The evolution of duplicate gene expression in mammalian organs.
The evolution of duplicate gene expression in mammalian organs.
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DOI：
10.1101/gr.215566.116
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发表时间：
2017-09
期刊：
影响因子：
7
通讯作者：
Kaessmann H
中科院分区：
文献类型：
--
作者：
Guschanski K;Warnefors M;Kaessmann H
基因复制产生基因组原料，允许新功能的出现，可能促进适应性进化创新。然而，直到最近，由于缺乏适当的比较数据，对哺乳动物重复基因的功能和进化相关性的全球评估受到限制。在这里，我们报告了一项基于RNA测序（RNA-seq）的大规模研究，研究了三种主要哺乳动物谱系（胎盘哺乳动物、有袋动物、产卵单孔目动物）和鸟类中基于DNA的功能基因重复的表达进化。来自九个物种和八个器官的数据。我们观察到不同重复年龄的旁系同源物的组织表达偏好的动态变化，表明在脊椎动物进化过程中旁系同源物对特定器官功能的不同贡献。具体来说，我们发现，旁系同源出现在共同祖先的脊椎动物丰富的基因与大脑特异性表达，并提供证据的差异力量优先出现年轻的睾丸和肝脏特异性表达的基因。进一步的分析发现，基因家族的整体空间表达谱往往是保守的，除了几个明显的组织特异性变化之间的谱系特异性基因家族的扩展。最后，我们追踪新的谱系特异性基因，这些基因可能有助于哺乳动物器官的特定生物学，包括很少研究的胎盘。总的来说，我们的研究提供了新的和分类学上广泛的证据，重复基因的组织特异性转录组的差异贡献和它们的重要性，脊椎动物的表型进化。
Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data. Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe dynamic changes in tissue expression preference of paralogs with different duplication ages, suggesting differential contribution of paralogs to specific organ functions during vertebrate evolution. Specifically, we show that paralogs that emerged in the common ancestor of bony vertebrates are enriched for genes with brain-specific expression and provide evidence for differential forces underlying the preferential emergence of young testis- and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved, with several exceptions of pronounced tissue specificity shifts among lineage-specific gene family expansions. Finally, we trace new lineage-specific genes that may have contributed to the specific biology of mammalian organs, including the little-studied placenta. Overall, our study provides novel and taxonomically broad evidence for the differential contribution of duplicate genes to tissue-specific transcriptomes and for their importance for the phenotypic evolution of vertebrates.
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影响因子：
4.5
作者：
Emerson RO;Thomas JH
通讯作者：
Thomas JH
影响因子：
7
作者：
Carelli FN;Hayakawa T;Go Y;Imai H;Warnefors M;Kaessmann H
通讯作者：
Kaessmann H
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
7
作者：
Grishkevich V;Yanai I
通讯作者：
Yanai I
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium