School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand.
School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia.
J Phycol. 2021 Jun;57(3):1035-1044. doi: 10.1111/jpy.13159. Epub 2021 Apr 13.
The advent of high-throughput sequencing (HTS) has allowed for the use of large numbers of coding regions to produce robust phylogenies. These phylogenies have been used to highlight relationships at ancient diversifications (subphyla, class) and highlight the evolution of plastid genome structure. The Erythropeltales are an order in the Compsopogonophyceae, a group with unusual plastid genomes but with low taxon sampling. We use HTS to produce near complete plastid genomes of all genera, and multiple species within some genera, to produce robust phylogenies to investigate character evolution, dating of divergence in the group, and plastid organization, including intron patterns. Our results produce a fully supported phylogeny of the genera in the Erythropeltales and suggest that morphologies (upright versus crustose) have evolved multiple times. Our dated phylogeny also indicates that the order is very old (~800 Ma), with diversification occurring after the ice ages of the Cryogenian period (750-635 Ma). Plastid gene order is congruent with phylogenetic relationships and suggests that genome architecture does not change often. Our data also highlight the abundance of introns in the plastid genomes of this order. We also produce a nearly complete plastid genome of Tsunamia transpacifica (Stylonematophyceae) to add to the taxon sampling of genomes of this class. The use of plastid genomes clearly produces robust phylogenetic relationships that can be used to infer evolutionary events, and increased taxon sampling, especially in less well-known red algal groups, will provide additional insights into their evolution.
高通量测序（HTS）的出现使得使用大量编码区域来产生稳健的系统发育成为可能。这些系统发育被用来突出古老分化（亚门、纲）的关系，并强调质体基因组结构的进化。Erythropeltales 是 Compsopogonophyceae 中的一个目，该目具有不寻常的质体基因组，但分类群采样较少。我们使用 HTS 来产生所有属的近乎完整的质体基因组，以及一些属内的多个物种，以产生稳健的系统发育来研究特征进化、该组的分化时间以及质体组织，包括内含子模式。我们的结果产生了 Erythropeltales 属的完全支持的系统发育，并表明形态（直立与壳状）已经进化了多次。我们的定年系统发育也表明该目非常古老（~800 Ma），其多样化发生在 Cryogenian 冰期（750-635 Ma）之后。质体基因顺序与系统发育关系一致，表明基因组结构不会经常改变。我们的数据还突出了该目质体基因组中内含子的丰富性。我们还产生了 Tsunamia transpacifica（Stylonematophyceae）的近乎完整的质体基因组，以增加该纲基因组的分类群采样。质体基因组的使用显然可以产生稳健的系统发育关系，可用于推断进化事件，并且增加分类群采样，特别是在不太知名的红藻群中，将为它们的进化提供更多的见解。
