi Ebihara, Joel H Nitta, Motomi Ito
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/85b81d768f5241a2a8105a26f80296a2
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spelling	oai:doaj.org-article:85b81d768f5241a2a8105a26f80296a22021-11-18T07:01:58ZMolecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.1932-620310.1371/journal.pone.0015136https://doaj.org/article/85b81d768f5241a2a8105a26f80296a22010-12-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21170336/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>DNA barcoding is expected to be an effective identification tool for organisms with heteromorphic generations such as pteridophytes, which possess a morphologically simple gametophyte generation. Although a reference data set including complete coverage of the target local flora/fauna is necessary for accurate identification, DNA barcode studies including such rich taxonomic sampling on a countrywide scale are lacking.<h4>Methodology/principal findings</h4>The Japanese pteridophyte flora (733 taxa including subspecies and varieties) was used to test the utility of two plastid DNA barcode regions (rbcL and trnH-psbA) with the intention of developing an identification system for native gametophytes. DNA sequences were obtained from each of 689 (94.0%) taxa for rbcL and 617 (84.2%) taxa for trnH-psbA. Mean interspecific divergence values across all taxon pairs (K2P genetic distances) did not reveal a significant difference in rate between trnH-psbA and rbcL, but mean K2P distances of each genus showed significant heterogeneity according to systematic position. The minimum fail rate of taxon discrimination in an identification test using BLAST (12.52%) was obtained when rbcL and trnH-psbA were combined, and became lower in datasets excluding infraspecific taxa or apogamous taxa, or including sexual diploids only.<h4>Conclusions/significance</h4>This study demonstrates the overall effectiveness of DNA barcodes for species identification in the Japanese pteridophyte flora. Although this flora is characterized by a high occurrence of apogamous taxa that pose a serious challenge to identification using DNA barcodes, such taxa are limited to a small number of genera, and only minimally detract from the overall success rate. In the case that a query sequence is matched to a known apogamous genus, routine species identification may not be possible. Otherwise, DNA barcoding is a practical tool for identification of most Japanese pteridophytes, and is especially anticipated to be helpful for identification of non-hybridizing gametophytes.Atsushi EbiharaJoel H NittaMotomi ItoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 12, p e15136 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Atsushi Ebihara Joel H Nitta Motomi Ito Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.
description	<h4>Background</h4>DNA barcoding is expected to be an effective identification tool for organisms with heteromorphic generations such as pteridophytes, which possess a morphologically simple gametophyte generation. Although a reference data set including complete coverage of the target local flora/fauna is necessary for accurate identification, DNA barcode studies including such rich taxonomic sampling on a countrywide scale are lacking.<h4>Methodology/principal findings</h4>The Japanese pteridophyte flora (733 taxa including subspecies and varieties) was used to test the utility of two plastid DNA barcode regions (rbcL and trnH-psbA) with the intention of developing an identification system for native gametophytes. DNA sequences were obtained from each of 689 (94.0%) taxa for rbcL and 617 (84.2%) taxa for trnH-psbA. Mean interspecific divergence values across all taxon pairs (K2P genetic distances) did not reveal a significant difference in rate between trnH-psbA and rbcL, but mean K2P distances of each genus showed significant heterogeneity according to systematic position. The minimum fail rate of taxon discrimination in an identification test using BLAST (12.52%) was obtained when rbcL and trnH-psbA were combined, and became lower in datasets excluding infraspecific taxa or apogamous taxa, or including sexual diploids only.<h4>Conclusions/significance</h4>This study demonstrates the overall effectiveness of DNA barcodes for species identification in the Japanese pteridophyte flora. Although this flora is characterized by a high occurrence of apogamous taxa that pose a serious challenge to identification using DNA barcodes, such taxa are limited to a small number of genera, and only minimally detract from the overall success rate. In the case that a query sequence is matched to a known apogamous genus, routine species identification may not be possible. Otherwise, DNA barcoding is a practical tool for identification of most Japanese pteridophytes, and is especially anticipated to be helpful for identification of non-hybridizing gametophytes.
format	article
author	Atsushi Ebihara Joel H Nitta Motomi Ito
author_facet	Atsushi Ebihara Joel H Nitta Motomi Ito
author_sort	Atsushi Ebihara
title	Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.
title_short	Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.
title_full	Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.
title_fullStr	Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.
title_full_unstemmed	Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.
title_sort	molecular species identification with rich floristic sampling: dna barcoding the pteridophyte flora of japan.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/85b81d768f5241a2a8105a26f80296a2
work_keys_str_mv	AT atsushiebihara molecularspeciesidentificationwithrichfloristicsamplingdnabarcodingthepteridophytefloraofjapan AT joelhnitta molecularspeciesidentificationwithrichfloristicsamplingdnabarcodingthepteridophytefloraofjapan AT motomiito molecularspeciesidentificationwithrichfloristicsamplingdnabarcodingthepteridophytefloraofjapan
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Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.

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