Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing
Copepods of the zooplankton genus Calanus play a key role in marine ecosystems in the northern seas. Although being among the most studied organisms on Earth, due to their ecological importance, genomic resources for Calanus spp. remain scarce, mostly due to their large genome size (from 6 to 12 Gbp...
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ftpubmed:oai:pubmedcentral.nih.gov:8861592 2023-05-15T15:48:06+02:00 Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing Lizano, Apollo Marco Smolina, Irina Choquet, Marvin Kopp, Martina Hoarau, Galice 2022-02-22 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8861592/ http://www.ncbi.nlm.nih.gov/pubmed/35228861 https://doi.org/10.1002/ece3.8606 en eng John Wiley and Sons Inc. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8861592/ http://www.ncbi.nlm.nih.gov/pubmed/35228861 http://dx.doi.org/10.1002/ece3.8606 © 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. CC-BY Ecol Evol Research Articles Text 2022 ftpubmed https://doi.org/10.1002/ece3.8606 2022-03-06T01:47:01Z Copepods of the zooplankton genus Calanus play a key role in marine ecosystems in the northern seas. Although being among the most studied organisms on Earth, due to their ecological importance, genomic resources for Calanus spp. remain scarce, mostly due to their large genome size (from 6 to 12 Gbps). As an alternative to whole‐genome sequencing in Calanus spp., we sequenced and de novo assembled transcriptomes of five Calanus species: Calanus glacialis, C. hyperboreus, C. marshallae, C. pacificus, and C. helgolandicus. Functional assignment of protein families based on clusters of orthologous genes (COG) and gene ontology (GO) annotations showed analogous patterns of protein functions across species. Phylogenetic analyses using maximum likelihood (ML) of 191 protein‐coding genes mined from RNA‐seq data fully resolved evolutionary relationships among seven Calanus species investigated (five species sequenced for this study and two species with published datasets), with gene and site concordance factors showing that 109 out of 191 protein‐coding genes support a separation between three groups: the C. finmarchicus group (including C. finmarchicus, C. glacialis, and C. marshallae), the C. helgolandicus group (including C. helgolandicus, C. sinicus, and C. pacificus) and the monophyletic C. hyperboreus group. The tree topology obtained in ML analyses was similar to a previously proposed phylogeny based on morphological criteria and cleared certain ambiguities from past studies on evolutionary relationships among Calanus species. Text Calanus glacialis Copepods PubMed Central (PMC) Ecology and Evolution 12 2 |
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Research Articles |
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Research Articles Lizano, Apollo Marco Smolina, Irina Choquet, Marvin Kopp, Martina Hoarau, Galice Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing |
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Research Articles |
description |
Copepods of the zooplankton genus Calanus play a key role in marine ecosystems in the northern seas. Although being among the most studied organisms on Earth, due to their ecological importance, genomic resources for Calanus spp. remain scarce, mostly due to their large genome size (from 6 to 12 Gbps). As an alternative to whole‐genome sequencing in Calanus spp., we sequenced and de novo assembled transcriptomes of five Calanus species: Calanus glacialis, C. hyperboreus, C. marshallae, C. pacificus, and C. helgolandicus. Functional assignment of protein families based on clusters of orthologous genes (COG) and gene ontology (GO) annotations showed analogous patterns of protein functions across species. Phylogenetic analyses using maximum likelihood (ML) of 191 protein‐coding genes mined from RNA‐seq data fully resolved evolutionary relationships among seven Calanus species investigated (five species sequenced for this study and two species with published datasets), with gene and site concordance factors showing that 109 out of 191 protein‐coding genes support a separation between three groups: the C. finmarchicus group (including C. finmarchicus, C. glacialis, and C. marshallae), the C. helgolandicus group (including C. helgolandicus, C. sinicus, and C. pacificus) and the monophyletic C. hyperboreus group. The tree topology obtained in ML analyses was similar to a previously proposed phylogeny based on morphological criteria and cleared certain ambiguities from past studies on evolutionary relationships among Calanus species. |
format |
Text |
author |
Lizano, Apollo Marco Smolina, Irina Choquet, Marvin Kopp, Martina Hoarau, Galice |
author_facet |
Lizano, Apollo Marco Smolina, Irina Choquet, Marvin Kopp, Martina Hoarau, Galice |
author_sort |
Lizano, Apollo Marco |
title |
Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing |
title_short |
Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing |
title_full |
Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing |
title_fullStr |
Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing |
title_full_unstemmed |
Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing |
title_sort |
insights into the species evolution of calanus copepods in the northern seas revealed by de novo transcriptome sequencing |
publisher |
John Wiley and Sons Inc. |
publishDate |
2022 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8861592/ http://www.ncbi.nlm.nih.gov/pubmed/35228861 https://doi.org/10.1002/ece3.8606 |
genre |
Calanus glacialis Copepods |
genre_facet |
Calanus glacialis Copepods |
op_source |
Ecol Evol |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8861592/ http://www.ncbi.nlm.nih.gov/pubmed/35228861 http://dx.doi.org/10.1002/ece3.8606 |
op_rights |
© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1002/ece3.8606 |
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Ecology and Evolution |
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12 |
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2 |
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1766383102858362880 |