Research Data

Acanthochromis polyacanthus genome sequencing and assembly

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General
Title
Acanthochromis polyacanthus genome sequencing and assembly
Type
Dataset
Date Record Created
2017-11-10
Date Record Modified
2018-01-05
Language
English
Coverage
Date Coverage
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Time Period
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Geospatial Location
Description
Descriptions
  1. Type: full

    Genome sequencing and assembly data for Acanthochromis polyacanthus (study on the effects of ocean acidifcation) from the National Center for Biotechnology Information (NCBI) BioProject number PRJNA328211. Submitted by King Abdullah University of Science and Technology.

    Abstract [Related Publication]: The impact of ocean acidification on marine ecosystems will depend on species capacity to adapt1,2. Recent studies show that the behaviour of reef fishes is impaired at projected CO 2 levels3,4; however, individual variation exists that might promote adaptation. Here, we show a clear signature of parental sensitivity to high CO 2 in the brain molecular phenotype of juvenile spiny damselfish, Acanthochromis polyacanthus, primarily driven by circadian rhythm genes. Offspring of CO 2-tolerant and CO 2-sensitive parents were reared at near-future CO 2 (754 μatm) or present-day control levels (414 μatm). By integrating 33 brain transcriptomes and proteomes with a de novo assembled genome we investigate the molecular responses of the fish brain to increased CO 2 and the expression of parental tolerance to high CO 2 in the offspring molecular phenotype. Exposure to high CO 2 resulted in differential regulation of 173 and 62 genes and 109 and 68 proteins in the tolerant and sensitive groups, respectively. Importantly, the majority of differences between offspring of tolerant and sensitive parents occurred in high CO 2 conditions. This transgenerational molecular signature suggests that individual variation in CO 2 sensitivity could facilitate adaptation of fish populations to ocean acidification.

    The full methodology for genome sequencing and assembly is included in the Supplementary Information (PDF) file with the Related Publication.

Related Publications
  1. Schunter, Celia, Welch, Megan J., Ryu, Taewoo, Zhang, Huoming, Berumen, Michael L., Nilsson, Goeran E., Munday, Philip L., and Ravasi, Timothy (2016) Molecular signatures of transgenerational response to ocean acidification in a species of reef fish. Nature Climate Change, 6 (11). pp. 1014-1018.
Related Websites
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Related Data
  1. Has part: >> Acanthochromis polyacanthus, whole genome shotgun sequencing project
    • ID: https://www.ncbi.nlm.nih.gov/nuccore/1185913644 (EXTERNAL)
    • Note(s): Nucleotide (WGS master)
    • Publish to RDA: This related object (and relationship) is NOT being published to RDA.
  2. Has part: >> RNAseq of Acanthochromis polyacanthus brain, ocean acidification
    • ID: https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=311159 (EXTERNAL)
    • Note(s): SRA Experiments (36)
    • Publish to RDA: This related object (and relationship) is NOT being published to RDA.
  3. Has part: >> MIGS Eukaryotic sample from Acanthochromis polyacanthus and Model organism or animal sample from Acanthochromis polyacanthus (36)
    • ID: https://www.ncbi.nlm.nih.gov/biosample?Db=biosample&DbFrom=bioproject&Cmd=Link&LinkName=bioproject_biosample&LinkReadableName=BioSample&ordinalpos=1&IdsFromResult=311159 (EXTERNAL)
    • Note(s): BioSamples (37)
    • Publish to RDA: This related object (and relationship) is NOT being published to RDA.
  4. Has part: >> Assembly ASM210954v1
    • ID: https://www.ncbi.nlm.nih.gov/assembly/GCF_002109545.1 (EXTERNAL)
    • Note(s): Assembly
    • Publish to RDA: This related object (and relationship) is NOT being published to RDA.
Related Services
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Technical metadata
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People
Creators
  1. Associated with: Ms Megan Welch , meg.welch@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies
  2. Associated with: Prof Philip Munday , philip.munday@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies, Zoology and Ecology
Primary Contact
Prof Philip Munday, philip.munday@jcu.edu.au
Supervisors
(no information)
Collaborators
  1. Celia Schunter, King Abdullah University of Science and Technology, Saudi Arabia
  2. Taewoo Ryu, APEC Climate Center, South Korea
  3. Huoming Zhang, King Abdullah University of Science and Technology, Saudi Arabia
  4. Michael L. Berumen, King Abdullah University of Science and Technology, Saudi Arabia
  5. Goeran E. Nilsson, University of Oslo, Norway
Subject
Fields of Research
  1. 050101 - Ecological Impacts of Climate Change (050101)
Socio-Economic Objective
(no information)
Keywords
  1. Acanthochromis polyacanthus
  2. genome sequences
  3. RNA sequences
  4. genome assembly
  5. ARC Centre of Excellence for Coral Reef Studies
Research Activity
(no information)
Research Themes
Tropical Ecosystems, Conservation and Climate Change
Rights
License
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License - Other
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Access Rights/Conditions
NCBI places no restrictions on the use or distribution of data.
Type
open
Rights
(no information)
Data
Data Location
Online Locations
  1. https://www.ncbi.nlm.nih.gov/bioproject/311159
Stored At
(no information)
Citation
Cite:
Schunter, C.; Welch, M.; Ryu, T.; Zhang, H.; Berumen, M.; Nilsson, G.; Munday, P.; Ravasi, T. (2017). Acanthochromis polyacanthus genome sequencing and assembly. James Cook University. (dataset). 8af60bb9a15e79258237292ba0e45b24