Transcriptome analysis to characterize the genes related to gonad growth and fatty acid metabolism in the sea urchin Strongylocentrotus intermedius
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.
KeywordsStrongylocentrotus 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
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 regulatory networks
Kyoto Encyclopedia of Genes and Genomes
Non-redundant protein database
Omega-6 fatty acid desaturase
Ovary at stage 1
Ovary at stage 2
Polyunsaturated fatty acids
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 , 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 . 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.
This article does not contain any studies with human participants or animals performed by any of the authors.
- Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry. 5th edition. New York: W H Freeman; Chapter 22, Fatty Acid Metabolism. https://www.ncbi.nlm.nih.gov/books/NBK21173/
- Chang Y, Ding J, Song J, Yang W (2004) Biology research and breeding of sea cucumber and sea urchin. Ocean Press, Beijing (in Chinese) Google Scholar
- Ding W, Ding J, Zhang W, Ding Y, He P (2015a) A preliminary study of rising temperature on immune-related enzyme and MDA content in family of sea urchins (Strongylocentrotus intermedius) with different tube feet colors. J Agric 5(9):110–116 (in Chinese) Google Scholar
- Ding J, Zhao L, Chang Y, Zhao W, Du Z, Hao Z (2015b) Transcriptome sequencing and characterization of Japanese scallop Patinopecten yessoensis from different shell color lines. PLoS ONE 10(2):e011640Google Scholar
- Food and Agriculture Organization of the United Nations (2018) Yearbook of fishery and aquaculture statistics 2016Google Scholar
- Klinger TS, Lawrence JM, Lawrence AL (1997) Gonad and somatic production of Strongylocentrotus droebachiensis fed manufactured feeds. Bull Aquac Assoc Can 97:35–37Google Scholar
- Kober KM, Pogson GH (2013) Genome-wide patterns of codon bias are shaped by natural selection in the purple sea urchin Strongylocentrotus purpuratus. G3-Genes Genom Genet 3(7):1069–1083Google Scholar
- Pearse JS (1981) Synchronization of gametogenesis in the sea urchins Strongylocentrotus purpuratus and S. franciscanus. In: Clark WH, Adams TS (eds) Advances in invertebrate reproduction. Elsevier, North Holland Inc, New York, pp 53–68Google Scholar
- Sun Z (2016) Signal-dependent regulation of skeletogenesis in the sea urchin embryo. PhD thesis of Carnegie Mellon UniversityGoogle Scholar
- Wang H, Ding J, Ding S, Chang Y (2019) Metabolomic changes and polyunsaturated fatty acid biosynthesis during gonadal growth and development in the sea urchin Strongylocentrotus intermedius. Comp Biochem Phys D 32:100611Google Scholar