Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros.
Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different envir...
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ftdoajarticles:oai:doaj.org/article:dea12fd7c0564b158c1bef107af9057d 2023-05-15T14:54:42+02:00 Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. Charlotte Nef Mohammed-Amin Madoui Éric Pelletier Chris Bowler 2022-11-01T00:00:00Z https://doi.org/10.1371/journal.pbio.3001893 https://doaj.org/article/dea12fd7c0564b158c1bef107af9057d EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pbio.3001893 https://doaj.org/toc/1544-9173 https://doaj.org/toc/1545-7885 1544-9173 1545-7885 doi:10.1371/journal.pbio.3001893 https://doaj.org/article/dea12fd7c0564b158c1bef107af9057d PLoS Biology, Vol 20, Iss 11, p e3001893 (2022) Biology (General) QH301-705.5 article 2022 ftdoajarticles https://doi.org/10.1371/journal.pbio.3001893 2022-12-30T19:28:53Z Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data. Article in Journal/Newspaper Arctic Arctic Ocean Climate change Directory of Open Access Journals: DOAJ Articles Arctic Arctic Ocean Pacific PLOS Biology 20 11 e3001893 |
institution |
Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Biology (General) QH301-705.5 |
spellingShingle |
Biology (General) QH301-705.5 Charlotte Nef Mohammed-Amin Madoui Éric Pelletier Chris Bowler Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. |
topic_facet |
Biology (General) QH301-705.5 |
description |
Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data. |
format |
Article in Journal/Newspaper |
author |
Charlotte Nef Mohammed-Amin Madoui Éric Pelletier Chris Bowler |
author_facet |
Charlotte Nef Mohammed-Amin Madoui Éric Pelletier Chris Bowler |
author_sort |
Charlotte Nef |
title |
Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. |
title_short |
Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. |
title_full |
Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. |
title_fullStr |
Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. |
title_full_unstemmed |
Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros. |
title_sort |
whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom chaetoceros. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2022 |
url |
https://doi.org/10.1371/journal.pbio.3001893 https://doaj.org/article/dea12fd7c0564b158c1bef107af9057d |
geographic |
Arctic Arctic Ocean Pacific |
geographic_facet |
Arctic Arctic Ocean Pacific |
genre |
Arctic Arctic Ocean Climate change |
genre_facet |
Arctic Arctic Ocean Climate change |
op_source |
PLoS Biology, Vol 20, Iss 11, p e3001893 (2022) |
op_relation |
https://doi.org/10.1371/journal.pbio.3001893 https://doaj.org/toc/1544-9173 https://doaj.org/toc/1545-7885 1544-9173 1545-7885 doi:10.1371/journal.pbio.3001893 https://doaj.org/article/dea12fd7c0564b158c1bef107af9057d |
op_doi |
https://doi.org/10.1371/journal.pbio.3001893 |
container_title |
PLOS Biology |
container_volume |
20 |
container_issue |
11 |
container_start_page |
e3001893 |
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1766326454511992832 |