Fungal Diversity ( IF 20.3 ) Pub Date : 2020-09-16 , DOI: 10.1007/s13225-020-00455-5 Natalie Vandepol 1 , Julian Liber 2 , Alessandro Desirò 3 , Hyunsoo Na 4 , Megan Kennedy 4 , Kerrie Barry 4 , Igor V Grigoriev 4 , Andrew N Miller 5 , Kerry O'Donnell 6 , Jason E Stajich 7 , Gregory Bonito 1, 3
Early efforts to classify Mortierellaceae were based on macro- and micromorphology, but sequencing and phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conflicting taxonomic groupings and polyphyletic genera. Although some taxonomic confusion in the family has been clarified, rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae. In this study, we applied two parallel approaches to resolve the Mortierellaceae phylogeny: low coverage genome (LCG) sequencing and high-throughput, multiplexed targeted amplicon sequencing to generate sequence data for multi-gene phylogenetics. We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic genera resulted in 13 genera, 7 of which are newly proposed. Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a high-confidence phylogeny. The multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach, but has limitations too. We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity and evolution.
中文翻译:
通过多基因系统发育和系统基因组学的综合解决被孢霉科系统发育
早期对被孢霉科进行分类的努力是基于宏观和微观形态学,但使用核糖体 DNA (rDNA) 标记进行的测序和系统发育研究表明,分类学分组和多系属相互矛盾。尽管该科中的一些分类混乱已得到澄清,但仅靠 rDNA 数据无法解决被孢霉科内更高级别的系统发育关系。在这项研究中,我们应用了两种并行方法来解决被孢霉科系统发育:低覆盖基因组 (LCG) 测序和高通量、多重靶向扩增子测序,以生成多基因系统发育的序列数据。然后,我们结合了我们的数据集,以提供一个得到充分支持的基于基因组的系统发育,该系统发育具有来自扩增子数据集的广泛采样深度。将被孢霉属系统发育分解为单系属,得到 13 个属,其中 7 个属是新提出的。事实证明,低覆盖率基因组测序是一种相对经济高效的生成高可信度系统发育的方法。多基因系统发生学方法比 LCG 方法实现了更大的采样深度和广度,但也有局限性。我们提出这项工作是为了解决一些分类混乱,并提供一个属级框架,以促进未来对被孢霉科多样性和进化的研究。