Chromosome-Level Clam Genome Helps Elucidate the Molecular Basis of Adaptation to a Buried Lifestyle.

Min Wei,Yihua Chen,Xiwu Yan,Haibao Duan,Zhiguo Dong,Min Zhang,Dongdong Zhang,Hongtao Nie,Xiaoting Liao,Changwei Shao,Hongxing Ge

doi:10.1016/j.isci.2020.101148

Abstract

SummaryBivalve mollusks are economically important invertebrates that exhibit marked diversity in benthic lifestyle and provide valuable resources for understanding the molecular basis of adaptation to benthic life. In this report, we present a high-quality, chromosome-anchored reference genome of the Venus clam, Cyclina sinensis. The chromosome-level genome was assembled by Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 10× Genomics, and high-throughput chromosome conformation capture technologies. The final genome assembly of C. sinensis is 903.2 Mb in size, with a contig N50 size of 2.6 Mb and a scaffold N50 size of 46.5 Mb. Enrichment analyses of significantly expanded and positively selected genes suggested evolutionary adaptation of this clam to buried life. In addition, a change in shell color represents another mechanism of adaptation to burial in sediment. The high-quality genome generated in this work provides a valuable resource for investigating the molecular mechanisms of adaptation to buried lifestyle.

Highlights

Bivalves are a large superclade of mollusks, consisting of approximate 10,000 species with a global distribution in diverse marine, freshwater, and terrestrial environments (Appeltans et al, 2012)
Ecological, and economic significance of these bivalves, available genomes are still limited to a few species (Yan et al, 2019; Ran et al, 2019; Bai et al, 2019), which hinders our understanding of the molecular basis of adaptation to a buried lifestyle in sediment
Genome Sequencing and Assembly A total of 58.02 Genome Complete size BUSCO (Gb) of reads (67.23) with an insert size of 350 bp was obtained with the Illumina HiSeq PE150 platform, and a total of 103.29 Gb of reads (119.63) was obtained with the PacBio Sequel platform

Summary

Introduction

Bivalves are a large superclade of mollusks, consisting of approximate 10,000 species with a global distribution in diverse marine, freshwater, and terrestrial environments (Appeltans et al, 2012). The sediment microenvironment is especially complex, because it consists of both water and soil, and benthic bivalves have adapted to extreme environments with a low oxygen content, pathogens, and high reducing power (Wang et al, 2012; Costa et al, 2015; Collins et al, 2017; Santos et al, 2019). The most burrowing and buried bivalves play critical roles in bioturbation and the breakdown of organic matter in sediment, improving the sediment microenvironment for the growth of bacteria and protists (Newel, 2004; Norkko and Shumway, 2011). Ecological, and economic significance of these bivalves, available genomes are still limited to a few species (Yan et al, 2019; Ran et al, 2019; Bai et al, 2019), which hinders our understanding of the molecular basis of adaptation to a buried lifestyle in sediment

Methods

Results

Discussion

Conclusion