Genome-wide analysis to uncover how Pocillopora acuta survives the challenging intertidal environment

Characterisation of genomic variation among corals can help uncover variants underlying trait differences and contribute towards genotype prioritisation in coastal restoration projects. For example, there is growing interest in identifying resilient genotypes for transplantation, and to better under...

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Published in:Scientific reports Vol. 14; no. 1; pp. 8538 - 11
Main Authors: Poquita-Du, Rosa Celia, Huang, Danwei, Todd, Peter A.
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 12.04.2024
Nature Publishing Group
Nature Portfolio
Subjects:
631/158
631/181
Animals
Anthozoa - genetics
Artificial reefs
Colonies
Copy number
Coral reefs
Corals
DNA Copy Number Variations
Engineering
Environmental engineering
Exons
Extreme environment
Genome-wide association study
Genomes
Genomics
Genotype
Genotypes
Homeostasis
Humanities and Social Sciences
Humans
Intertidal
Intertidal environment
Local adaptation
multidisciplinary
Pocillopora acuta
Science
Science (multidisciplinary)
Single-nucleotide polymorphism
Transplantation
Genome-wide association study
Intertidal
Extreme environment
Local adaptation
ISSN:2045-2322, 2045-2322
Online Access:Get full text
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Summary:Characterisation of genomic variation among corals can help uncover variants underlying trait differences and contribute towards genotype prioritisation in coastal restoration projects. For example, there is growing interest in identifying resilient genotypes for transplantation, and to better understand the genetic processes that allow some individuals to survive in specific conditions better than others. The coral species Pocillopora acuta is known to survive in a wide range of habitats, from reefs artificial coastal defences, suggesting its potential use as a starter species for ecological engineering efforts involving coral transplantation onto intertidal seawalls. However, the intertidal section of coastal armour is a challenging environment for corals, with conditions during periods of emersion being particularly stressful. Here, we scanned the entire genome of P. acuta corals to identify the regions harbouring single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) that separate intertidal colonies ( n  = 18) from those found in subtidal areas ( n  = 21). Findings revealed 74,391 high quality SNPs distributed across 386 regions of the P. acuta genome. While the majority of the detected SNPs were in non-coding regions, 12% were identified in exons (i.e. coding regions). Functional SNPs that were significantly associated with intertidal colonies were found in overrepresented genomic regions linked to cellular homeostasis, metabolism, and signalling processes, which may represent local environmental adaptation in the intertidal. Interestingly, regions that exhibited CNVs were also associated with metabolic and signalling processes, suggesting P. acuta corals living in the intertidal have a high capacity to perform biological functions critical for survival in extreme environments.
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ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-024-59268-0