Genome Sequences of Marine Shrimp Exopalaemon carinicauda Holthuis Provide Insights into Genome Size Evolution of Caridea.

Jianbo Yuan,Yi Gao,Jianhai Xiang,Chengzhang Liu,Fuhua Li,Jiankai Wei,Xiaojun Zhang

doi:10.3390/md15070213

Abstract

Crustacea, particularly Decapoda, contains many economically important species, such as shrimps and crabs. Crustaceans exhibit enormous (nearly 500-fold) variability in genome size. However, limited genome resources are available for investigating these species. Exopalaemon carinicauda Holthuis, an economical caridean shrimp, is a potential ideal experimental animal for research on crustaceans. In this study, we performed low-coverage sequencing and de novo assembly of the E. carinicauda genome. The assembly covers more than 95% of coding regions. E. carinicauda possesses a large complex genome (5.73 Gb), with size twice higher than those of many decapod shrimps. As such, comparative genomic analyses were implied to investigate factors affecting genome size evolution of decapods. However, clues associated with genome duplication were not identified, and few horizontally transferred sequences were detected. Ultimately, the burst of transposable elements, especially retrotransposons, was determined as the major factor influencing genome expansion. A total of 2 Gb repeats were identified, and RTE-BovB, Jockey, Gypsy, and DIRS were the four major retrotransposons that significantly expanded. Both recent (Jockey and Gypsy) and ancestral (DIRS) originated retrotransposons responsible for the genome evolution. The E. carinicauda genome also exhibited potential for the genomic and experimental research of shrimps.

Highlights

Crustacea and Hexapoda are two species-rich groups of Arthropoda, which is the phylum with the highest number of species identified worldwide [1].Abundant genome resources have been identified from insects, whereas few crustaceans genomes, except those of the branchiopod Daphnia pulex and the amphipodParhyale hawaiensis [2,3], have been completely sequenced
In contrast to the bimodal distribution of K-mer frequencies in L. vannamei and P. hawaiensis [3,4], a single peak was observed in E. carinicauda; this peak corresponds to K-mers present on homozygous regions (Figure 1A)
This study provides a valuable genome resource of E. carinicauda for research on decapod shrimps, the 5.57 Gb sequences covering about 97% of the genome and more than 95% of coding regions

Summary

Introduction

Crustacea (such as shrimps and crabs) and Hexapoda (mainly insects) are two species-rich groups of Arthropoda, which is the phylum with the highest number of species identified worldwide [1].Abundant genome resources have been identified from insects (more than 40 species), whereas few crustaceans genomes, except those of the branchiopod Daphnia pulex and the amphipodParhyale hawaiensis [2,3], have been completely sequenced. Crustacea (such as shrimps and crabs) and Hexapoda (mainly insects) are two species-rich groups of Arthropoda, which is the phylum with the highest number of species identified worldwide [1]. Abundant genome resources have been identified from insects (more than 40 species), whereas few crustaceans genomes, except those of the branchiopod Daphnia pulex and the amphipod. The genomes of decapods are difficult to sequence and assemble due to the large size and complexity of the genome; these economically important species include Litopenaeus vannamei, Penaeus monodon, Macrobrachium rosenbergii, Exopalaemon carinicauda, and Eriocheir sinensis [4,5]. The low-coverage sequencing of the cherry shrimp Neocaridina denticulata and the Chinese mitten crab E. sinensis impels research on the genomic characteristics of crustaceans [6,7].

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Conclusion