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Transcriptome analysis of the differences in gene expression between testis and ovary in green mud crab (Scylla paramamosain)

Jie Gao1, Xiaowei Wang1, Zhihua Zou1, Xiwei Jia1, Yilei Wang1* and Ziping Zhang2*

Author Affiliations

1 Key Laboratory of Healthy Mariculture in the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, 361021 Xiamen, China

2 Department of Natural Sciences and Mathematics, State University of New York at Cobleskill, 12043 Cobleskill, NY, USA

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BMC Genomics 2014, 15:585  doi:10.1186/1471-2164-15-585

Published: 11 July 2014



The green mud crab (Scylla paramamosain) is the most prevalent crustacean on the southeast coast of China. The molecular regulatory mechanism of sex determination and gonadal differentiation in this species has received considerable attention in recent years because of the huge differences—both biological and economic—between male and female crabs. In this study, next-generation sequencing technology was used to develop deep-coverage transcriptomic sequencing data for the testis and ovary of S. paramamosain.


A total of 365,116 reads (testis 171,962, ovary 193,154) with an average sequence length of 285 bp were produced from testis and ovary cDNA libraries. After filtering out contaminating reads, the clean reads were assembled, producing a total of 21,791 isotigs and leaving 22,814 reads as singlets. Using the BLASTX program, 3,471 unique sequences (2,275 isotigs and 1,196 singletons) were annotated with known protein sequences from the NCBI non-redundant (Nr) protein sequence database. The Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses allowed the 224 unique sequences that were annotated with enzyme code (EC) numbers to be mapped into 174 KEGG pathways. After comparing the ovary and testis libraries, 4,021 gonad-differentially, 10,522 ovary-specifically, and 19,013 testis-specifically expressed genes were identified. Moreover, 33 ovary-specific, 14 testis-specific, and 34 gonad-differential transcripts were confirmed by semi-quantitative PCR and quantitative real-time PCR. In addition, 8,610 putative simple sequence repeats (SSRs) and 23,879 potential single nucleotide polymorphisms (SNPs) were identified.


This is the first large-scale RNA sequencing of S. paramamosain to be reported. We have identified many important functional genes and made a preliminary attempt to construct the regulatory network involved in the gonadal development of crustaceans. The annotated transcriptome data will provide fundamental support for future research into the reproduction biology of S. paramamosain. A large number of candidate SSRs and SNPs were detected, which could be used as genetic markers for population genetics and functional genomics in this species.

Testis; Ovary; Specifically/differentially expressed genes; Transcriptome; Scylla paramamosain