The evolution of vertebrate tetraspanins: gene loss, retention, and massive positive selection after whole genome duplications.
The evolution of vertebrate tetraspanins: gene loss, retention, and massive positive selection after whole genome duplications.
复制标题
DOI：
10.1186/1471-2148-10-306
复制
发表时间：
2010-10-13
影响因子：
3.4
通讯作者：
Xu A
中科院分区：
文献类型：
--
作者：
Huang S;Tian H;Chen Z;Yu T;Xu A
脊椎动物四跨膜蛋白家族具有许多特征，这些特征使其适合于保存古老序列进化的印记，并适合于基因组分析。因此，我们认为，对四跨膜蛋白进化的深入分析不仅可以提供对四跨膜蛋白生物学的更全面的理解，而且可以为脊椎动物起源中两轮全基因组复制（2 R-WGD）的影响提供新的见解。利用多条信息线构建了脊椎动物四跨膜蛋白的详细基因组学，包括基于序列的基因组遗传学、关键结构特征、内含子构型和基因组同线性。特别是，总共有38个现代四跨膜蛋白直系同源物谱系的脊椎动物已被确定，并随后分为17个祖先谱系存在于2 R-WGD之前。基于此，我们发现2 R-WGD后四跨膜蛋白的ohnolog保留率留存率是平均值的三倍（与转录因子和蛋白激酶的保留率相似）。这种高比率并没有增加tetrapanin家族的规模，但改变了家庭的组成，可能是通过取代脊椎动物特有的基因谱系与整个后口动物保守的谱系。我们还发现从2 R-WGD到最近的时间是由基因丢失控制的。同时，在2 R-WGD之后的80%的分支上检测到了正选择，在随后的物种形成分支上，正选择的幅度和广度都显著下降。值得注意的是，哺乳动物RDS 2的丢失伴随着对哺乳动物ROM 1的强阳性选择，这可能是由于基因丢失诱导的补偿性进化。首先，与转录因子和激酶不同的是，2 R-WGD后高重复留存率并没有增加四跨膜蛋白家族的大小，而只是重塑了家族的组成。其次，在2 R-WGD之后，四跨膜蛋白的进化受到了大量基因丢失和编码序列正选择的影响。第三，2 R-WGD对四跨膜蛋白基因丢失和正选择的影响可能持续3亿至4亿年。
The vertebrate tetraspanin family has many features which make it suitable for preserving the imprint of ancient sequence evolution and amenable for phylogenomic analysis. So we believe that an in-depth analysis of the tetraspanin evolution not only provides more complete understanding of tetraspanin biology, but offers new insights into the influence of the two rounds of whole genome duplication (2R-WGD) at the origin of vertebrates. A detailed phylogeny of vertebrate tetraspanins was constructed by using multiple lines of information, including sequence-based phylogenetics, key structural features, intron configuration and genomic synteny. In particular, a total of 38 modern tetraspanin ortholog lineages in bony vertebrates have been identified and subsequently classified into 17 ancestral lineages existing before 2R-WGD. Based on this phylogeny, we found that the ohnolog retention rate of tetraspanins after 2R-WGD was three times as the average (a rate similar to those of transcription factors and protein kinases). This high rate didn't increase the tetrapanin family size, but changed the family composition, possibly by displacing vertebrate-specific gene lineages with the lineages conserved across deuterostomes. We also found that the period from 2R-WGD to recent time is controlled by gene losses. Meanwhile, positive selection has been detected on 80% of the branches right after 2R-WGDs, which declines significantly on both magnitude and extensity on the following speciation branches. Notably, the loss of mammalian RDS2 is accompanied by strong positive selection on mammalian ROM1, possibly due to gene loss-induced compensatory evolution. First, different from transcription factors and kinases, high duplicate retention rate after 2R-WGD didn't increase the tetraspanin family size but just reshaped the family composition. Second, the evolution of tetraspanins right after 2R-WGD had been impacted by a massive wave of gene loss and positive selection on coding sequences. Third, the lingering effect of 2R-WGD on tetraspanin gene loss and positive selection might last for 300-400 million years.
登录
查看更多内容
影响因子：
10.7
作者：
Ding, KY;Zhou, K;Shen, Y
通讯作者：
Shen, Y
影响因子：
10.7
作者：
Gu, X
通讯作者：
Gu, X
影响因子：
10.7
作者：
Anisimova, Maria;Yang, Ziheng
通讯作者：
Yang, Ziheng
影响因子：
10.7
作者：
Brunet, Frederic G.;Roest Crollius, Hugues;Robinson-Rechavi, Marc
通讯作者：
Robinson-Rechavi, Marc
影响因子：
3.7
作者：
Garcia-Espana, Antonio;Mares, Roso;DeSalle, Rob
通讯作者：
DeSalle, Rob