Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin.
Whole-genome positive selection and habitat-driven evolution in a shallow and a deep-sea urchin.
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DOI：
10.1093/gbe/evq063
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发表时间：
2010
影响因子：
3.3
通讯作者：
Palumbi SR
中科院分区：
文献类型：
--
作者：
Oliver TA;Garfield DA;Manier MK;Haygood R;Wray GA;Palumbi SR
不同物种之间基因组序列的比较可以深入了解许多不同类别蛋白质的自然选择作用。在这里，我们研究了两种密切相关的海胆（浅水Strongylocentrotus purpuratus和深海Allocentrotus fragilis）中组织特异性和阶段特异性基因表达的正选择程度，这两种海胆在成体但在幼体栖息地方面存在很大差异。在成体体细胞组织中特异性表达的基因的 dN/dS 比率显着高于全基因组平均值，而幼虫中的基因与全基因组平均值无法区分。睾丸特异性基因的 dN/dS 值最高，而卵巢特异性基因的 dN/dS 值最低。涉及外群 S. franciscanus 的分支位点模型表明，沿着 A. fragilis 分支比沿着 S. purpuratus 分支有更大的选择（ωFG）。 A. fragilis 分支还显示出较高比例的正选择基因，包括涉及骨骼发育、内吞作用和硫代谢的基因。两个谱系在参与免疫、发育和细胞间通讯的基因的正选择富集方面大致相等。分支位点模型进一步表明，成虫特异性基因比幼虫中表达的基因经历了更大的正选择，而卵巢特异性基因比成虫体细胞组织和睾丸中特异表达的基因更保守（即经历了更大的负选择）。我们的结果绘制了这两个物种栖息地分化后发生的蛋白质变化模式，并表明基因发挥作用的发育或功能背景可以在不同物种如何适应新环境中发挥重要作用。
Comparisons of genomic sequence between divergent species can provide insight into the action of natural selection across many distinct classes of proteins. Here, we examine the extent of positive selection as a function of tissue-specific and stage-specific gene expression in two closely-related sea urchins, the shallow-water Strongylocentrotus purpuratus and the deep-sea Allocentrotus fragilis, which have diverged greatly in their adult but not larval habitats. Genes that are expressed specifically in adult somatic tissue have significantly higher dN/dS ratios than the genome-wide average, whereas those in larvae are indistinguishable from the genome-wide average. Testis-specific genes have the highest dN/dS values, whereas ovary-specific have the lowest. Branch-site models involving the outgroup S. franciscanus indicate greater selection (ωFG) along the A. fragilis branch than along the S. purpuratus branch. The A. fragilis branch also shows a higher proportion of genes under positive selection, including those involved in skeletal development, endocytosis, and sulfur metabolism. Both lineages are approximately equal in enrichment for positive selection of genes involved in immunity, development, and cell–cell communication. The branch-site models further suggest that adult-specific genes have experienced greater positive selection than those expressed in larvae and that ovary-specific genes are more conserved (i.e., experienced greater negative selection) than those expressed specifically in adult somatic tissues and testis. Our results chart the patterns of protein change that have occurred after habitat divergence in these two species and show that the developmental or functional context in which a gene acts can play an important role in how divergent species adapt to new environments.
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影响因子：
12.3
作者：
Huse SM;Huber JA;Morrison HG;Sogin ML;Welch DM
通讯作者：
Welch DM
影响因子：
4.3
作者：
Arbiza L;Dopazo J;Dopazo H
通讯作者：
Dopazo H
DOI：
10.1186/jbiol161
发表时间：
2009-07-21
期刊：
Journal of Biology (London)
影响因子：
--
作者：
Garfield, David A.;Wray, Gregory A.
通讯作者：
Wray, Gregory A.
DOI：
10.1073/pnas.0701705104
发表时间：
2007-05-01
影响因子：
11.1
作者：
Bakewell, Margaret A.;Shi, Peng;Zhang, Jianzhi
通讯作者：
Zhang, Jianzhi
种群基因组学：果蝇果蝇中多态性和差异的全基因组分析。
影响因子：
9.8
作者：
Begun, David J.;Holloway, Alisha K.;Stevens, Kristian;Hillier, LaDeana W.;Poh, Yu-Ping;Hahn, Matthew W.;Nista, Phillip M.;Jones, Corbin D.;Kern, Andrew D.;Dewey, Colin N.;Pachter, Lior;Myers, Eugene;Langley, Charles H.
通讯作者：
Langley, Charles H.