Marine Biotechnology

, Volume 20, Issue 2, pp 193–205 | Cite as

Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids

  • Zhicheng Wang
  • Jun Cui
  • Jian Song
  • Haoze Wang
  • Kailun Gao
  • Xuemei Qiu
  • Meng Gou
  • Xin Li
  • Ziwen Hu
  • Xiuli Wang
  • Yaqing Chang
Original Article
  • 142 Downloads

Abstract

Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.

Keywords

Sea cucumber Transcriptome Growth-related genes Heterosis 

Notes

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no competing interests.

Supplementary material

10126_2018_9796_Fig7_ESM.gif (109 kb)
Supplementary Figure 1.

Transcript length distribution (GIF 108 kb)

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High resolution image (TIFF 11658 kb)
10126_2018_9796_Fig8_ESM.gif (45 kb)
Supplementary Figure 2.

Box plot of FPKM and the correlation coefficients of gene expression levels. T01 to T04 represent RR, CC, CR and RC at 45 DAF, respectively. T05 to T08 represent RR, CC, CR and RC at 75 DAF, respectively. (GIF 44 kb)

10126_2018_9796_MOESM2_ESM.tif (5.4 mb)
High resolution image (TIFF 5579 kb)
10126_2018_9796_Fig9_ESM.gif (116 kb)
Supplementary Figure 3.

GO enrichment analysis. T01 to T04 represent RR, CC, CR and RC at 45 DAF, respectively. T05 to T08 represent RR, CC, CR and RC at 75 DAF, respectively. (GIF 115 kb)

10126_2018_9796_MOESM3_ESM.tif (13.3 mb)
High resolution image (TIFF 13588 kb)
10126_2018_9796_Fig10_ESM.gif (79 kb)
Supplementary Figure 4.

COG functional classification. T01 to T04 represent RR, CC, CR and RC at 45 DAF, respectively. T05 to T08 represent RR, CC, CR and RC at 75 DAF, respectively. (GIF 78 kb)

10126_2018_9796_MOESM4_ESM.tif (10 mb)
High resolution image (TIFF 10251 kb)
10126_2018_9796_Fig11_ESM.jpg (2.8 mb)
Supplementary Figure 5.

KEGG enrichment analysis. T01 to T04 represent RR, CC, CR and RC at 45 DAF, respectively. T05 to T08 represent RR, CC, CR and RC at 75 DAF, respectively. (JPEG 2828 kb)

10126_2018_9796_MOESM5_ESM.tif (20.8 mb)
High resolution image (TIFF 21292 kb)
10126_2018_9796_MOESM6_ESM.docx (22 kb)
Supplementary Table 1 (DOCX 22 kb)
10126_2018_9796_MOESM7_ESM.docx (18 kb)
Supplementary Table 2 (DOCX 17 kb)
10126_2018_9796_MOESM8_ESM.xlsx (17 kb)
Supplementary Table 3 (XLSX 16 kb)
10126_2018_9796_MOESM9_ESM.xlsx (20 kb)
Supplementary Table 4 (XLSX 19 kb)
10126_2018_9796_MOESM10_ESM.xlsx (20.1 mb)
Supplementary Table 5 (XLSX 20535 kb)
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Supplementary Table 6 (XLSX 176 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Zhicheng Wang
    • 1
    • 2
  • Jun Cui
    • 2
  • Jian Song
    • 1
  • Haoze Wang
    • 2
  • Kailun Gao
    • 2
  • Xuemei Qiu
    • 2
  • Meng Gou
    • 3
  • Xin Li
    • 2
  • Ziwen Hu
    • 2
  • Xiuli Wang
    • 1
    • 2
  • Yaqing Chang
    • 1
    • 2
  1. 1.Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of AgricultureDalian Ocean UniversityDalianChina
  2. 2.College of Fisheries and Life ScienceDalian Ocean UniversityDalianChina
  3. 3.School of Life ScienceLiaoning Normal UniversityDalianChina

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