Comparative De Novo transcriptome analysis of the Australian black-lip and Sydney rock oysters reveals expansion of repetitive elements in Saccostrea genomes

Ostreid oysters (the ‘true oysters’) represent a large and commercially important family of bivalve molluscs. Several species, such as the Pacific oyster (Magallana gigas), the American oyster (Crassostrea virginica), the European oyster (Ostrea edulis) and the Sydney rock oyster (Saccostrea glomerata), are currently farmed at a large scale. However a number of other species may also be suitable for commercial-scale aquaculture. One such species is the ‘black-lip oyster’, a large Saccostrea species of uncertain taxonomic affinity found in northern Australia. Here, phylogenetic analysis of the COI gene places this oyster within a clade identified in a previous study of Japanese Saccostrea species, ‘Saccostrea lineage J’. To facilitate comparisons between this oyster and the better-studied S. glomerata, de novo transcriptomes were generated from larval stages and adult tissues of both species. Patterns of orthology indicated an expansion of repetitive elements within Saccostrea genomes when compared to M. gigas and C. virginica, which may be reflected in increased evolutionary rates and/or genome sizes. The generation of high-quality transcriptomes for these two commercially relevant oysters provides a valuable resource for gene identification and comparison of molecular processes in these and other mollusc species.

牡蛎（又称‘真牡蛎’）是一类庞大的双壳贝类软体动物，在商业上具有重要价值。其中，诸如太平洋牡蛎（Magallana gigas）、美国牡蛎（Crassostrea virginica）、欧洲牡蛎（Ostrea edulis）以及悉尼岩牡蛎（Saccostrea glomerata）等物种，目前已被大规模养殖。然而，还有其他多种物种也可能适用于商业规模的养殖。其中一种为‘黑唇牡蛎’，这是一种在澳大利亚北部发现的、分类学关系不明的巨型Saccostrea物种。在此，通过对COI基因的系统发育分析，将该牡蛎归类于先前研究中在日本的Saccostrea物种中识别出的一个类群，即‘Saccostrea lineage J’。为了便于与更广泛研究的S. glomerata进行比较，从两种物种的幼虫阶段和成年组织中新构建了转录组。同源模式表明，与Magallana gigas和Crassostrea virginica相比，Saccostrea基因组中重复元件的扩张可能反映了进化速率的增加和/或基因组大小的增加。为这两种具有商业重要性的牡蛎生成高质量的转录组，为基因识别以及这些以及其他软体动物物种分子过程的比较提供了宝贵的资源。