Rapid Functional and Sequence Differentiation of a Tandemly Repeated Species-Specific Multigene Family in Drosophila
Rapid Functional and Sequence Differentiation of a Tandemly Repeated Species-Specific Multigene Family in Drosophila
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DOI：
10.1093/molbev/msw212
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发表时间：
2017-01-01
影响因子：
10.7
通讯作者：
Ranz, Jose M.
中科院分区：
文献类型：
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作者：
Clifton, Bryan D.;Librado, Pablo;Ranz, Jose M.
新近复制的基因簇是进化变化的温床。然而，我们对突变机制和进化力量如何塑造这些集群的结构和功能进化的理解受到拷贝之间高度序列同一性的阻碍，这通常导致它们在基因组组装中的不准确表示。据推测，睾丸特异性嵌合基因Sdic起源于黑腹果蝇，并在黑腹果蝇中不断扩增，从而增加了雄性之间的竞争。利用各种类型的大规模并行测序数据，我们研究了不同Sdic拷贝的组织、序列进化和功能属性。通过利用长读测序数据，我们发现了当前接受的Sdic区域注释的拷贝数和顺序差异。尽管有证据表明普遍存在影响Sdic拷贝的基因转换，但我们也发现了两段多样化选择的特征，这有助于多种c -末端和miRNA结合位点组成的进化。表达分析涉及来自59种不同生物学条件的RNA-seq数据集，揭示了拷贝之间的不同表达宽度，其中三个拷贝在雌性中转录，开启了性别拮抗效应的可能性。使用Sdic敲除菌株的表型分析表明，如果这种拮抗作用存在，它不会损害女性的生育能力。我们的研究结果强烈表明，Sdic基因簇的基因组整合更多的是不同拷贝对不同分子修补路径的快速探索的结果，而不仅仅是剂量的增加，这可能是存在持续性选择的反复进化结果。
Gene clusters of recently duplicated genes are hotbeds for evolutionary change. However, our understanding of how mutational mechanisms and evolutionary forces shape the structural and functional evolution of these clusters is hindered by the high sequence identity among the copies, which typically results in their inaccurate representation in genome assemblies. The presumed testis-specific, chimeric gene Sdic originated, and tandemly expanded in Drosophila melanogaster, contributing to increased male-male competition. Using various types of massively parallel sequencing data, we studied the organization, sequence evolution, and functional attributes of the different Sdic copies. By leveraging long-read sequencing data, we uncovered both copy number and order differences from the currently accepted annotation for the Sdic region. Despite evidence for pervasive gene conversion affecting the Sdic copies, we also detected signatures of two episodes of diversifying selection, which have contributed to the evolution of a variety of C-termini and miRNA binding site compositions. Expression analyses involving RNA-seq datasets from 59 different biological conditions revealed distinctive expression breadths among the copies, with three copies being transcribed in females, opening the possibility to a sexually antagonistic effect. Phenotypic assays using Sdic knock-out strains indicated that should this antagonistic effect exist, it does not compromise female fertility. Our results strongly suggest that the genome consolidation of the Sdic gene cluster is more the result of a quick exploration of different paths of molecular tinkering by different copies than a mere dosage increase, which could be a recurrent evolutionary outcome in the presence of persistent sexual selection.