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



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.


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.


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.


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.


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


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



Very long-chain specific acyl-CoA dehydrogenase


Acyl-CoA synthetase family member 2, mitochondrial-like


Apolipoprotein A-II


Coenzyme A


Carnitine O-palmitoyltransferase 1


Differentially expressed genes


Non-supervised Orthologous Groups


Fatty acid elongation protein 3


Fatty acid 2-hydroxylase


Fatty acyl desaturases


Fibroblast growth factor


Gene ontology


Gene regulatory networks


Gonado-somatic index


High-density lipoproteins


Kyoto Encyclopedia of Genes and Genomes


Non-redundant protein database


Omega-6 fatty acid desaturase


Ovary at stage 1


Ovary at stage 2


Protein family


Polyunsaturated fatty acids


Single-nucleotide polymorphisms


Simple sequence repeats


Transcripts per million


Testis at stage 1


Testis at stage 2


Vascular endothelial growth factor


Very long-chain fatty acids

18S rRNA

18S ribosomal RNA gene



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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