Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus
The copepod Calanus finmarchicus (Crustacea, Copepoda) is a key zooplanktonic species with a crucial position in the North Atlantic food web and significant contributor to ocean carbon flux. Like many other high latitude animals, it has evolved a programmed arrested development called diapause to co...
Published in: | Ecology and Evolution |
---|---|
Main Authors: | , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2022
|
Subjects: | |
Online Access: | https://hal.inrae.fr/hal-04096227 https://hal.inrae.fr/hal-04096227/document https://hal.inrae.fr/hal-04096227/file/2022_Payton_Ecol_Evol.pdf https://doi.org/10.1002/ece3.8605 |
id |
ftccsdartic:oai:HAL:hal-04096227v1 |
---|---|
record_format |
openpolar |
institution |
Open Polar |
collection |
Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
annual rhythms copepods diapause transcriptome wildlife zooplankton [SDE]Environmental Sciences |
spellingShingle |
annual rhythms copepods diapause transcriptome wildlife zooplankton [SDE]Environmental Sciences Payton, Laura Noirot, Céline Last, Kim, S Grigor, Jordan Hüppe, Lukas Conway, David, V P Dannemeyer, Mona Suin, Amandine Meyer, Bettina Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus |
topic_facet |
annual rhythms copepods diapause transcriptome wildlife zooplankton [SDE]Environmental Sciences |
description |
The copepod Calanus finmarchicus (Crustacea, Copepoda) is a key zooplanktonic species with a crucial position in the North Atlantic food web and significant contributor to ocean carbon flux. Like many other high latitude animals, it has evolved a programmed arrested development called diapause to cope with long periods of limited food supply, while growth and reproduction are timed to take advantage of seasonal peaks in primary production. However, anthropogenic warming is inducing changes in the expected timing of phytoplankton blooms, suggesting phenological mismatches with negative consequences for the N. Atlantic ecosystem. While diapause mechanisms are mainly studied in terrestrial arthropods, specifically on laboratory model species, such as the fruit fly Drosophila, the molecular investigations of annual rhythms in wild marine species remain fragmentary. Here we performed a rigorous year-long monthly sampling campaign of C. finmarchicus in a Scottish Loch (UK; 56.45 degrees N, 5.18 degrees W) to generate an annual transcriptome. The mRNA of 36 samples (monthly triplicate of 25 individuals) have been deeply sequenced with an average depth of 137 +/- 4 million reads (mean +/- SE) per sample, aligned to the reference transcriptome, and filtered. We detail the quality assessment of the datasets and provide a high-quality resource for the investigation of wild annual transcriptomic rhythms (35,357 components) in a key diapausing zooplanktonic species. |
author2 |
Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS) Helmholtz Ctr Polar & Marine Res, Alfred Wegener Inst, D-27570 Bremerhaven, Germany Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE) Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Scottish Association for Marine Science (SAMS) University of Würzburg Marine Biological Association Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe) Plateforme Génome & Transcriptome (GET) Génopole Toulouse Midi-Pyrénées Auzeville (GENOTOUL) Université Toulouse III - Paul Sabatier (UT3) Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT) Institut National Polytechnique (Toulouse) (Toulouse INP) Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP) Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3) Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées Auzeville (GENOTOUL) Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) |
format |
Article in Journal/Newspaper |
author |
Payton, Laura Noirot, Céline Last, Kim, S Grigor, Jordan Hüppe, Lukas Conway, David, V P Dannemeyer, Mona Suin, Amandine Meyer, Bettina |
author_facet |
Payton, Laura Noirot, Céline Last, Kim, S Grigor, Jordan Hüppe, Lukas Conway, David, V P Dannemeyer, Mona Suin, Amandine Meyer, Bettina |
author_sort |
Payton, Laura |
title |
Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus |
title_short |
Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus |
title_full |
Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus |
title_fullStr |
Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus |
title_full_unstemmed |
Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus |
title_sort |
annual transcriptome of a key zooplankton species, the copepod calanus finmarchicus |
publisher |
HAL CCSD |
publishDate |
2022 |
url |
https://hal.inrae.fr/hal-04096227 https://hal.inrae.fr/hal-04096227/document https://hal.inrae.fr/hal-04096227/file/2022_Payton_Ecol_Evol.pdf https://doi.org/10.1002/ece3.8605 |
genre |
Calanus finmarchicus North Atlantic Copepods |
genre_facet |
Calanus finmarchicus North Atlantic Copepods |
op_source |
EISSN: 2045-7758 Ecology and Evolution https://hal.inrae.fr/hal-04096227 Ecology and Evolution, 2022, 12 (2), pp.e8605. ⟨10.1002/ece3.8605⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1002/ece3.8605 info:eu-repo/semantics/altIdentifier/pmid/35228860 hal-04096227 https://hal.inrae.fr/hal-04096227 https://hal.inrae.fr/hal-04096227/document https://hal.inrae.fr/hal-04096227/file/2022_Payton_Ecol_Evol.pdf doi:10.1002/ece3.8605 PUBMED: 35228860 WOS: 000760366500040 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1002/ece3.8605 |
container_title |
Ecology and Evolution |
container_volume |
12 |
container_issue |
2 |
_version_ |
1786202780618194944 |
spelling |
ftccsdartic:oai:HAL:hal-04096227v1 2023-12-24T10:15:42+01:00 Annual transcriptome of a key zooplankton species, the copepod Calanus finmarchicus Payton, Laura Noirot, Céline Last, Kim, S Grigor, Jordan Hüppe, Lukas Conway, David, V P Dannemeyer, Mona Suin, Amandine Meyer, Bettina Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS) Helmholtz Ctr Polar & Marine Res, Alfred Wegener Inst, D-27570 Bremerhaven, Germany Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE) Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) Scottish Association for Marine Science (SAMS) University of Würzburg Marine Biological Association Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe) Plateforme Génome & Transcriptome (GET) Génopole Toulouse Midi-Pyrénées Auzeville (GENOTOUL) Université Toulouse III - Paul Sabatier (UT3) Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT) Institut National Polytechnique (Toulouse) (Toulouse INP) Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP) Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3) Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées Auzeville (GENOTOUL) Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) 2022-02 https://hal.inrae.fr/hal-04096227 https://hal.inrae.fr/hal-04096227/document https://hal.inrae.fr/hal-04096227/file/2022_Payton_Ecol_Evol.pdf https://doi.org/10.1002/ece3.8605 en eng HAL CCSD Wiley Open Access info:eu-repo/semantics/altIdentifier/doi/10.1002/ece3.8605 info:eu-repo/semantics/altIdentifier/pmid/35228860 hal-04096227 https://hal.inrae.fr/hal-04096227 https://hal.inrae.fr/hal-04096227/document https://hal.inrae.fr/hal-04096227/file/2022_Payton_Ecol_Evol.pdf doi:10.1002/ece3.8605 PUBMED: 35228860 WOS: 000760366500040 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess EISSN: 2045-7758 Ecology and Evolution https://hal.inrae.fr/hal-04096227 Ecology and Evolution, 2022, 12 (2), pp.e8605. ⟨10.1002/ece3.8605⟩ annual rhythms copepods diapause transcriptome wildlife zooplankton [SDE]Environmental Sciences info:eu-repo/semantics/article Journal articles 2022 ftccsdartic https://doi.org/10.1002/ece3.8605 2023-11-25T23:48:16Z The copepod Calanus finmarchicus (Crustacea, Copepoda) is a key zooplanktonic species with a crucial position in the North Atlantic food web and significant contributor to ocean carbon flux. Like many other high latitude animals, it has evolved a programmed arrested development called diapause to cope with long periods of limited food supply, while growth and reproduction are timed to take advantage of seasonal peaks in primary production. However, anthropogenic warming is inducing changes in the expected timing of phytoplankton blooms, suggesting phenological mismatches with negative consequences for the N. Atlantic ecosystem. While diapause mechanisms are mainly studied in terrestrial arthropods, specifically on laboratory model species, such as the fruit fly Drosophila, the molecular investigations of annual rhythms in wild marine species remain fragmentary. Here we performed a rigorous year-long monthly sampling campaign of C. finmarchicus in a Scottish Loch (UK; 56.45 degrees N, 5.18 degrees W) to generate an annual transcriptome. The mRNA of 36 samples (monthly triplicate of 25 individuals) have been deeply sequenced with an average depth of 137 +/- 4 million reads (mean +/- SE) per sample, aligned to the reference transcriptome, and filtered. We detail the quality assessment of the datasets and provide a high-quality resource for the investigation of wild annual transcriptomic rhythms (35,357 components) in a key diapausing zooplanktonic species. Article in Journal/Newspaper Calanus finmarchicus North Atlantic Copepods Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Ecology and Evolution 12 2 |