Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions
BACKGROUND: Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form s...
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ftpubmed:oai:pubmedcentral.nih.gov:7245778 2023-05-15T13:38:57+02:00 Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions Stephens, Timothy G. González-Pech, Raúl A. Cheng, Yuanyuan Mohamed, Amin R. Burt, David W. Bhattacharya, Debashish Ragan, Mark A. Chan, Cheong Xin 2020-05-24 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245778/ http://www.ncbi.nlm.nih.gov/pubmed/32448240 https://doi.org/10.1186/s12915-020-00782-8 en eng BioMed Central http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245778/ http://www.ncbi.nlm.nih.gov/pubmed/32448240 http://dx.doi.org/10.1186/s12915-020-00782-8 © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. CC0 PDM CC-BY BMC Biol Research Article Text 2020 ftpubmed https://doi.org/10.1186/s12915-020-00782-8 2020-06-07T00:38:27Z BACKGROUND: Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free-living species is still lacking. RESULTS: Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates. CONCLUSIONS: Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a ... Text Antarc* Antarctica Arctic Phytoplankton PubMed Central (PMC) Arctic BMC Biology 18 1 |
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Research Article Stephens, Timothy G. González-Pech, Raúl A. Cheng, Yuanyuan Mohamed, Amin R. Burt, David W. Bhattacharya, Debashish Ragan, Mark A. Chan, Cheong Xin Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions |
topic_facet |
Research Article |
description |
BACKGROUND: Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free-living species is still lacking. RESULTS: Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates. CONCLUSIONS: Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a ... |
format |
Text |
author |
Stephens, Timothy G. González-Pech, Raúl A. Cheng, Yuanyuan Mohamed, Amin R. Burt, David W. Bhattacharya, Debashish Ragan, Mark A. Chan, Cheong Xin |
author_facet |
Stephens, Timothy G. González-Pech, Raúl A. Cheng, Yuanyuan Mohamed, Amin R. Burt, David W. Bhattacharya, Debashish Ragan, Mark A. Chan, Cheong Xin |
author_sort |
Stephens, Timothy G. |
title |
Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions |
title_short |
Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions |
title_full |
Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions |
title_fullStr |
Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions |
title_full_unstemmed |
Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions |
title_sort |
genomes of the dinoflagellate polarella glacialis encode tandemly repeated single-exon genes with adaptive functions |
publisher |
BioMed Central |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245778/ http://www.ncbi.nlm.nih.gov/pubmed/32448240 https://doi.org/10.1186/s12915-020-00782-8 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Antarc* Antarctica Arctic Phytoplankton |
genre_facet |
Antarc* Antarctica Arctic Phytoplankton |
op_source |
BMC Biol |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245778/ http://www.ncbi.nlm.nih.gov/pubmed/32448240 http://dx.doi.org/10.1186/s12915-020-00782-8 |
op_rights |
© The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
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CC0 PDM CC-BY |
op_doi |
https://doi.org/10.1186/s12915-020-00782-8 |
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BMC Biology |
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18 |
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