ABSTRACT This study is the first to determine the transcriptomes of eight colonial volvocine algae: Pandorina morum, P. colemaniae, Volvulina compacta, Eudorina elegans, E. cylindrica, Yamagishiella unicocca, Colemanosphaera charkowiensis and C. angeleri. By analysing these data together with the whole-genome data of Chlamydomonas reinhardtii and other colonial volvocine algae, we determined 26 979 gene families and 105 single-copy orthogroups. Using the single-copy orthogroups, we adopted a supermatrix and coalescent-based approach to perform phylotranscriptomic analysis of colonial volvocine algae. The phylogenetic relationships of most species were consistent with those of a previous study, and the results showed paraphyly of the genus Pandorina. Then, we analysed gene family expansion and contraction in colonial volvocine algae and found that they exhibited a large number of expanded and contracted gene families. In particular, the common ancestor of the Volvocaceae had the largest number of expanded gene families, which may be associated with the increased volume of extracellular matrix. Finally, using the ML method to analyse the substitution rates among colonial volvocine algae based on single-copy orthogroups, we showed a significantly higher non-synonymous substitution (dN) rate in Tetrabaena socialis. By analysing the differences in the dN/dS ratio, we found that more orthogroups exhibited a significantly higher dN/dS in T. socialis; we speculate that the higher dN/dS could indicate relaxed selection pressure and that this lower constraint allows the accumulation of more non-synonymous mutations in T. socialis.

中文翻译：

---

基于基因家族进化和自然选择的系统转录组学分析比较群落藻类

摘要 本研究首次确定了八种菌落藻类的转录组：Pandorina morum、P. colemaniae、Volvulina compacta、Eudorina elegans、E. cylindrica、Yamagishiella unicocca、Colemanosphaera charkowiensis 和 C. angeleri。通过分析这些数据以及莱茵衣藻和其他菌落藻类的全基因组数据，我们确定了 26 979 个基因家族和 105 个单拷贝正群。使用单拷贝 orthogroups，我们采用了基于超矩阵和聚结的方法对殖民地 volvocine 藻类进行系统转录组学分析。大多数物种的系统发育关系与之前的研究一致，结果显示潘多丽娜属的并系。然后，我们分析了菌落藻类中基因家族的扩张和收缩，发现它们表现出大量扩张和收缩的基因家族。尤其是沃尔沃卡科的共同祖先拥有最多数量的扩展基因家族，这可能与细胞外基质体积增加有关。最后，使用 ML 方法分析基于单拷贝正群的殖民地 volvocine 藻类之间的替代率，我们在 Tetrabaena socialis 中显示出显着更高的非同义替代 (dN) 率。通过分析 dN/dS 比值的差异，我们发现更多的正群在 T. socialis 中表现出显着更高的 dN/dS；