Chen Bing, Shao Jingru, Zhuang Huifu, Wen Jianfan
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
Gene. 2017 Feb 20;602:24-32. doi: 10.1016/j.gene.2016.11.027. Epub 2016 Nov 15.
Intron evolution, including its dynamics in the evolutionary transitions and diversification of eukaryotes, remains elusive. Inadequate taxon sampling due to data shortage, unclear phylogenetic framework, and inappropriate outgroup application might be among the causes. Besides, the integrity of all the introns within a gene was often neglected previously. Taking advantage of the ancient conserved triosephosphate isomerase gene (tim), the relatively robust phylogeny of Metazoa, and choanoflagellates as outgroup, the evolutionary dynamics of tim intron location pattern (ILP) in Metazoa was investigated. From 133 representative species of ten phyla, 30 types of ILPs were identified. A most common one, which harbors the maximum six intron positions, is deduced to be the common ancestral tim ILP of Metazoa, which almost had formed in their protozoan ancestor and was surprisingly retained and passed down till to each ancestors of metazoan phyla. In the subsequent animal diversification, it underwent different evolutionary trajectories: within Deuterostomia, it was almost completely retained only with changes in a few species with relatively recently fast-evolving histories, while within the rapidly radiating Protostomia, besides few but remarkable retention, it usually displayed extensive intron losses and a few gains. Therefore, a common ancestral exon-intron arrangement pattern of an animal gene is definitely discovered; besides the 'intron-rich view' of early animal genes being confirmed, the novel insight that high exon-intron re-arrangements of genes seem to be associated with the relatively recently rapid evolution of lineages/species/genomes but have no correlation with the ancient major evolutionary transitions in animal evolution, is revealed.
内含子的进化，包括其在真核生物进化转变和多样化过程中的动态变化，仍然难以捉摸。数据短缺导致的分类群抽样不足、系统发育框架不明确以及外类群应用不当可能是原因之一。此外，以前常常忽略一个基因内所有内含子的完整性。利用古老的保守磷酸丙糖异构酶基因（tim）、后生动物相对可靠的系统发育以及作为外类群的领鞭毛虫，研究了后生动物中tim内含子定位模式（ILP）的进化动态。从十个门的133个代表性物种中，鉴定出30种ILP类型。推断出一种最常见的类型，其内含子位置最多有六个，是后生动物tim的共同祖先ILP，它几乎在其原生动物祖先中就已形成，并且令人惊讶地保留下来并一直传承到后生动物各门类的每个祖先。在随后的动物多样化过程中，它经历了不同的进化轨迹：在后口动物中，除了少数具有相对近期快速进化历史的物种有变化外，它几乎完全保留下来；而在快速辐射的原口动物中，除了少数但显著的保留外，它通常表现出广泛的内含子丢失和少量增加。因此，确实发现了一个动物基因的共同祖先外显子 - 内含子排列模式；除了证实早期动物基因的“富含内含子观点”外，还揭示了一个新的见解，即基因的高外显子 - 内含子重排似乎与谱系/物种/基因组相对近期的快速进化相关，但与动物进化中的古代主要进化转变无关。
