Optimal markers for the identification of Colletotrichum species
Optimal markers for the identification of Colletotrichum species
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DOI：
10.1016/j.ympev.2019.106694
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发表时间：
2020-02-01
影响因子：
4.1
通讯作者：
Doyle, Vinson Patrick
中科院分区：
文献类型：
--
作者：
dos Santos Vieira, Willie Anderson;Bezerra, Priscila Alves;Doyle, Vinson Patrick
炭疽菌是植物真菌病原菌中最重要的属之一。在过去的十年中，分子系统发育的研究使我们对属内的进化关系和物种边界有了更好的理解。目前已被接受的物种约有200种，其中大部分分布在13个物种复合体中。鉴于炭疽菌在世界各地农作物中的突出作用，植物病理学家、监管官员和真菌生物学家通常需要快速鉴定大量的炭疽菌分离物。然而，在每个物种复合体中区分物种的最佳分子标记尚未达成一致。在这里，我们计算了条形码间隙距离和种内/种间距离重叠，以评估每种最常用的分子标记作为物种识别条形码的效用。甘油醛-3-磷酸脱氢酶（GAPDH）、组蛋白-3 （HIS3）、DNA裂解酶（APN2）、DNA裂解酶与交配型位点MAT1-2-1之间的基因间间隔物（APN2/MAT-IGS）、GAPDH与假设蛋白（GAP2-IGS）之间的基因间间隔物（GAP2-IGS）具有良好的条形码特性，而肌动蛋白（ACT）、几丁质合成酶（CHS-1）和核rDNA内部转录间隔物（nrITS）序列无法区分大多数物种。最后，我们利用系统发育信息性分析、谱系分类指数（GSI）和贝叶斯一致性分析（BCA）评估了这些标记在系统发育研究中的效用。虽然GAPDH、HIS3和β -微管蛋白（TUB2）经常是最好的标记，但没有一组标记对所有物种复合物都是最好的。消除低系统发育信号的标记倾向于减少拓扑结构的不确定性，无论物种复杂程度如何，并导致在贝叶斯一致性分析中支持每个谱系的标记比例更大。最后，我们利用具有最强系统发育信号的最小系统发育标记集重建了每个物种复合体的系统发育，并发现大多数物种被强烈支持为单系统。
Colletotrichum is among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection of Colletotrichum isolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and beta-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.