Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR

Arash Akbarzadeh, Aimee Lee S. Houde, View ORCID ProfileBen J.G. Sutherland, Oliver P. Günther, Kristina M. Miller
doi: https://doi.org/10.1101/2020.05.14.086090
Arash Akbarzadeh
aDepartment of Fisheries, Faculty of Marine Science and technology, University of Hormozgan, P.O. Box: 3995, Bandar Abbas, Iran
bPacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: kristi.saunders@dfo-mpo.gc.ca akbarzadeh@ut.ac.ir
Aimee Lee S. Houde
bPacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
cDepartment of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ben J.G. Sutherland
bPacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ben J.G. Sutherland
Oliver P. Günther
dGünther Analytics, Vancouver, BC Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kristina M. Miller
bPacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, V9T 6N7, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: kristi.saunders@dfo-mpo.gc.ca akbarzadeh@ut.ac.ir
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (Oncorhynchus tshawytscha), held in normoxia [dissolved oxygen (DO) > 8 mg L−1] and hypoxia (DO = 4□5 mg L−1) in 10 and 18°C temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; p < 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Aimee Lee Houde, Email: Aimee.Houde{at}dfo-mpo.gc.ca, Ben J.G. Sutherland: Ben.Sutherland{at}dfo-mpo.gc.ca, Oliver P. Günther, Email: oliver{at}guntheranalytics.com, Kristina M. Miller, Email: Kristi.Saunders{at}dfo-mpo.gc.ca

  • Identifying early gene expression responses to hypoxia (i.e., low dissolved oxygen) as a tool to assess the degree of exposure to this stressor is crucial for salmonids, because they are increasingly exposed to hypoxic stress due to anthropogenic habitat change, e.g., global warming, excessive nutrient loading, and persistent algal blooms. Our goal was to discover and validate gill gene expression biomarkers specific to the hypoxia response in salmonids across multi-stressor conditions. Gill tissue was collected from 24 freshwater juvenile Chinook salmon (Oncorhynchus tshawytscha), held in normoxia [dissolved oxygen (DO) > 8 mg L-1] and hypoxia (DO = 4‒5 mg L-1) in 10 and 18 C temperatures for up to six days. RNA-sequencing (RNA-seq) was then used to discover 240 differentially expressed genes between hypoxic and normoxic conditions, but not affected by temperature. The most significantly differentially expressed genes had functional roles in the cell cycle and suppression of cell proliferation associated with hypoxic conditions. The most significant genes (n = 30) were selected for real-time qPCR assay development. These assays demonstrated a strong correlation (r = 0.88; p < 0.001) between the expression values from RNA-seq and the fold changes from qPCR. Further, qPCR of the 30 candidate hypoxia biomarkers was applied to an additional 322 Chinook salmon exposed to hypoxic and normoxic conditions to reveal the top biomarkers to define hypoxic stress. Multivariate analyses revealed that smolt stage, water salinity, and morbidity status were relevant factors to consider with the expression of these genes in relation to hypoxic stress. These hypoxia candidate genes will be put into application screening Chinook salmon to determine the identity of stressors impacting the fish.

  • https://github.com/bensutherland/Simple_reads_to_counts

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted July 13, 2020.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR
Arash Akbarzadeh, Aimee Lee S. Houde, Ben J.G. Sutherland, Oliver P. Günther, Kristina M. Miller
bioRxiv 2020.05.14.086090; doi: https://doi.org/10.1101/2020.05.14.086090
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR
Arash Akbarzadeh, Aimee Lee S. Houde, Ben J.G. Sutherland, Oliver P. Günther, Kristina M. Miller
bioRxiv 2020.05.14.086090; doi: https://doi.org/10.1101/2020.05.14.086090

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4113)
  • Biochemistry (8815)
  • Bioengineering (6519)
  • Bioinformatics (23463)
  • Biophysics (11790)
  • Cancer Biology (9209)
  • Cell Biology (13323)
  • Clinical Trials (138)
  • Developmental Biology (7438)
  • Ecology (11410)
  • Epidemiology (2066)
  • Evolutionary Biology (15151)
  • Genetics (10436)
  • Genomics (14044)
  • Immunology (9171)
  • Microbiology (22154)
  • Molecular Biology (8812)
  • Neuroscience (47570)
  • Paleontology (350)
  • Pathology (1428)
  • Pharmacology and Toxicology (2491)
  • Physiology (3730)
  • Plant Biology (8080)
  • Scientific Communication and Education (1437)
  • Synthetic Biology (2221)
  • Systems Biology (6037)
  • Zoology (1253)