Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification
Abstract Background There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but me...
Published in: | BMC Genomics |
---|---|
Main Authors: | , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
BMC
2022
|
Subjects: | |
Online Access: | https://doi.org/10.1186/s12864-022-08781-5 https://doaj.org/article/1a5cd635bd1c49b2b1fe43c7b3f5bab2 |
id |
ftdoajarticles:oai:doaj.org/article:1a5cd635bd1c49b2b1fe43c7b3f5bab2 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:1a5cd635bd1c49b2b1fe43c7b3f5bab2 2023-05-15T15:59:04+02:00 Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification Yaamini R. Venkataraman Samuel J. White Steven B. Roberts 2022-08-01T00:00:00Z https://doi.org/10.1186/s12864-022-08781-5 https://doaj.org/article/1a5cd635bd1c49b2b1fe43c7b3f5bab2 EN eng BMC https://doi.org/10.1186/s12864-022-08781-5 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-022-08781-5 1471-2164 https://doaj.org/article/1a5cd635bd1c49b2b1fe43c7b3f5bab2 BMC Genomics, Vol 23, Iss 1, Pp 1-16 (2022) Pacific oyster Bivalve Ocean acidification DNA methylation Gonad development Biotechnology TP248.13-248.65 Genetics QH426-470 article 2022 ftdoajarticles https://doi.org/10.1186/s12864-022-08781-5 2022-12-30T20:40:28Z Abstract Background There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific ... Article in Journal/Newspaper Crassostrea gigas DML Ocean acidification Pacific oyster Directory of Open Access Journals: DOAJ Articles Pacific BMC Genomics 23 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Pacific oyster Bivalve Ocean acidification DNA methylation Gonad development Biotechnology TP248.13-248.65 Genetics QH426-470 |
spellingShingle |
Pacific oyster Bivalve Ocean acidification DNA methylation Gonad development Biotechnology TP248.13-248.65 Genetics QH426-470 Yaamini R. Venkataraman Samuel J. White Steven B. Roberts Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification |
topic_facet |
Pacific oyster Bivalve Ocean acidification DNA methylation Gonad development Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization. Results Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation. Conclusions Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific ... |
format |
Article in Journal/Newspaper |
author |
Yaamini R. Venkataraman Samuel J. White Steven B. Roberts |
author_facet |
Yaamini R. Venkataraman Samuel J. White Steven B. Roberts |
author_sort |
Yaamini R. Venkataraman |
title |
Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification |
title_short |
Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification |
title_full |
Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification |
title_fullStr |
Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification |
title_full_unstemmed |
Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification |
title_sort |
differential dna methylation in pacific oyster reproductive tissue in response to ocean acidification |
publisher |
BMC |
publishDate |
2022 |
url |
https://doi.org/10.1186/s12864-022-08781-5 https://doaj.org/article/1a5cd635bd1c49b2b1fe43c7b3f5bab2 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas DML Ocean acidification Pacific oyster |
genre_facet |
Crassostrea gigas DML Ocean acidification Pacific oyster |
op_source |
BMC Genomics, Vol 23, Iss 1, Pp 1-16 (2022) |
op_relation |
https://doi.org/10.1186/s12864-022-08781-5 https://doaj.org/toc/1471-2164 doi:10.1186/s12864-022-08781-5 1471-2164 https://doaj.org/article/1a5cd635bd1c49b2b1fe43c7b3f5bab2 |
op_doi |
https://doi.org/10.1186/s12864-022-08781-5 |
container_title |
BMC Genomics |
container_volume |
23 |
container_issue |
1 |
_version_ |
1766394849251033088 |