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Reconsideration of species boundaries and proposed DNA barcodes for Calonectria
Studies in Mycology ( IF 16.5 ) Pub Date : 2020-10-07 , DOI: 10.1016/j.simyco.2020.08.001
Q L Liu 1, 2, 3 , J Q Li 1, 2, 3 , M J Wingfield 3 , T A Duong 3 , B D Wingfield 3 , P W Crous 3, 4 , S F Chen 1, 2
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Calonectria represents a genus of phytopathogenic ascomycetous fungi with a worldwide distribution. In recent years, there has been an increase in the number of taxonomic studies on these fungi. Currently, there are 169 described species of Calonectria based on comparisons of DNA sequence data, combined with morphological characteristics. However, for some of these species, the sequence data utilised at the time of their description were relatively limited. This has justified an urgent need to reconsider the species boundaries for Calonectria based on robust genus-wide phylogenetic analyses. In this study, we utilised 240 available isolates including the ex-types of 128 Calonectria species, and re-sequenced eight gene regions (act, cmdA, his3, ITS, LSU, rpb2, tef1 and tub2) for them. Sequences for 44 Calonectria species, for which cultures could not be obtained, were downloaded from GenBank. DNA sequence data of all the 169 Calonectria species were then used to determine their phylogenetic relationships. As a consequence, 51 species were reduced to synonymy, two new species were identified, and the name Ca. lauri was validated. This resulted in the acceptance of 120 clearly defined Calonectria spp. The overall data revealed that the genus includes 11 species complexes, distributed across the Prolate and Sphaero-Naviculate Groups known to divide Calonectria. The results also made it possible to develop a robust set of DNA barcodes for Calonectria spp. To accomplish this goal, we evaluated the outcomes of each of the eight candidate DNA barcodes for the genus, as well as for each of the 11 species complexes. No single gene region provided a clear identity for all Calonectria species. Sequences of the tef1 and tub2 genes were the most reliable markers; those for the cmdA, his3, rpb2 and act gene regions also provided a relatively effective resolution for Calonectria spp., while the ITS and LSU failed to produce useful barcodes for species discrimination. At the species complex level, results showed that the most informative barcodes were inconsistent, but that a combination of six candidate barcodes (tef1, tub2, cmdA, his3, rpb2 and act) provided stable and reliable resolution for all 11 species complexes. A six-gene combined phylogeny resolved all 120 Calonectria species, and revealed that tef1, tub2, cmdA, his3, rpb2 and act gene regions are effective DNA barcodes for Calonectria.



中文翻译:

重新考虑物种边界和提议的 Calonectria 的 DNA 条形码

Calonectria代表植物致病性子囊菌属真菌,在世界范围内分布。近年来,对这些真菌的分类学研究有所增加。目前,基于 DNA 序列数据的比较,结合形态特征,描述了 169 种Calonectria。然而,对于其中一些物种,在描述它们时使用的序列数据相对有限。这证明迫切需要基于稳健的全属系统发育分析重新考虑Calonectria的物种边界。在这项研究中,我们使用了 240 个可用的分离物,包括 128 个Calonectria物种的前类型,并对 8 个基因区域进行了重新测序(act, cmdA , his3 , ITS, LSU, rpb2, tef1tub2 )。从 GenBank 下载了 44种无法获得培养物的Calonectria物种的序列。然后使用所有 169 个Calonectria物种的DNA 序列数据来确定它们的系统发育关系。结果,51 种被简化为同义词,发现了两个新种,命名为Ca. lauri得到验证。这导致接受了 120 种明确定义的Calonectria spp。总体数据显示,该属包括 11 个物种复合体,分布在已知分裂的长骨和球形-舟形组中月见草。结果还使得为Calonectria spp开发一套强大的 DNA 条形码成为可能。为了实现这一目标,我们评估了该属的八个候选 DNA 条形码中的每一个以及 11 个物种复合体中的每一个的结果。没有单个基因区域为所有Calonectria物种提供明确的身份。该序列TEF1TUB2基因是最可靠的指标; 者为CMDAHIS3RPB2行为基因区域也提供了一种用于比较有效分辨率Calonectriaspp.,而 ITS 和 LSU 未能产生用于物种歧视的有用条形码。在物种复合体水平上,结果显示信息量最大的条形码不一致,但六个候选条形码(tef1tub2cmdAhis3rpb2act)的组合为所有 11 个物种复合体提供了稳定可靠的分辨率。六基因组合系统发育解析了所有 120 个Calonectria物种,并揭示了tef1tub2cmdAhis3rpb2act基因区域是Calonectria 的有效 DNA 条形码。

更新日期:2020-12-02
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