Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
University of Chinese Academy of Sciences, Beijing, 100039, China.
BMC Genomics. 2020 Jun 26;21(1):442. doi: 10.1186/s12864-020-06845-y.
Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. The phylogenetic relationships of Chaetophorales have been inferred primarily based on short and less informative rDNA sequences. This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme, and to further understand the evolution of order Chaetophorales.
In the present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales. Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships.
chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.
Order Chaetophorales 目前包括六个科，即 Schizomeridaceae、Aphanochaetaceae、Barrancaceae、Uronemataceae、Fritschiellaceae 和 Chaetophoraceae。Chaetophorales 的系统发育关系主要是基于短的、信息量较少的 rDNA 序列推断的。本研究旨在重建 Chaetophorales 的系统发育，确定分类方案，并进一步了解 Chaetophorales 的进化。
本研究共采集了七个完整的和五个片段的叶绿体基因组。进行了系统基因组学和比较基因组学分析，以确定 Chaetophorales 内的分类方案。结果表明，Oedogoniales 与 Chaetophorales 和 Chaetopeltidales 的一个分支是姐妹群。Schizomeriaceae 和 Aphanochaetaceae 在 Chaetophorales 中聚为一个很好解决的基部分支，与基于 rDNA 序列的系统发育分析结果不一致。比较基因组分析显示，Schizomeriaceae 和 Aphanochaetaceae 的叶绿体基因组高度保守且同源，突出了该目内的最密切关系。游动孢子的萌发类型与系统发育关系精确相关。
叶绿体基因组结构分析、同线性分析和游动孢子萌发分析与基于叶绿体基因组的系统发育分析一致，所有这些都强有力地确定了 Chaetophorales 的独特分类方案以及 Oedogoniales、Chaetophorales 和 Chaetopeltidales 的关系。
