Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication.
Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication.
复制标题
DOI：
10.1186/1471-2148-9-127
复制
发表时间：
2009-06-05
影响因子：
3.4
通讯作者：
Nishida M
中科院分区：
文献类型：
--
作者：
Sato Y;Hashiguchi Y;Nishida M
最近的基因组研究揭示了硬骨鱼特异性第三轮全基因组复制（3R-WGD）事件发生在硬骨鱼的共同祖先中。然而，目前尚不清楚在该事件中复制的基因如何在硬骨鱼多样化过程中丢失或持续存在，因此，有多少复制基因导致了硬骨鱼之间的遗传差异。该主题对于通过 WGD 事件了解脊椎动物进化过程也很重要。我们基于四种硬骨鱼的全基因组序列，采用比较进化方法来解决这个问题，重点关注参与长期增强、味觉和嗅觉转导以及三羧酸循环的基因；斑马鱼、青鳉鱼、刺鱼和绿斑河豚鱼。我们对人类上述生物系统中涉及的 130 个基因中的每一个都应用了最先进的最大似然系统发育推断和保守同线性分析方法。这些分析鉴定出硬骨鱼和四足动物之间的 116 个直系同源基因组，以及其中的 45 对 3R-WGD 衍生的重复基因。这表明四种硬骨鱼共同祖先中存在的超过一半[(45×2)/(116+45)] = 56.5%)的基因座，可能超过一万个基因，在3R-WGD之后仍然被复制。估计的基因丢失时间模式表明，在3R-WGD之后，许多（71/116）重复基因在最初的7500万年（MY）内迅速丢失，而四种硬骨鱼（45/116）祖先中平均有超过一半（27.3/45）的重复基因持续存在了约275 MY。 3R-WGD 衍生的重复体持续了很长的进化时间，具有明显更多数量的相互作用伙伴和更长的蛋白质编码序列，这意味着它们往往比 3R-WGD 之后的单体更具多功能性。我们首先基于硬骨鱼系统发育和分化时间框架展示了 3R-WGD 后基因丢失过程的时间模式。 3R-WGD 衍生的重复项并未经历恒定的指数衰减，这表明选择有利于往往具有多功能的重复项子集的长期持续存在。基于对 116 个直系同源基因组的分析获得的结果，我们提出超过一万个 3R-WGD 衍生的重复体经历了谱系特异性进化，即谱系之间的差异亚/新功能化或次生损失，并促成了硬骨鱼多样性。
Recent genomic studies have revealed a teleost-specific third-round whole genome duplication (3R-WGD) event occurred in a common ancestor of teleost fishes. However, it is unclear how the genes duplicated in this event were lost or persisted during the diversification of teleosts, and therefore, how many of the duplicated genes contribute to the genetic differences among teleosts. This subject is also important for understanding the process of vertebrate evolution through WGD events. We applied a comparative evolutionary approach to this question by focusing on the genes involved in long-term potentiation, taste and olfactory transduction, and the tricarboxylic acid cycle, based on the whole genome sequences of four teleosts; zebrafish, medaka, stickleback, and green spotted puffer fish. We applied a state-of-the-art method of maximum-likelihood phylogenetic inference and conserved synteny analyses to each of 130 genes involved in the above biological systems of human. These analyses identified 116 orthologous gene groups between teleosts and tetrapods, and 45 pairs of 3R-WGD-derived duplicate genes among them. This suggests that more than half [(45×2)/(116+45)] = 56.5%) of the loci, probably more than ten thousand genes, present in a common ancestor of the four teleosts were still duplicated after the 3R-WGD. The estimated temporal pattern of gene loss suggested that, after the 3R-WGD, many (71/116) of the duplicated genes were rapidly lost during the initial 75 million years (MY), whereas on average more than half (27.3/45) of the duplicated genes remaining in the ancestor of the four teleosts (45/116) have persisted for about 275 MY. The 3R-WGD-derived duplicates that have persisted for a long evolutionary periods of time had significantly larger number of interacting partners and longer length of protein coding sequence, implying that they tend to be more multifunctional than the singletons after the 3R-WGD. We have shown firstly the temporal pattern of gene loss process after 3R-WGD on the basis of teleost phylogeny and divergence time frameworks. The 3R-WGD-derived duplicates have not undergone constant exponential decay, suggesting that selection favoured the long-term persistence of a subset of duplicates that tend to be multi-functional. On the basis of these results obtained from the analysis of 116 orthologous gene groups, we propose that more than ten thousand of 3R-WGD-derived duplicates have experienced lineage-specific evolution, that is, the differential sub-/neo-functionalization or secondary loss between lineages, and contributed to teleost diversity.
登录
查看更多内容
影响因子：
7
作者：
Gilad, Y;Man, O;Glusman, G
通讯作者：
Glusman, G
影响因子：
64.8
作者：
Aury, Jean-Marc;Jaillon, Olivier;Wincker, Patrick
通讯作者：
Wincker, Patrick
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：
11.4
作者：
Hoegg, S;Meyer, A
通讯作者：
Meyer, A
影响因子：
14.9
作者：
Flicek P;Aken BL;Beal K;Ballester B;Caccamo M;Chen Y;Clarke L;Coates G;Cunningham F;Cutts T;Down T;Dyer SC;Eyre T;Fitzgerald S;Fernandez-Banet J;Gräf S;Haider S;Hammond M;Holland R;Howe KL;Howe K;Johnson N;Jenkinson A;Kähäri A;Keefe D;Kokocinski F;Kulesha E;Lawson D;Longden I;Megy K;Meidl P;Overduin B;Parker A;Pritchard B;Prlic A;Rice S;Rios D;Schuster M;Sealy I;Slater G;Smedley D;Spudich G;Trevanion S;Vilella AJ;Vogel J;White S;Wood M;Birney E;Cox T;Curwen V;Durbin R;Fernandez-Suarez XM;Herrero J;Hubbard TJ;Kasprzyk A;Proctor G;Smith J;Ureta-Vidal A;Searle S
通讯作者：
Searle S