Integrative Transcriptome Sequencing Reveals the Molecular Difference of Maturation Process of Ovary and Testis in Mud Crab Scylla paramamosain

Wenxiao Cui,Shengkang Li,Ardavan Farhadi,Hongyu Ma,Huan Fang,Huaiping Zheng,Mhd Ikhwanuddin,Qin Yang,Yueling Zhang,Yin Zhang

doi:10.3389/fmars.2021.658091

Wenxiao Cui, Shengkang Li + Show 8 more

Open Access

https://doi.org/10.3389/fmars.2021.658091

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Abstract

The mud crab Scylla paramamosain is a species with significant sexual dimorphism in growth rate and body size, of which the females are of higher economic and nutritional values than the males. Accordingly, there is an urgent need to explore the molecular mechanism underlying sex determination and gonadal differentiation. The single-molecule long-read technology combining with RNA sequencing was employed to construct a full-length transcriptome for gonads of S. paramamosain. In total, 1,562,819 FLNC reads were obtained from 1,813,758 reads of inserts (ROIs). Among them, the 10,739 fusion isoforms corresponded to 23,634 reads and were involved in 5,369 genes in the reference annotation. According to the criteria for new transcripts, a total of 213,809 isoforms were recognized as novel transcripts and then matched against Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), NR, Swissprot, and KOG databases. We also identified 22,313 SSRs, 169,559 lncRNAs, and 25,451 SNPs. Additionally, 349,854 alternative splicing (AS) events from 8,430 gene models were detected, and 5,129 polyadenylation sites were profiled from 3,090 genes. GO and KEGG annotation indicated that AS and APA probably play important roles in the gonadal development and maturation. Besides, the DEGs associated with gonadal development and maturation were identified and analyzed based on the RNA-Seq data.

Highlights

The mud crab (Scylla paramamosain), which is widely distributed along the southeast Asia coasts, is one of the most prevalent aquaculture crustaceans in China due to its huge economic value and superior growth performance (Shi et al, 2019)
2019; Wan et al, 2019), little full-length transcriptome resources are available for gonads of mud crab
Unique isoform sequences were obtained from the gonad transcriptome by using single molecular long-read sequencing with the PacBio Sequel platform

Summary

Introduction

The mud crab (Scylla paramamosain), which is widely distributed along the southeast Asia coasts, is one of the most prevalent aquaculture crustaceans in China due to its huge economic value and superior growth performance (Shi et al, 2019). The molecular mechanism underlying sex determination and gonadal differentiation of the mud crab has received considerable attention due to the remarkable biological and economic differences between sexes (Yang et al, 2018). Multiple omics and sequencing technologies have recently focused on the understanding of sexual differentiation, gonadal maturation, and gametogenesis in mud crab. Comparative profiling of ovarian and testicular piRNAs in the S. paramamosain, which provided baseline information of mud crab piRNAs and their differential expression, suggested that piRNAs play an essential role in regulating gametogenesis and gonadal development (Waiho et al, 2019). Some achievements have been implemented, the understanding of gonadal development and sexual differentiation which facilitates monosexual crab breeding and culture, remains lacking

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