Application of community phylogenetic approaches to understand gene expression: differential exploration of venom gene space in predatory marine gastropods
Application of community phylogenetic approaches to understand gene expression: differential exploration of venom gene space in predatory marine gastropods
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DOI：
10.1186/1471-2148-14-123
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发表时间：
2014-06-05
影响因子：
3.4
通讯作者：
Duda, Thomas F., Jr.
中科院分区：
文献类型：
--
作者：
Chang, Dan;Duda, Thomas F., Jr.
背景：圆锥属的掠食性海洋腹足类动物在物种内部和物种之间的毒液组成都有很大的变化。除了与基因家族的广泛更新和编码毒液成分（“conotoxin”）的基因的快速进化相关的机制外，不同conotoxin表达模式的进化是另一个变异来源，可能导致物种对“毒液基因空间”的利用存在种间差异。为了确定Conus物种毒液基因表达模式的进化，我们通过比较从这些物种基因组中恢复的a -超家族基因转录本，评估了一组密切相关的Conus物种的a -超家族concontoxin基因的表达。我们改进了群落系统发育方法，结合系统发育历史和基因差异及其表达谱来确定毒液基因空间利用模式。结果：这些物种的a超家族基因库中只有不到一半的基因被表达，只有少数同源基因在物种之间共表达。物种表现出截然不同的表达策略，一些表达密切相关的基因座组（可用基因的“欠分散”表达），而另一些表达更不同的基因组（“过度分散”表达）。此外，表达基因的d(N)/d(S)值高于未表达基因或祖先基因；这意味着表达使基因暴露于选择，并促进了这些基因的快速进化。最近的谱系特异性基因副本很少同时表达，这表明冗余基因副本之间的表达差异可能在基因复制后不久就建立起来。结论：我们的研究表明，Conus物种对毒液基因空间的探索是不同的，这一过程有效地允许了这些物种毒液的独立和快速进化。
Background: Predatory marine gastropods of the genus Conus exhibit substantial variation in venom composition both within and among species. Apart from mechanisms associated with extensive turnover of gene families and rapid evolution of genes that encode venom components ('conotoxins'), the evolution of distinct conotoxin expression patterns is an additional source of variation that may drive interspecific differences in the utilization of species' 'venom gene space'. To determine the evolution of expression patterns of venom genes of Conus species, we evaluated the expression of A-superfamily conotoxin genes of a set of closely related Conus species by comparing recovered transcripts of A-superfamily genes that were previously identified from the genomes of these species. We modified community phylogenetics approaches to incorporate phylogenetic history and disparity of genes and their expression profiles to determine patterns of venom gene space utilization.Results: Less than half of the A-superfamily gene repertoire of these species is expressed, and only a few orthologous genes are coexpressed among species. Species exhibit substantially distinct expression strategies, with some expressing sets of closely related loci ('under-dispersed' expression of available genes) while others express sets of more disparate genes ('over-dispersed' expression). In addition, expressed genes show higher d(N)/d(S) values than either unexpressed or ancestral genes; this implies that expression exposes genes to selection and facilitates rapid evolution of these genes. Few recent lineage-specific gene duplicates are expressed simultaneously, suggesting that expression divergence among redundant gene copies may be established shortly after gene duplication.Conclusions: Our study demonstrates that venom gene space is explored differentially by Conus species, a process that effectively permits the independent and rapid evolution of venoms in these species.