文蛤成長轉錄體與微生物組、藻類群落綜合分析

Abstract

文蛤是台灣主要養殖的雙殼類，是重要的經濟與生態物種。文蛤產地主要集中在彰化、雲林、和台南。然而近年來出現文蛤生長速度緩慢的現象，但目前仍尚不清楚發生的原因。本研究旨在透過RNA-seq技術，探討大文蛤與小文蛤在基因表現上的差異，並結合16 S 和18S rRNA資料，找出影響文蛤大小的關鍵因素。每批次蒐集回來的文蛤以體重前四分之一定義為大文蛤，最後四分之一為小文蛤。之後進行文蛤轉錄體組裝，並進行差異性表達基因的分析，結果發現有31個基因差異性表現基因上調，69個基因下調。以COG和KEGG資料庫註釋差異性表達基因後發現許多DEGs與脂質和碳水化合物代謝相關。在微生物方面，根據LEfSe結果發現Romboutsia 和 Ulivibacter 屬在大隻文蛤組中顯著富集，PICRUSt2功能預測中顯示大隻文蛤組在代謝相關的多條路徑(碳水化合物與脂質代謝) 顯著富集，推測腸道菌可能有助於提升宿主的營養吸收效率與整體代謝能力。而在網絡分析顯示，一些與細胞生長調控相關的宿主基因與特定的藻類或細菌高度相關。本結果表明，文蛤的生長表現可能不僅受其遺傳背景所限制，還可能受到腸道環境因子的共同調控，這些發現有助於識別與文蛤生長相關的基因與環境，為水產養殖技術提供嶄新見解。

Bivalve species hold significant economic and ecological value, with the hard clam (Meretrix meretrix) being one of the farmed species in Taiwan. The main production areas for hard clams are concentrated in Changhua, Yunlin, and Tainan. However, in recent years, there has been a noticeable trend of slow growth in the clams. Although the reasons behind this slow growth remain unclear, existing literature suggests that growth is regulated by factors such as RNA expression and environmental conditions. In this study, hard clams from each batch were classified into large and small groups by the first and last quartile of size, respectively. RNA-seq was employed to investigate differential gene expression, alongside 16S and 18S rRNA analyses to identify key microbial factors associated with clam size. After transcriptome assembly, differential expression analysis was conducted to identify genes associated with size-related phenotypic differences. Overall, 31 genes were up-regulated and 69 genes were down-regulated when comparing the large group to the small group. Based on functional annotations from the COG and KEGG databases, several differentially expressed genes (DEGs) were associated with lipid and carbohydrate metabolism. In microbiome part, LEfSe analysis revealed that Romboutsia and Ulivibacter genus were significantly enriched in the large-size clam group. The results of functional prediction using PICRUSt2 indicated that various metabolism-related pathways were also enriched in the large-size group. Network analysis revealed that certain host genes associated with cell growth regulation were highly correlated with specific algae or bacteria. This suggests that the growth phenotype of clams may not only be constrained by their genetic background, but also be co-regulated by intestinal environmental factors. These findings provide valuable insights into identifying key genes and microbial factors related to clam growth, offering scientific guidance for improving aquaculture techniques in the future.