Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
PLoS One. 2011;6(9):e25081. doi: 10.1371/journal.pone.0025081. Epub 2011 Sep 22.
DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (450 bp) representing ~100 morphospecies from ~650 collections of Agaricomycotina using several sets of new primers. Large introns (1500 bp) at variable locations were detected in 5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms.
DNA 条形码是一种使用短的标准遗传标记快速识别物种的方法。线粒体细胞色素氧化酶 I 基因（COI）已被提议作为通用的条形码基因座，但它在蘑菇（约 20,000 种）中的条形码功能尚未得到证实。我们使用多套新的引物，成功地从 Agaricomycotina 的约 650 个采集物中生成了代表约 100 个形态种的 167 个 COI 部分序列（450bp）。在所获得的序列中，约 5%的序列检测到了位置可变的大内含子（1500bp）。我们怀疑这种基因座广泛存在的大内含子是导致我们 PCR 成功率低（~30%）的原因。我们还对核内转录间隔区 rDNA 区（ITS）进行了测序，以便与 COI 进行比较。在 COI 可以测序的少数分类群中，COI 和 ITS 的条形码功能相似。然而，在一个紧密相关的分类群的密集采样中，COI 的变异性小于 ITS，并且无法区分所有末端分支。鉴于我们的结果和公共数据库中已经存在的大量 ITS 数据，我们建议放弃 COI，转而将 ITS 作为蘑菇的主要 DNA 条形码基因座。
