Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, 3000 Santa Fe, Argentina.
Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia.
Gene. 2023 Jun 15;869:147393. doi: 10.1016/j.gene.2023.147393. Epub 2023 Mar 24.
In angiosperms, the mitochondrial cox2 gene harbors up to two introns, commonly referred to as cox2i373 and cox2i691. We studied the cox2 from 222 fully-sequenced mitogenomes from 30 angiosperm orders and analyzed the evolution of their introns. Unlike cox2i373, cox2i691 shows a distribution among plants that is shaped by frequent intron loss events driven by localized retroprocessing. In addition, cox2i691 exhibits sporadic elongations, frequently in domain IV of introns. Such elongations are poorly related to repeat content and two of them showed the presence of LINE transposons, suggesting that increasing intron size is very likely due to nuclear intracelular DNA transfer followed by incorporation into the mitochondrial DNA. Surprisingly, we found that cox2i691 is erroneously annotated as absent in 30 mitogenomes deposited in public databases. Although each of the cox2 introns is ∼1.5 kb in length, a cox2i691 of 4.2 kb has been reported in Acacia ligulata (Fabaceae). It is still unclear whether its unusual length is due to a trans-splicing arrangement or the loss of functionality of the interrupted cox2. Through analyzing short-read RNA sequencing of Acacia with a multi-step computational strategy, we found that the Acacia cox2 is functional and its long intron is spliced in cis in a very efficient manner despite its length.
在被子植物中，线粒体 cox2 基因含有多达两个内含子，通常称为 cox2i373 和 cox2i691。我们研究了来自 30 个被子植物目中的 222 个完全测序的线粒体基因组中的 cox2，并分析了它们内含子的进化。与 cox2i373 不同，cox2i691 在植物中的分布是由局部 retroprocessing 驱动的频繁内含子丢失事件形成的。此外，cox2i691 在结构域 IV 中表现出零星的延长，这在内含子中很常见。这种延长与重复序列的含量没有关系，其中两个表现出线粒体 DNA 内转位酶（LINE transposons）的存在，表明内含子大小的增加很可能是由于核内细胞内 DNA 转移，然后整合到线粒体 DNA 中。令人惊讶的是，我们发现 30 个公共数据库中存储的线粒体基因组错误地注释为 cox2i691 缺失。尽管每个 cox2 内含子的长度约为 1.5kb，但在金合欢属（豆科）中已经报道了一个长度为 4.2kb 的 cox2i691。其不寻常的长度是否是由于反式剪接排列或被中断的 cox2 的功能丧失，目前尚不清楚。通过对金合欢属的短读 RNA 测序进行多步计算策略分析，我们发现尽管 Acacia 的 cox2 内含子很长，但它的功能是正常的，并且以非常有效的方式在顺式中进行剪接。
