Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing
Abstract 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...
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crwiley:10.1002/ece3.8606 2024-09-15T18:00:43+00:00 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 Nord universitet 2022 http://dx.doi.org/10.1002/ece3.8606 https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.8606 https://onlinelibrary.wiley.com/doi/full-xml/10.1002/ece3.8606 en eng Wiley http://creativecommons.org/licenses/by/4.0/ Ecology and Evolution volume 12, issue 2 ISSN 2045-7758 2045-7758 journal-article 2022 crwiley https://doi.org/10.1002/ece3.8606 2024-06-27T04:21:15Z Abstract 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. Article in Journal/Newspaper Calanus glacialis Copepods Wiley Online Library Ecology and Evolution 12 2 |
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Wiley Online Library |
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English |
description |
Abstract 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. |
author2 |
Nord universitet |
format |
Article in Journal/Newspaper |
author |
Lizano, Apollo Marco Smolina, Irina Choquet, Marvin Kopp, Martina Hoarau, Galice |
spellingShingle |
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 |
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 |
Wiley |
publishDate |
2022 |
url |
http://dx.doi.org/10.1002/ece3.8606 https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.8606 https://onlinelibrary.wiley.com/doi/full-xml/10.1002/ece3.8606 |
genre |
Calanus glacialis Copepods |
genre_facet |
Calanus glacialis Copepods |
op_source |
Ecology and Evolution volume 12, issue 2 ISSN 2045-7758 2045-7758 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1002/ece3.8606 |
container_title |
Ecology and Evolution |
container_volume |
12 |
container_issue |
2 |
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1810437886114267136 |