Clam Genome and Transcriptomes Provide Insights into Molecular Basis of Morphological Novelties and Adaptations in Mollusks
文献类型： 外文期刊
作者： Sun, Xiujun 1 ; Chen, Xi 1 ; Wu, Biao 1 ; Zhou, Liqing 1 ; Chen, Yancui 3 ; Zheng, Sichen 1 ; Wang, Songlin 1 ; Liu, Zhihong 1 ;
作者机构： 1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, State Key Lab Mariculture Biobreeding & Sustainabl, Qingdao 266071, Peoples R China
2.Laoshan Lab, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao 266071, Peoples R China
3.Zhangzhou Aquat Technol Promot Stn, Zhangzhou 363000, Peoples R China
4.Shanghai Ocean Univ, Coll Fisheries & Life Sci, Shanghai 201306, Peoples R China
5.Jiangsu Ocean Univ, Coll Marine Sci & Fisheries, Lianyungang 222005, Peoples R China
关键词： clam; genome; transcriptome; phenotype evolution; transposable elements
期刊名称：BIOLOGY-BASEL （ 影响因子：3.5； 五年影响因子：4.0 ）
ISSN：
年卷期： 2024 年 13 卷 11 期
页码：
收录情况： SCI
摘要： Bivalve mollusks, comprising animals enclosed in two shell valves, are well-adapted to benthic life in many intertidal zones. Clams have evolved the buried lifestyle, which depends on their unique soft tissue structure and their wedge-shaped muscular foot and long extendible siphons. However, molecular mechanisms of adaptative phenotype evolution remain largely unknown. In the present study, we obtain the high-quality chromosome-level genome of Manila clam R. philippinarum, an economically important marine bivalve in many coastal areas. The genome is constructed by the Hi-C assisted assembly, which yields 19 chromosomes with a total of 1.17 Gb and BUSCO integrity of 92.23%. The de novo assembled genome has a contig N50 length of 307.7 kb and scaffold N50 of 59.5 Mb. Gene family expansion analysis reveals that a total of 24 single-copy gene families have undergone the significant expansion or contraction, including E3 ubiquitin ligase and dynein heavy chain. The significant expansion of transposable elements has been also identified, including long terminal repeats (LTR) and non-LTR retrotransposons. The comparative transcriptomics among different clam tissues reveals that extracellular matrix (ECM) receptors and neuroactive ligand receptors may play the important roles in tissue structural support and neurotransmission during their infaunal life. These findings of gene family expansion and tissue-specific expression may reflect the unique soft tissue structure of clams, suggesting the evolution of lineage-specific morphological novelties. The high-quality genome and transcriptome data of R. philippinarum will not only facilitate the genetic studies on clams but will also provide valuable information on morphological novelties in mollusks.
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