Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy.
Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, USA.
Genome Biol Evol. 2018 Jun 1;10(6):1389-1402. doi: 10.1093/gbe/evy082.
Comparative genomics has become a central tool for evolutionary biology, and a better knowledge of understudied taxa represents the foundation for future work. In this study, we characterized the transcriptome of male and female mature gonads in the European clam Ruditapes decussatus, compared with that in the Manila clam Ruditapes philippinarum providing, for the first time in bivalves, information about transcription dynamics and sequence evolution of sex-biased genes. In both the species, we found a relatively low number of sex-biased genes (1,284, corresponding to 41.3% of the orthologous genes between the two species), probably due to the absence of sexual dimorphism, and the transcriptional bias is maintained in only 33% of the orthologs. The dN/dS is generally low, indicating purifying selection, with genes where the female-biased transcription is maintained between the two species showing a significantly higher dN/dS. Genes involved in embryo development, cell proliferation, and maintenance of genome stability show a faster sequence evolution. Finally, we report a lack of clear correlation between transcription level and evolutionary rate in these species, in contrast with studies that reported a negative correlation. We discuss such discrepancy and call into question some methodological approaches and rationales generally used in this type of comparative studies.
比较基因组学已成为进化生物学的主要工具，而对研究较少的分类群有更好的了解则代表了未来工作的基础。在这项研究中，我们对欧洲贻贝（Ruditapes decussatus）的雄性和雌性成熟性腺的转录组进行了特征描述，与菲律宾蛤仔（Ruditapes philippinarum）的转录组进行了比较，这是双壳类动物中首次提供有关性别偏向基因转录动态和序列进化的信息。在这两个物种中，我们发现了相对较少的性别偏向基因（1284 个，对应于两个物种之间的同源基因的 41.3%），这可能是由于没有性二态性，并且只有 33%的同源基因保持转录偏倚。dN/dS 通常较低，表明存在纯化选择，在这两个物种中维持雌性偏转录的基因具有明显更高的 dN/dS。涉及胚胎发育、细胞增殖和基因组稳定性维持的基因表现出更快的序列进化。最后，我们报告了在这些物种中，转录水平和进化率之间缺乏明显的相关性，这与报道负相关的研究形成了对比。我们讨论了这种差异，并对这种类型的比较研究中通常使用的一些方法学方法和推理提出了质疑。
