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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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Autores principales: Lizano, Apollo Marco, Smolina, Irina, Choquet, Marvin, Kopp, Martina, Hoarau, Galice
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8861592/
https://www.ncbi.nlm.nih.gov/pubmed/35228861
http://dx.doi.org/10.1002/ece3.8606
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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
collection PubMed
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.
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spelling pubmed-88615922022-02-27 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 Ecol Evol Research Articles 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. John Wiley and Sons Inc. 2022-02-22 /pmc/articles/PMC8861592/ /pubmed/35228861 http://dx.doi.org/10.1002/ece3.8606 Text en © 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.
spellingShingle 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
title 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_short 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
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8861592/
https://www.ncbi.nlm.nih.gov/pubmed/35228861
http://dx.doi.org/10.1002/ece3.8606
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