Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
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DOI：
10.1073/pnas.1117018109
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发表时间：
2012-04-17
影响因子：
11.1
通讯作者：
Schindel, David
中科院分区：
文献类型：
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作者：
Schoch, Conrad L.;Seifert, Keith A.;Schindel, David
六个DNA区域被评估为真菌的潜在DNA条形码，真菌是真核生物的第二大王国，由多国，多实验室财团。用作动物条形码的线粒体细胞色素c氧化酶亚基1的区域被排除作为潜在的标记物，因为它难以在真菌中扩增，通常包括大的内含子，并且可能不够可变。从核核糖体RNA顺反子的三个亚基进行了比较，连同三个代表性的蛋白质编码基因（RNA聚合酶II的最大亚基，RNA聚合酶II的第二大亚基，和微型染色体维持蛋白）的区域。虽然蛋白质编码基因区域与核糖体标记物相比通常具有更高的正确识别率，但低PCR扩增和测序成功率使其无法作为通用真菌条形码的候选者。在核糖体顺反子的区域中，内部转录间隔区（ITS）区域具有最大的概率成功识别最广泛的真菌，种间和种内变异之间具有最明确定义的条形码间隙。核核糖体大亚基，在某些群体中流行的系统发育标记，具有优越的上级的物种分辨率在一些分类群体，如早期分歧的谱系和子囊菌酵母，但在其他方面稍逊于ITS。核核糖体小亚基在真菌中具有较差的种水平分辨率。ITS将被正式提议作为生命条形码联盟的主要真菌条形码标记，并有可能为特定的狭义分类群开发补充条形码。
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter-and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.