Clam Genome Sequence Clarifies the Molecular Basis of Its Benthic Adaptation and Extraordinary Shell Color Diversity

Xiwu Yan; Hongtao Nie; Zhongming Huo; Jianfeng Ding; Zhenzhen Li; Lulu Yan; Liwen Jiang; Zhengqiang Mu; Huamin Wang; Xiangyu Meng; Peng Chen; Mengyan Zhou; Md Golam Rbbani; Guangjian Liu; Dongdong Li

doi:10.1016/j.isci.2019.08.049

Clam Genome Sequence Clarifies the Molecular Basis of Its Benthic Adaptation and Extraordinary Shell Color Diversity

iScience. 2019 Sep 27:19:1225-1237. doi: 10.1016/j.isci.2019.08.049. Epub 2019 Aug 30.

Authors

Affiliations

¹ Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China. Electronic address: yanxiwu@dlou.edu.cn.
² Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China. Electronic address: htnie@dlou.edu.cn.
³ Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China.
⁴ Novogene Bioinformatics Institute, Beijing 100083, China.
⁵ Novogene Bioinformatics Institute, Beijing 100083, China. Electronic address: liuguangjian@novogene.com.

Abstract

Ruditapes philippinarum is an economically important bivalve with remarkable diversity in its shell coloration patterns. In this study, we sequenced the whole genome of the Manila clam and investigated the molecular basis of its adaptation to hypoxia, acidification, and parasite stress with transcriptome sequencing and an RNA sequence analysis of different tissues and developmental stages to clarify these major issues. A number of immune-related gene families are expanded in the R. philippinarum genome, such as TEP, C3, C1qDC, Hsp70, SABL, and lysozyme, which are potentially important for its stress resistance and adaptation to a coastal benthic life. The transcriptome analyses demonstrated the dynamic and orchestrated specific expression of numerous innate immune-related genes in response to experimental challenge with pathogens. These findings suggest that the expansion of immune- and stress-related genes may play vital roles in resistance to adverse environments and has a profound effect on the clam's adaptation to benthic life.

Keywords: Biological Sciences; Genetics; Genomics.