A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes
A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes
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DOI：
10.1186/s43008-019-0002-x
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发表时间：
2019-06-07
期刊：
影响因子：
5.4
通讯作者：
Townsend, Jeffrey P.
中科院分区：
文献类型：
--
作者：
Johnston, Peter R.;Quijada, Luis;Townsend, Jeffrey P.
真菌在生态上是多样的，包括菌根、根和叶的内生菌、植物病原体、水生和空气水生菌丝菌、哺乳动物病原体和腐殖菌。这些真菌通常在病变组织和环境DNA提取物的培养物中检测到。从这些特征差的样本中鉴定标本越来越依赖于DNA测序。然而，目前对利多菌的分类仍然主要是基于形态学定义的分类群，特别是在更高的分类水平上。因此，正式的利多菌分类往往与DNA测序研究提出的关系不一致。以往的利多菌属全类系统发育都是基于核糖体DNA标记，大多数已发表的多基因研究都集中在特定的属或科上。在本文中，我们整理了来自该类遗传广度的有性和无性形态标本的可用数据，重点是通用型物种，以279个标本中多达15个连接基因为基础，提出了一个系统发育。数据集中包括从72个可用于该类的基因组中提取的基因，其中包括与本研究一起发布的10个新基因组。为了验证系统发育中最深层分支的统计支持，本文还提出了一个基于51个选定基因组的3156个基因的系统发育。为了填补15个基因系统发育的分类空白，我们进一步提出了ITS基因树，特别是针对属型物种的前型标本。提出了少数新分类群：Marthamycetales ord. nov.、Drepanopezizaceae和Mniaeciaceae fams。11 .正式的分类学变化是有限的，部分原因是分类单元和标本选择的特殊性质，纯粹基于数据的可得性。系统发育构成了一个框架，使未来的分类学目标研究使用故意标本选择。理想情况下，这类研究将包括为那些无法从原始模式标本中提取DNA的属的模式种指定表型，并考虑形态学特征，无论何时遗传定义的进化枝被认为是一个分类中的正式分类群。
Fungi in the class Leotiomycetes are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic and aero-aquatic hyphomycetes, mammalian pathogens, and saprobes. These fungi are commonly detected in cultures from diseased tissue and from environmental DNA extracts. The identification of specimens from such character-poor samples increasingly relies on DNA sequencing. However, the current classification of Leotiomycetes is still largely based on morphologically defined taxa, especially at higher taxonomic levels. Consequently, the formal Leotiomycetes classification is frequently poorly congruent with the relationships suggested by DNA sequencing studies. Previous class-wide phylogenies of Leotiomycetes have been based on ribosomal DNA markers, with most of the published multi-gene studies being focussed on particular genera or families. In this paper we collate data available from specimens representing both sexual and asexual morphs from across the genetic breadth of the class, with a focus on generic type species, to present a phylogeny based on up to 15 concatenated genes across 279 specimens. Included in the dataset are genes that were extracted from 72 of the genomes available for the class, including 10 new genomes released with this study. To test the statistical support for the deepest branches in the phylogeny, an additional phylogeny based on 3156 genes from 51 selected genomes is also presented. To fill some of the taxonomic gaps in the 15-gene phylogeny, we further present an ITS gene tree, particularly targeting ex-type specimens of generic type species. A small number of novel taxa are proposed: Marthamycetales ord. nov., and Drepanopezizaceae and Mniaeciaceae fams. nov. The formal taxonomic changes are limited in part because of the ad hoc nature of taxon and specimen selection, based purely on the availability of data. The phylogeny constitutes a framework for enabling future taxonomically targeted studies using deliberate specimen selection. Such studies will ideally include designation of epitypes for the type species of those genera for which DNA is not able to be extracted from the original type specimen, and consideration of morphological characters whenever genetically defined clades are recognized as formal taxa within a classification.