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Marine Biotechnology

, Volume 20, Issue 1, pp 20–34 | Cite as

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

  • Xiaolong Yang
  • Mhd Ikhwanuddin
  • Xincang Li
  • Fan Lin
  • Qingyang Wu
  • Yueling Zhang
  • Cuihong You
  • Wenhua Liu
  • Yinwei Cheng
  • Xi Shi
  • Shuqi Wang
  • Hongyu MaEmail author
Original Article

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.

Keywords

Scylla paramamosain RNA sequencing Unigenes lncRNAs Sex differentiation 

Abbreviations

lncRNAs

long non-coding RNAs

DEGs

differentially expressed genes

qRT-PCR

quantitative reverse transcription polymerase chain reaction

PFAM

Pfam-san

CPC

Coding Potential Calculator

CNCI

Coding-Non-Coding Index

GO

Gene Ontology

KEGG

Kyoto Encyclopedia of Genes and Genomes

ORFs

open reading frames

ELSPBP1

epididymal sperm-binding protein 1

Igfals

insulin-like growth factor-binding protein complex acid labile chain

Eps15l1

epidermal growth factor receptor substrate 15-like 1

HR97b

hormone receptor-like 97b

ER

estrogen receptor

FSTL1

follistatin-related protein 1

SRA1

steroid receptor RNA activator 1

mMHC

muscle myosin heavy chain

Fsh

female sterile homeotic

Peg3

paternally expressed gene 3

Notes

Funding Information

This study was supported by the STU Scientific Research Foundation for Talents (No. NTF17006), the National Program for Support of Top-Notch Young Professionals, the National Natural Science Foundation of China (No. 31772837), and the “Sail Plan” Program for the Introduction of Outstanding Talents of Guangdong Province, China.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Supplementary material

10126_2017_9784_MOESM1_ESM.docx (81 kb)
Online Resource 1 Fig. S1. Expression level of partial lncRNAs and its putative target genes (DOCX 81 kb)
10126_2017_9784_MOESM2_ESM.docx (23 kb)
Online Resource 2 Table S1. Primers used in validation of Illumina sequencing by qRT-PCR (DOCX 22 kb)
10126_2017_9784_MOESM3_ESM.docx (30 kb)
Online Resource 3 Table S2. Candidate genes involved in the regulation of gonadal development in S. paramamosain (DOCX 30 kb)
10126_2017_9784_MOESM4_ESM.xls (18 kb)
Online Resource 4 Table S3. Analysis results of differential expressed unigenes (XLS 17 kb)
10126_2017_9784_MOESM5_ESM.xls (8 kb)
Online Resource 5 Table S4. Analysis results of differential expressed lncRNAs (XLS 8 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Guangdong Provincial Key Laboratory of Marine BiotechnologyShantou UniversityShantouChina
  2. 2.Institute of Tropical AquacultureUniversiti Malaysia TerengganuKuala TerengganuMalaysia
  3. 3.East China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesShanghaiChina

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