Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes.

AIMS Genetics Pub Date : 2018-01-17 eCollection Date: 2018-01-01 DOI:10.3934/genet.2018.1.1
Jeffrey M Marcus
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引用次数: 32

Abstract

DNA barcodes are very useful for species identification especially when identification by traditional morphological characters is difficult. However, the short mitochondrial and chloroplast barcodes currently in use often fail to distinguish between closely related species, are prone to lateral transfer, and provide inadequate phylogenetic resolution, particularly at deeper nodes. The deficiencies of short barcode identifiers are similar to the deficiencies of the short year identifiers that caused the Y2K problem in computer science. The resolution of the Y2K problem was to increase the size of the year identifiers. The performance of conventional mitochondrial COI barcodes for phylogenetics was compared with the performance of complete mitochondrial genomes and nuclear ribosomal RNA repeats obtained by genome skimming for a set of caddisfly taxa (Insect Order Trichoptera). The analysis focused on Trichoptera Family Hydropsychidae, the net-spinning caddisflies, which demonstrates many of the frustrating limitations of current barcodes. To conduct phylogenetic comparisons, complete mitochondrial genomes (15 kb each) and nuclear ribosomal repeats (9 kb each) from six caddisfly species were sequenced, assembled, and are reported for the first time. These sequences were analyzed in comparison with eight previously published trichopteran mitochondrial genomes and two triochopteran rRNA repeats, plus outgroup sequences from sister clade Lepidoptera (butterflies and moths). COI trees were not well-resolved, had low bootstrap support, and differed in topology from prior phylogenetic analyses of the Trichoptera. Phylogenetic trees based on mitochondrial genomes or rRNA repeats were well-resolved with high bootstrap support and were largely congruent with each other. Because they are easily sequenced by genome skimming, provide robust phylogenetic resolution at various phylogenetic depths, can better distinguish between closely related species, and (in the case of mitochondrial genomes), are backwards compatible with existing mitochondrial barcodes, it is proposed that mitochondrial genomes and rRNA repeats be used as next generation DNA barcodes.

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我们与DNA条形码、Y2K问题以及下一代条形码的搜索之间的爱恨交织关系。
DNA条形码在物种识别中非常有用,尤其是当传统形态特征难以识别时。然而,目前使用的短线粒体和叶绿体条形码往往无法区分亲缘关系密切的物种,容易发生横向转移,并且提供的系统发育分辨率不足,尤其是在更深的节点。短条形码标识符的缺陷类似于导致计算机科学中Y2K问题的短年份标识符的缺陷。Y2K问题的解决方案是增加年份标识符的大小。将传统线粒体COI条形码在系统发育学中的性能与通过基因组撇除获得的完整线粒体基因组和核核糖体RNA重复序列在一组昆虫分类群(昆虫目毛翅目)中的性能进行了比较。分析的重点是毛翅目水螅科,即网络旋转球童,这表明了当前条形码的许多令人沮丧的局限性。为了进行系统发育比较,对6个caddisfly物种的完整线粒体基因组(每个15 kb)和核核糖体重复序列(每个9 kb)进行了测序、组装,并首次报道。这些序列与之前发表的八个毛翅目线粒体基因组和两个三翅目rRNA重复序列,以及鳞翅目姐妹分支(蝴蝶和蛾)的外群序列进行了比较分析。COI树没有很好地解析,具有较低的bootstrap支持,并且在拓扑结构上与先前的毛翅目系统发育分析不同。基于线粒体基因组或rRNA重复序列的系统发育树在高度自举支持下得到了很好的解析,并且在很大程度上彼此一致。由于它们很容易通过基因组掠过进行测序,在不同的系统发育深度提供了强大的系统发育分辨率,可以更好地区分亲缘关系密切的物种,并且(在线粒体基因组的情况下)与现有的线粒体条形码向后兼容,因此建议将线粒体基因组和rRNA重复序列用作下一代DNA条形码。
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AIMS Genetics
AIMS Genetics GENETICS & HEREDITY-
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