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

Marine Biotechnology
Zhicheng WangYaqing Chang

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 role...Continue Reading

References

Jan 1, 1987·Annual Review of Biochemistry·M Barbacid
Jan 1, 1982·Advances in Protein Chemistry·C B Klee, T C Vanaman
Dec 1, 1993·Genes & Development·L Powell-BraxtonT A Stewart
Jan 30, 1999·The International Journal of Biochemistry & Cell Biology·G SchenkP F Nixon
Feb 27, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jinping HuaQifa Zhang
Mar 15, 2003·Nature Reviews. Cancer·Erik Sahai, Christopher J Marshall
Oct 3, 2003·The Plant Cell·James A BirchlerNicole C Riddle
Dec 19, 2003·Nucleic Acids Research·Minoru KanehisaMasahiro Hattori
Jan 28, 2004·Annual Review of Pharmacology and Toxicology·Thomas Holbro, Nancy E Hynes
Nov 3, 2004·Nature Reviews. Molecular Cell Biology·Claudia WellbrockRichard Marais
Jul 16, 2005·Genetics·Marnik VuylstekeMarc Zabeau
Mar 2, 2006·Molecular and Cellular Biology·Linda K RushworthWalter Kolch
Jul 11, 2006·Nature Reviews. Molecular Cell Biology·Ami Citri, Yosef Yarden
Mar 10, 2007·Current Medicinal Chemistry·Armin ZebischJakob Troppmair
Mar 27, 2007·Nature Reviews. Cancer·Suzanne SchubbertGideon Bollag
May 15, 2007·Oncogene·A S DhillonW Kolch
Jun 9, 2007·Biochimica Et Biophysica Acta·Deborah T LeichtGuri Tzivion
Nov 21, 2008·PLoS Biology·Zachary B LippmanDani Zamir
Mar 14, 2009·PLoS Genetics·Beth A HollowayMary C Mullins
Mar 28, 2009·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Jason B Wolf, Michael J Wade
Apr 18, 2009·Proceedings of the National Academy of Sciences of the United States of America·Gang WeiLihuang Zhu
Apr 17, 2010·Genes & Development·Luis de la Torre-UbietaAzad Bonni
May 25, 2010·Nature Reviews. Molecular Cell Biology·Boris N KholodenkoWalter Kolch
Mar 29, 2011·Endocrine Reviews·Julian C Lui, Jeffrey Baron
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Jun 24, 2011·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Elizabeth M H TankCynthia Kenyon
Jul 23, 2011·Genes & Cancer·David MatallanasWalter Kolch
Jan 17, 2012·BMC Systems Biology·Pınar PirStephen G Oliver
Mar 3, 2012·PLoS Computational Biology·Purvesh KhatriAtul J Butte
Mar 7, 2012·Clinical Science·Shaobin WangMing-Hui Zou
Jun 6, 2012·Annual Review of Biochemistry·Alexander Varshavsky
Sep 8, 2012·Nature·Sarah DjebaliThomas R Gingeras
Oct 5, 2012·BMC Genomics·Stefan K SchulzeAndreas S Beutler
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Nov 17, 2012·Cell Adhesion & Migration·Johan Holmberg, Madeleine Durbeej
Dec 25, 2012·Cell Adhesion & Migration·Patricia Rousselle, Konrad Beck

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Datasets Mentioned

BETA
SRR6040821

Methods Mentioned

BETA
PCR
RNA-Seq

Software Mentioned

STAR
R package
DEGseq
Trinity
KOBAS
topGO R package
Tophat2
cBot Cluster Generation System

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