Comparative transcriptome analysis of Rimicaris sp. reveals novel molecular features associated with survival in deep-sea hydrothermal vent

Scientific Reports
Jian ZhangLi Sun

Abstract

Shrimp of the family Alvinocarididae are the predominant megafauna of deep-sea hydrothermal vents. However, genome information on this family is currently unavailable. In the present study, by employing Illumina sequencing, we performed the first de novo transcriptome analysis of the gills of the shrimp Rimicaris sp. from the hydrothermal vent in Desmos, Manus Basin. The analysis was conducted in a comparative manner with the shrimp taken directly from the vent (GR samples) and the shrimp that had been maintained for ten days under normal laboratory condition (mGR samples). Among the 128,938 unigenes identified, a large number of differentially expressed genes (DEGs) between the GR and mGR samples were detected, including 2365 and 1607 genes significantly upregulated and downregulated, respectively, in GR. The DEGs covered diverse functional categories. Most of the DEGs associated with immunity were downregulated in GR, while most of the DEGs associated with sulfur metabolism and detoxification were upregulated in GR. These results provide the first comprehensive transcriptomic resource for hydrothermal vent Rimicaris and revealed varied categories of genes likely involved in deep-sea survival.

References

Jan 1, 1983·Transactions of the New York Academy of Sciences·W B Jakoby
Oct 19, 1999·The Journal of Clinical Investigation·M D LevittE DeMaster
Aug 29, 2000·Immunopharmacology·P Moseley
Jun 5, 2002·Annual Review of Biochemistry·Jeffrey D Esko, Scott B Selleck
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Jan 1, 1997·Annual Review of Entomology·M J Lehane
Apr 14, 2005·Journal of Biochemistry and Molecular Biology·Sadaaki Iwanaga, Bok Luel Lee
Dec 3, 2005·Toxicological Sciences : an Official Journal of the Society of Toxicology·Niranjali GamageMichael E McManus
Nov 18, 2006·Nature Immunology·Matthew J RobinsonCaetano Reis e Sousa
Apr 12, 2007·The Plant Journal : for Cell and Molecular Biology·Galina BrychkovaMoshe Sagi
Apr 25, 2007·IUBMB Life·Rita CipollonePaolo Visca
May 29, 2007·Nucleic Acids Research·Yuki MoriyaMinoru Kanehisa
Oct 25, 2007·Antioxidants & Redox Signaling·Miguel Angel García-BereguiaínCarlos Gutiérrez-Merino
Nov 28, 2007·Nucleic Acids Research·Robert D FinnAlex Bateman
Apr 24, 2008·Molecular Microbiology·Girbe BuistOscar P Kuipers
May 1, 2008·Nucleic Acids Research·Stefan GötzAna Conesa
May 28, 2008·FEMS Microbiology Ecology·Satoshi Nakagawa, Ken Takai
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Mar 18, 2009·Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology·J MarchandB Chénais
Mar 31, 2009·Physiological and Biochemical Zoology : PBZ·Joanna Joyner-MatosDavid Julian
Jun 2, 2009·Genome Génome / Conseil National De Recherches Canada·Eric BonnivardDominique Higuet
Jan 12, 2010·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Shams Tabrez, Masood Ahmad
Feb 6, 2010·Genome Biology·Matthew D YoungAlicia Oshlack
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Oct 14, 2011·The ISME Journal·Mathieu GuriMarie-Anne Cambon-Bonavita
Mar 28, 2012·The International Journal of Biochemistry & Cell Biology·C GarridoH H Kampinga
Apr 10, 2012·Developmental and Comparative Immunology·Fuhua Li, Jianhai Xiang
Sep 11, 2012·Fish & Shellfish Immunology·Xian-Wei Wang, Jin-Xing Wang
Sep 19, 2012·Briefings in Bioinformatics·Marie-Agnès DilliesUNKNOWN French StatOmique Consortium
Jun 24, 2014·Genes & Cancer·Luena PapaDoris Germain
Jan 16, 2015·Current Genetics·Gunseli Bayram AkcapinarVerena Seidl-Seiboth

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Datasets Mentioned

BETA
SRR4342052
ACB42236
ADD63783.1
AIY69132.1
AFA26603.1
KX228390
KX228389

Methods Mentioned

BETA
RNA-Seq
PCR
electrophoresis
RNA assay
reverse transcription-PCR

Software Mentioned

cBot Cluster generation system
DESeq R package
GeoMapApp
DNASTAR
KEXUE
Clustal V
MEGA
KEGG Automatic Annotation
RSEM
KASS

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