Universidade Federal Rural de Pernambuco - UFRPE, Departamento de Agronomia, Rua Manuel de Medeiros, s/n - Dois Irmãos, Recife, Pernambuco 52171-900, Brazil.
Universidade Federal Rural de Pernambuco - UFRPE, Departamento de Agronomia, Rua Manuel de Medeiros, s/n - Dois Irmãos, Recife, Pernambuco 52171-900, Brazil.
Mol Phylogenet Evol. 2020 Feb;143:106694. doi: 10.1016/j.ympev.2019.106694. Epub 2019 Nov 28.
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 β-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.
炭疽菌是最重要的真菌植物病原体属之一。过去十年的分子系统发育研究极大地增进了我们对该属内进化关系和物种界限的理解。目前约有 200 个被接受的种，其中大多数分布在 13 个种复合体中。鉴于炭疽菌在世界各地农作物上的重要性，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炭疽菌分离株。然而，对于每个种复合体中最好的分子标记来区分种，目前还没有达成共识。在这里，我们计算了条码间隙距离和种内/种间距离重叠，以评估最常用的分子标记在物种鉴定中的应用潜力。甘油醛-3-磷酸脱氢酶（GAPDH）、组蛋白-3（HIS3）、DNA 裂合酶（APN2）、DNA 裂合酶与交配型位点 MAT1-2-1 之间的基因间间隔（APN2/MAT-IGS）和 GAPDH 与假定蛋白之间的基因间间隔（GAP2-IGS）具有良好条码的特性，而肌动蛋白（ACT）、几丁质合酶（CHS-1）和核 rDNA 内转录间隔区（nrITS）的序列则无法区分大多数种。最后，我们使用系统发育信息量分析、系统发生分类指数（GSI）和贝叶斯一致分析（BCA）评估了这些标记在系统发育研究中的应用。虽然 GAPDH、HIS3 和 β-微管蛋白（TUB2）经常是最好的标记之一，但没有一套标记适用于所有种复合体。消除具有低系统发育信号的标记往往会降低拓扑结构的不确定性，无论种复合体如何，并且会导致更大比例的标记支持贝叶斯一致分析中的每个谱系。最后，我们使用具有最强系统发育信号的最小一组系统发育标记重建每个种复合体的系统发育，并发现大多数种都强烈支持为单系。
