Comparative Transcriptome Analysis Provides Insights into Differentially Expressed Genes and Long Non-Coding RNAs between Ovary and Testis of the Mud Crab (Scylla paramamosain)

Abstract

The molecular mechanism underlying sex determination and gonadal differentiation of the mud crab (Scylla paramamosain) has received considerable attention, due to the remarkably biological and economic differences between sexes. However, sex-biased genes, especially non-coding genes, which account for these differences, remain elusive in this crustacean species. In this study, the first de novo gonad transcriptome sequencing was performed to identify both differentially expressed genes and long non-coding RNAs (lncRNAs) between male and female S. paramamosain by using Illumina Hiseq2500. A total of 79,282,758 and 79,854,234 reads were generated from ovarian and testicular cDNA libraries, respectively. After filtrating and de novo assembly, 262,688 unigenes were produced from both libraries. Of these unigenes, 41,125 were annotated with known protein sequences in public databases. Homologous genes involved in sex determination and gonadal development pathways (Sxl-Tra/Tra-2-Dsx/Fru, Wnt4, thyroid hormone synthesis pathway, etc.) were identified. Three hundred and sixteen differentially expressed unigenes were further identified between both transcriptomes. Meanwhile, a total of 233,078 putative lncRNAs were predicted. Of these lncRNAs, 147 were differentially expressed between sexes. qRT-PCR results showed that nine lncRNAs negatively regulated the expression of eight genes, suggesting a potential role in sex differentiation. These findings will provide fundamental resources for further investigation on sex differentiation and regulatory mechanism in crustaceans.

Transcriptome sequencing and molecular markers discovery in the gonads of Portunus sanguinolentus

“…The presence of the Vibrio cholera infection pathway among the top five KEGG pathways suggests that virus might have infected the wild crabs used in the study. While this is uncommon due to the ineluctable microbial presence in the open habitat of crabs, it is synonymous with the previous observation where microbial metabolism in diverse environment was among the top 5 KEGG pathways found in gonadal transcriptome profiles of the mud crab, S. paramamosain 2 , 24 .…”

The Single-molecule long-read sequencing of Scylla paramamosain

“…The third-generation sequencing technology is the most advanced technology, which could obtain full-length transcripts on a large scale. In this study, a total of 79005 high-quality unique transcripts is obtained, among which 50% transcripts is full-length, which is more efficient than RACE and the second-generation sequencing technology 30,32,33,48 . These full-length transcripts identified in this study will facilitate further study of S .…”

“…In crab and shrimp, the high-throughput sequencing technology has been applied in Eriocheir sinensis 1–21 , Portunus trituberculatus 22–29 , S . paramamosain 30–33 , S . olivacea 34 , Carcinus maenas 35,36 , Gecarcinus lateralis 37–41 , P .…”

High-Density Genetic Linkage Maps Provide Novel Insights Into ZW/ZZ Sex Determination System and Growth Performance in Mud Crab (Scylla paramamosain)

“…Based on their transcriptomic profiles, some sex-related genes such as vasa , Dmrt , FEM1 , and Wnt6 were found to be differentially expressed in the gonad of S. paramamosain (Gao et al, 2014). Recently, we have also uncovered 147 gonadal differentially expressed long non-coding RNAs (lnc RNAs), nine of which showed regulation toward eight sex-related genes in S. paramamosain (Yang et al, 2017). The genome organization of sex chromosomes in S. paramamosain and the exact gene localization, however, remains unclear.…”