Abstract：
Considering the phylogenetic differences in the taxonomic framework of the Chaetophorales as determined by the use of nuclear molecular markers or chloroplast genes, the current study was the first to use phylotranscriptomic analyses comparing the transcriptomes of 12 Chaetophorales algal species. The results showed that a total of 240,133 gene families and 143 single-copy orthogroups were identified. Based on the single-copy orthogroups, supergene analysis and the coalescent-based approach were adopted to perform phylotranscriptomic analysis of the Chaetophorales. The phylogenetic relationships of most species were consistent with those of phylogenetic analyses based on the chloroplast genome data rather than nuclear molecular markers. The Schizomeriaceae and the Aphanochaetaceae clustered into a well-resolved basal clade in the Chaetophorales by either strategy. Evolutionary analyses of divergence time and substitution rate also revealed that the closest relationships existed between the Schizomeriaceae and Aphanochaetaceae. All species in the Chaetophorales exhibited a large number of expanded and contracted gene families, in particular the common ancestor of the Schizomeriaceae and Aphanochaetaceae. The only terrestrial alga, Fritschiella tuberosa, had the greatest number of expanded gene families, which were associated with increased fatty acid biosynthesis. Phylotranscriptomic and evolutionary analyses all robustly identified the unique taxonomic relationship of Chaetophorales consistent with chloroplast genome data, proving the advantages of high-throughput data in phylogeny.
摘要：
考虑到通过使用核分子标记或叶绿体基因确定的Chaetophorales分类学框架的系统发育差异，当前的研究是第一个使用基因转录组学分析，比较了12种Chaetophorales藻类的转录组。结果表明，共鉴定出240,133个基因家族和143个单拷贝正统。基于单副本正交组，采用超基因分析和基于合并的方法对Chaetophorales进行了基因组分析。大多数物种的系统发育关系与基于叶绿体基因组数据而不是核分子标记的系统发育分析一致。通过两种策略，裂殖科和落叶草科都聚集在Chaetophorales中的一个分辨率很好的基底进化枝。对分歧时间和取代率的进化分析还表明，裂子菌科和白菜科之间存在最紧密的关系。Chaetophorales中的所有物种都表现出大量扩展和收缩的基因家族，特别是五味子科和五味子科的共同祖先。唯一的陆地藻类，块菌，拥有最多数量的扩展基因家族，这与脂肪酸生物合成增加有关。植物转录组学和进化分析都有力地确定了与叶绿体基因组数据一致的Chaetophorales的独特分类学关系，证明了高通量数据在系统发育中的优势。
