The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation

Zhaoxia Cui,Gregory G Smith,Yanan Yang,Quinn P Fitzgibbon,Chengwen Song,Chengcheng Shi,Tin‐Yam Chan ,Jing Qin,Guangyi Fan,Fuhua Li,Xiaojun Zhang,Qingle Cai,Jianhai Xiang,Yuan Liu,Shijie Hao,Hourong Liu,Jianbo Yuan,Jing Du,Ka Yan ,Dongliang Zhan,Shuai Sun,Chenchang Bao,Tomer Ventura,Min Hui,Ka Hou Chu

doi:10.1038/s41467-021-22604-3

Abstract

The infraorder Brachyura (true or short-tailed crabs) represents a successful group of marine invertebrates yet with limited genomic resources. Here we report a chromosome-anchored reference genome and transcriptomes of the Chinese mitten crab Eriocheir sinensis, a catadromous crab and invasive species with wide environmental tolerance, strong osmoregulatory capacity and high fertility. We show the expansion of specific gene families in the crab, including F-ATPase, which enhances our knowledge on the adaptive plasticity of this successful invasive species. Our analysis of spatio-temporal transcriptomes and the genome of E. sinensis and other decapods shows that brachyurization development is associated with down-regulation of Hox genes at the megalopa stage when tail shortening occurs. A better understanding of the molecular mechanism regulating sexual development is achieved by integrated analysis of multiple omics. These genomic resources significantly expand the gene repertoire of Brachyura, and provide insights into the biology of this group, and Crustacea in general.

Highlights

IntroductionThe infraorder Brachyura (true or short-tailed crabs) represents a successful group of marine invertebrates yet with limited genomic resources
The infraorder Brachyura represents a successful group of marine invertebrates yet with limited genomic resources
We report a chromosome-anchored reference genome of E. sinensis, representing a major addition to the decapod highquality genome assemblies, which are only available for the Pacific white shrimp Litopenaeus vannamei[16], the marbled crayfish Procambarus virginalis[17] and the swimming crab Portunus trituberculatus[18]

Summary

Introduction

The infraorder Brachyura (true or short-tailed crabs) represents a successful group of marine invertebrates yet with limited genomic resources. We report a chromosome-anchored reference genome and transcriptomes of the Chinese mitten crab Eriocheir sinensis, a catadromous crab and invasive species with wide environmental tolerance, strong osmoregulatory capacity and high fertility. A better understanding of the molecular mechanism regulating sexual development is achieved by integrated analysis of multiple omics These genomic resources significantly expand the gene repertoire of Brachyura, and provide insights into the biology of this group, and Crustacea in general. E. sinensis has high fertility, dispersal ability, and wide environmental tolerance, facilitating its successful invasion[4] These traits have facilitated the rapid expansion of its aquaculture across China, making it the most important cultured crab globally, with net worth more than US $10 billion per year[7]. In this work, based on comparative genomic analysis with other arthropods, the highly adaptive plasticity of E. sinensis is linked with the chr[73 0]

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Conclusion