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Genes & Genomics

, Volume 41, Issue 12, pp 1397–1415 | Cite as

Transcriptome analysis to characterize the genes related to gonad growth and fatty acid metabolism in the sea urchin Strongylocentrotus intermedius

  • Heng Wang
  • Jun DingEmail author
  • Siyu Ding
  • Yaqing ChangEmail author
Research Article

Abstract

Background

Sea urchin gonads of both sexes, commonly termed “roe”, are highly valued seafood delicacies, and Strongylocentrotus intermedius is considered one of the tastiest sea urchins. In order to produce high-quality gonads for consumption and clarify the mechanism of gonad growth and development of the sea urchin, more genetic information, especially at the transcriptome level, is needed.

Objective

A more thorough understanding of sea urchin gonad growth and development in both sexes could enable regulation of these processes at several stages with the aim of suppressing gametogenesis in order to produce high-quality gonads for consumption.

Methods

The adult sea urchins S. intermedius were cultured for 3 months, and were sampled for the gonadal transcriptome analysis which has been performed on the RNAs of three male and female adults of S. intermedius in each gonad development stage.

Results

Illumina sequencing raw sequence data was deposited in the NCBI Sequence Read Archive (SRA) database (PRJNA532998). It generated 560,196,356 raw reads and 548,956,944 clean reads were acquired, which were assembled into 107,850 transcripts with 44,124 genes. Comparative analysis showed the differentially expressed genes (DEGs) from 114 to 2566. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to determine the functional significance of these DEGs. We have selected 9 genes related to growth and 12 genes related to fatty acid biosynthesis and metabolism in sea urchin gonads.

Conclusion

These data for sea urchins were intended to provide markers for gonad growth and development that can be accumulated for use in aquaculture applications.

Keywords

Strongylocentrotus intermedius Transcriptome Differential expression genes Gonad growth and development Fatty acid biosynthesis and metabolism 

Abbreviations

Acadvl

Very long-chain specific acyl-CoA dehydrogenase

Acsf2

Acyl-CoA synthetase family member 2, mitochondrial-like

Apoa2

Apolipoprotein A-II

CoA

Coenzyme A

Cpt1

Carnitine O-palmitoyltransferase 1

DEGs

Differentially expressed genes

eggNOG

Non-supervised Orthologous Groups

Elo3

Fatty acid elongation protein 3

Fa2h

Fatty acid 2-hydroxylase

Fads

Fatty acyl desaturases

FGF

Fibroblast growth factor

GO

Gene ontology

GRNs

Gene regulatory networks

GSI

Gonado-somatic index

HDL

High-density lipoproteins

KEGG

Kyoto Encyclopedia of Genes and Genomes

NR

Non-redundant protein database

Ofad

Omega-6 fatty acid desaturase

Ost1

Ovary at stage 1

Ost2

Ovary at stage 2

PFAM

Protein family

PUFA

Polyunsaturated fatty acids

SNPs

Single-nucleotide polymorphisms

SSRs

Simple sequence repeats

TPM

Transcripts per million

Tst1

Testis at stage 1

Tst2

Testis at stage 2

VEGF

Vascular endothelial growth factor

VLCFA

Very long-chain fatty acids

18S rRNA

18S ribosomal RNA gene

Notes

Acknowledgements

This work was supported by grants from the National Key Research and Development Program of China [2018YFD0901601], Marine and Fishery Scientific Research Project of Liaoning Province [201814], Key Laboratory of Mariculture& Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs [2018-KF-18], PhD research startup foundation of Dalian Ocean University [HDYJ201807] and National Natural Science Foundation of China [31672652]. Mr. Lei Li helped to feed the sea urchins in the study.

Compliance with ethical standards

Conflict of interest

Heng Wang, Jun Ding, Siyu Ding and Yaqing Chang declare that they do not have conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

13258_2019_864_MOESM1_ESM.docx (23 kb)
Supplementary material 1 (DOCX 22 kb)

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Copyright information

© The Genetics Society of Korea 2019

Authors and Affiliations

  1. 1.Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural AffairsDalian Ocean UniversityDalianChina

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