Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.
Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.
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DOI：
10.1371/journal.pone.0015136
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发表时间：
2010-12-08
期刊：
影响因子：
3.7
通讯作者：
Ito M
中科院分区：
文献类型：
--
作者：
Ebihara A;Nitta JH;Ito M
DNA条形码有望成为一种有效的鉴定工具，用于具有异形世代的生物，如蕨类植物，其具有形态简单的配子体世代。虽然一个参考数据集，包括完整的目标当地植物群/动物群的覆盖范围是必要的准确识别，DNA条形码研究，包括在全国范围内丰富的分类抽样缺乏。以日本蕨类植物植物群（包括亚种和变种）733个分类单元为材料，研究了质体DNA条形码区域（rbcL和trnH-psbA）的实用性，旨在建立天然配子体的鉴定系统。从rbcL的689个（94.0%）分类群和trnH-psbA的617个（84.2%）分类群中的每一个获得DNA序列。平均种间分歧值在所有的分类对（K2 P遗传距离）并没有发现显着差异率之间的trnH-psbA和rbcL，但平均K2 P距离的每个属表现出显着的异质性，根据系统位置。当rbcL和trnH-psbA组合时，在使用BLAST的鉴定测试中获得分类单元区分的最小失败率（12.52%），并且在不包括种下分类单元或无配子体分类单元或仅包括有性二倍体的数据集中变得更低。本研究证明了DNA条形码在日本蕨类植物植物群物种鉴定中的整体有效性。尽管该植物群的特征在于高发生率的无配生殖分类群，这对使用DNA条形码进行鉴定构成了严重挑战，但此类分类群仅限于少数属，并且仅最小程度地降低了总体成功率。在查询序列与已知的无配生殖属匹配的情况下，常规的物种识别可能是不可能的。另外，DNA条形码是鉴定大多数日本蕨类植物的实用工具，特别是预计将有助于鉴定非杂交配子体。
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. 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. 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.
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DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
影响因子：
2.4
作者：
Ebihara, Atsushi;Iwatsuki, Kunio;Dubuisson, Jean-Yves
通讯作者：
Dubuisson, Jean-Yves
影响因子：
56.9
作者：
FARRAR, DR
通讯作者：
FARRAR, DR
影响因子：
4.9
作者：
Ebihara, Atsushi;Matsumoto, Sadamu;Ito, Motomi
通讯作者：
Ito, Motomi
影响因子：
3
作者：
GASTONY, GJ;YATSKIEVYCH, G
通讯作者：
YATSKIEVYCH, G