Kamikawa Ryoma, Kolisko Martin, Nishimura Yuki, Yabuki Akinori, Brown Matthew W, Ishikawa Sohta A, Ishida Ken-ichiro, Roger Andrew J, Hashimoto Tetsuo, Inagaki Yuji
Graduate School of Global Environmental Studies and Graduate School of Human and Environmental Studies, Kyoto University, Japan.
Genome Biol Evol. 2014 Feb;6(2):306-15. doi: 10.1093/gbe/evu015.
The unicellular eukaryotic assemblage Discoba (Excavata) comprises four lineages: the Heterolobosea, Euglenozoa, Jakobida, and Tsukubamonadida. Discoba has been considered as a key assemblage for understanding the early evolution of mitochondrial (mt) genomes, as jakobids retain the most gene-rich (i.e., primitive) genomes compared with any other eukaryotes determined to date. However, to date, mt genome sequences have been completed for only a few groups within Discoba, including jakobids, two closely related heteroloboseans, and kinetoplastid euglenozoans. The Tsukubamonadida is the least studied lineage, as the order was only recently established with the description of a sole representative species, Tsukubamonas globosa. The evolutionary relationship between T. globosa and other discobids has yet to be resolved, and no mt genome data are available for this particular organism. Here, we use a "phylogenomic" approach to resolve the relationship between T. globosa, heteroloboseans, euglenozoans, and jakobids. In addition, we have characterized the mt genome of T. globosa (48,463 bp in length), which encodes 52 putative protein-coding and 29 RNA genes. By mapping the gene repertoires of discobid mt genomes onto the well-resolved Discoba tree, we model gene loss events during the evolution of discobid mt genomes.
单细胞真核生物类群双滴虫目（盘状动物门）由四个谱系组成：异叶足虫纲、眼虫纲、贾科比虫纲和筑波虫纲。双滴虫目被认为是理解线粒体（mt）基因组早期进化的关键类群，因为与迄今已确定的任何其他真核生物相比，贾科比虫纲保留了基因最丰富（即最原始）的基因组。然而，迄今为止，仅完成了双滴虫目内少数类群的mt基因组序列测定，包括贾科比虫纲、两种亲缘关系密切的异叶足虫以及动质体眼虫纲。筑波虫纲是研究最少的谱系，因为该目最近才随着唯一代表物种球形筑波虫的描述而建立。球形筑波虫与其他双滴虫目的进化关系尚未解决，且尚无该特定生物的mt基因组数据。在此，我们采用“系统发育基因组学”方法来解析球形筑波虫、异叶足虫纲、眼虫纲和贾科比虫纲之间的关系。此外，我们还对球形筑波虫的mt基因组（长度为48463 bp）进行了特征分析，该基因组编码52个推定的蛋白质编码基因和29个RNA基因。通过将双滴虫目mt基因组的基因库映射到解析良好的双滴虫目系统树上，我们对双滴虫目mt基因组进化过程中的基因丢失事件进行了建模。
