Comparative transcriptomics in two bivalve species offers different perspectives on the evolution of sex-biased genes

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 <i>Ruditapes decussatus</i>, compared to that in the Manila clam <i>Ruditapes philippinarum</i> 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.<br>

比较基因组学现已成为进化生物学的核心研究工具，对研究不足类群的深入认知更是后续研究的重要基础。本研究对欧洲缀锦蛤（Ruditapes decussatus）与菲律宾蛤仔（Ruditapes philippinarum）的雌雄成熟性腺转录组进行了表征并开展对比分析，首次在双壳类动物中提供了性偏倚基因的转录动态与序列演化相关数据。在两个物种中，我们均发现性偏倚基因的数量相对较少（共计1284个，占两物种间直系同源基因的41.3%），这可能与二者缺乏显著的性二态性有关；且仅有33%的直系同源基因保留了转录偏倚特性。dN/dS比值普遍较低，表明存在纯化选择；其中在两物种间均维持雌性转录偏倚的基因，其dN/dS比值显著更高。参与胚胎发育、细胞增殖及基因组稳定性维持的基因，序列演化速率更快。最后，本研究发现上述物种的转录水平与演化速率之间无明确相关性，这与此前报道二者呈负相关的研究结果相悖。我们针对这一差异展开了讨论，并对这类比较研究中普遍采用的部分研究方法与理论依据提出了质疑。