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Differential Gene expression related to morphological variation in the adductor muscle tissues of diploid and triploid fujian oysters,
 Crassostrea angulata

The Fujian oyster, Crassostrea angulata, accounts for approximately 50% of the total oyster production in China and is one of the most economically important marine products. In this study, we investigated differential gene expression profiles between diploid (n = 2) and triploid (n = 3) oysters that may indicate the specific adaptation associated with ploidy. A total of 14,626,126 and 15,492,551 reads were generated from diploid and triploid oyster muscle transcriptomes using Illumina RNA‐Seq respectively. Gene expression analysis revealed a total of 2,045 differentially expressed genes between 2n and 3n individuals, from which 814 genes were significantly up‐regulated in the 2n transcriptome while 1,231 were down‐regulated. In addition, 24 differentially expressed genes (DEGs) were uniquely expressed in 2n individuals while 28 DEGs were uniquely expressed in 3n individuals. Furthermore, our pathway analysis suggested that the DEGs up‐regulated in 2n oysters were enriched in the pathways related to normal growth, development and reproduction, whereas DEGs up‐regulated in 3n individuals may be involved in faster growth and metabolism. Finally, we validated the expression levels of 15 genes using quantitative real‐time PCR (qRT‐PCR), and 14 out of 15 genes showed consistent expression patterns with RNA‐Seq data. This study provides an important foundation for further investigations on distinct gene expression patterns and signalling pathways that differ between diploid and triploid oysters.