In this paper, we provide a phylogenetic overview of Basidiomycota and related phyla in relation to ten years of DNA based phylogenetic studies since the AFTOL publications in 2007. We selected 529 species to address phylogenetic relationships of higher-level taxa using a maximum-likelihood framework and sequence data from six genes traditionally used in fungal molecular systematics (nrLSU, nrSSU, 5.8S, tef1-α, rpb1 and rpb2). These species represent 18 classes, 62 orders, 183 families, and 392 genera from the phyla Basidiomycota (including the newly recognized subphylum Wallemiomycotina) and Entorrhizomycota, and 13 species representing 13 classes of Ascomycota as outgroup taxa. We also conducted a molecular dating analysis based on these six genes for 116 species representing 17 classes and 54 orders of Basidiomycota and Entorrhizomycota. Finally we performed a phyloproteomics analysis from 109 Basidiomycota species and 6 outgroup taxa using amino-acid sequences retrieved from 396 orthologous genes. Recognition of higher taxa follows the criteria in Zhao et al (Fungal Divers 78:239–292, 2016): (i) taxa must be monophyletic and statistically well-supported in molecular dating analyses, (ii) their respective stem ages should be roughly equivalent, and (iii) stem ages of higher taxa must be older than those of lower level taxa. The time-tree indicates that the mean of stem ages of Basidiomycota and Entorrhizomycota are ca. 530 Ma; subphyla of Basidiomycota are 406–490 Ma; most classes are 358–393 Ma for those of Agaricomycotina and 245–356 Ma for those of Pucciniomycotina and Ustilaginomycotina; most orders of those subphyla split 120–290 Ma. Monophyly of most higher-level taxa of Basidiomycota are generally supported, especially those taxa introduced in the recent ten years: phylum Entorrhizomycota, classes Malasseziomycetes, Moniliellomycetes, Spiculogloeomycetes, Tritirachiomycetes and orders Amylocorticiales, Golubeviales, Holtermanniales, Jaapiales, Lepidostromatales, Robbauerales, Stereopsidales and Trichosporonales. However, the younger divergence times of Leucosporidiales (Microbotryomycetes) indicate that its order status is not supported, thus we propose combining it under Microbotryales. On the other hand, the families Buckleyzymaceae and Sakaguchiaceae (Cystobasidiomycetes) are raised to Buckleyzymales and Sakaguchiales due to their older divergence times. Cystofilobasidiales (Tremellomycetes) has an older divergence time and should be amended to a higher rank. We however, do not introduce it as new class here for Cystofilobasidiales, as DNA sequences from these taxa are not from their respective types and thus await further studies. Divergence times for Exobasidiomycetes, Cantharellales, Gomphales and Hysterangiales were obtained based on limited species sequences in molecular dating study. More comprehensive phylogenetic studies on those four taxa are needed in the future because our ML analysis based on wider sampling, shows they are not monophyletic groups. In general, the six-gene phylogenies are in agreement with the phyloproteomics tree except for the placements of Wallemiomycotina, orders Amylocorticiales, Auriculariales, Cantharellales, Geastrales, Sebacinales and Trechisporales from Agaricomycetes. These conflicting placements in the six-gene phylogeny vs the phyloproteomics tree are discussed. This leads to future perspectives for assessing gene orthology and problems in deciphering taxon ranks using divergence times.

中文翻译：

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担子菌属和相关门的六基因系统发育概貌，具有较高分类群的发散时间，并具有系统进化学的观点

在本文中，我们提供了自2007年AFTOL发表以来十年来基于DNA的系统发育研究相关的担子菌属和相关系统发育的系统发育概述。我们选择了529种，以利用最大似然框架解决高等分类群的系统发育关系。和来自真菌分子系统中传统使用的六个基因的序列数据（nrLSU，nrSSU，5.8S，tef1-α，rpb1和rpb2）。这些物种代表18类，62台的订单，家庭183，以及从392个门属担子菌门（包括新识别的亚门Wallemiomycotina）和Entorrhizomycota，和13种表示13类的子囊菌作为外来生物群。我们还根据这六个基因对116种代表17类和54阶担子菌和肠菌菌的物种进行了分子测年分析。最后，我们使用从396个直系同源基因中检索到的氨基酸序列，对109种担子菌属和6种外类群进行了系统进化分析。较高的分类单元的识别遵循Zhao等人的标准（Fungal Divers 78：239–292，2016）：（i）分类单元必须是单系的，并且在分子测年分析中得到统计上的良好支持；（ii）它们各自的茎龄应该大致相同（iii）较高分类单元的茎年龄必须比较低分类单元的茎年龄大。时间树表明担子菌茎的平均年龄和Entorrhizomycota是ca. 530毫安; 担子菌属的亚门为406-490 Ma。大多数类是358-393毫安那些伞菌亚门和245-356马对于那些柄锈菌和黑粉菌; 这些亚门的大多数阶分裂120-290 Ma。一般支持大多数担子菌分类单元的单系类，特别是近十年来引入的那些类群：门生菌门类，Malasseziomycetes类，Moniliellomycetes，Spiculogloeomycetes，Tritirachiomycetes和支链淀粉菌类，Golubevial​​es，Holtermanniales，Jaapiales，Lepidostromatales，Robbauerales，Stereopsidales和Trichosporonales。然而，Leucosporidiales（Microbotryomycetes）的发散时间越短，表明其订单状态不被支持，因此我们建议在Microbotryales下对其进行组合。在另一方面，家庭Buckleyzymaceae和Sakaguchiaceae（囊担菌纲）升高到Buckleyzymales和Sakaguchiales由于他们年长的分歧时间。胞丝虫病（Tremellomycetes）的发散时间更长，应该修改为更高的等级。但是，在这里，我们不将其作为胞丝虫病的新种类，因为来自这些分类群的DNA序列并非来自其各自的类型，因此有待进一步研究。发散时间外担菌纲，鸡油菌目，钉菇目和辐片包目是在分子测年研究中基于有限物种序列获得的。将来需要对这四个类群进行更全面的系统发育研究，因为我们基于更广泛采样的ML分析显示它们不是单系类。一般情况下，六基因系统发育均符合除的展示位置phyloproteomics生成树协议Wallemiomycotina，订单Amylocorticiales，木耳目，鸡油菌目，Geastrales，蜡壳耳目和糙孢孔目从伞菌。讨论了六基因系统发育树与系统进化树中的这些冲突位置。这导致了将来评估基因正畸的观点以及使用发散时间来解密分类单元的问题。