農業部-水產試驗所全球資訊網農業部-水產試驗所全球資訊網

文蛤(Hard Clam, Meretrix spp.)屬於軟體動物門(Mollusca)、雙殼綱 (Bivalvia)、簾蛤目(Veneroida)、簾蛤科(Veneridae)、文蛤屬(Meretrix)，該屬 物種主要分布於印度-西太平洋地區的沿岸及河口地帶，文蛤為亞洲重要的經濟貝類 物種之一，文蛤具潛沙之習性，喜好棲息於具細沙之河口、內灣或淺海。臺灣於 1980至1981年間建立文蛤人工繁殖及育苗技術，並於1983年起開始大量繁殖，且西 海岸多為適合文蛤生產之沙地及河口，因此養殖面積及生產規模隨著消費需要快速 增加，依據行政院農業委員會漁業署臺灣地區漁業統計年報(2017)資料顯示，臺灣 文蛤養殖仍以內陸為主，面積約7,718公頃，產量約52,000公噸，其產值每年超過 50億以上，為臺灣內陸養殖最重要之養殖貝類，其產地集中在雲林、嘉義及臺南地 區，惟近年文蛤養殖會發生如生長停滯、偶發及季節性死亡等問題，是產量不甚穩 定的主因。初步推測可能原因為季節轉換氣溫變化劇烈、養殖密度過高、水質環境 惡化等因素所造成；另一方面，臺灣文蛤養殖之種苗來源多年來大多使用未經過育 種之國內或國外進口之種貝進行繁殖，並未對文蛤性狀如：成長速度、抗病及抗溫 能力等進行篩選培育，這些重要性狀之相關基因體學研究亦較為缺乏，可能是臺灣 文蛤養殖業受近年氣候變遷影響較大而影響產業發展的原因之一。本研究計畫屬具 導向性之基礎研究計畫，擬運用近年快速發展之第三世代定序技術(third generation sequencing)，對文蛤基因進行較為完整及全面性之解析，並解決以往 次世代定序(next generation sequencing)其一次可讀取之片段較短，僅100-150鹼 基對(bp)之限制，因較短的定序片段容易錯誤組合(misassembly)或欠損(gap)，增 加後續遺傳分析之困難度。本研究計畫希望能瞭解文蛤其基因序列組成特性及分析 其環境適應能力之相關基因，並預期這些解析之基因序列資料能夠作為後續文蛤品 種培育之起點與基石，本次研究共獲得717,585轉錄體序列，經由分析對應至 403,167個基因，並完成以14個貝類物種為參考資料的基因註解。

Hard clam (Meretrix spp.) is one of the major aquaculture shellfishes in Taiwan and the scale of aquaculture has increased because of higher consumption. In recent years, the production of hard clam farming are sometimes unstable because of growth retardation, seasonal and accidental deaths. These problems may be caused by drastically temperature changes, high density of aquaculture, and water quality deterioration, etc. In spite of the importance as a marine resource, the reference genome of bivalves for comprehensive genetic studies is largely unexplored. The lack of genomic resources of hard clam coupled with poor understanding of molecular and biochemical processes have hindered advances in aquaculture productivity. In the previous study of this project, the 2nd generation sequencing is applied for transcriptome analysis in hard clam. However, the limitation of 2nd generation sequencing is shorter reads (100-150 bp). These short-reads combined by assembly programs are still fragmented contigs of mRNA sequences and has lower similarity to the other bivalve mRNA sequences. These abovementioned issues lead to misassemblies and gaps in sequences and increase the difficulty of genetic analysis. In order to obtain effective genetic information for breeding and artificial selection, 3rd generation (long-read) sequencing would be applied for hard clam transcriptome. We hope that third revolution in sequencing technology promise to bring exciting new developments and discoveries in hard clam aquaculture. In total, 717,585 transcripts were collected, which could be grouped into 403,167 gene candidates. Taxonomic distribution of de novo assemble in 14 reference clam species is also completed.