RT-qPCR normalization genes in the red alga Chondrus crispus.
International audience Chondrus crispus is a common red macroalga living on the rocky shores of the North Atlantic Ocean. It has a long research history, being a major source of carrageenan, a thickener widely used in the food industry, but also for physiological and ecological studies. To establish...
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Online Access: | https://hal.sorbonne-universite.fr/hal-01002409 https://hal.sorbonne-universite.fr/hal-01002409/document https://hal.sorbonne-universite.fr/hal-01002409/file/fetchObject.pdf https://doi.org/10.1371/journal.pone.0086574 |
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ftsorbonneuniv:oai:HAL:hal-01002409v1 2023-06-11T04:14:58+02:00 RT-qPCR normalization genes in the red alga Chondrus crispus. Kowalczyk, Nathalie Rousvoal, Sylvie Hervé, Cécile Boyen, Catherine Collén, Jonas Végétaux marins et biomolécules Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS) Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) 2014 https://hal.sorbonne-universite.fr/hal-01002409 https://hal.sorbonne-universite.fr/hal-01002409/document https://hal.sorbonne-universite.fr/hal-01002409/file/fetchObject.pdf https://doi.org/10.1371/journal.pone.0086574 en eng HAL CCSD Public Library of Science info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0086574 info:eu-repo/semantics/altIdentifier/pmid/24498277 hal-01002409 https://hal.sorbonne-universite.fr/hal-01002409 https://hal.sorbonne-universite.fr/hal-01002409/document https://hal.sorbonne-universite.fr/hal-01002409/file/fetchObject.pdf doi:10.1371/journal.pone.0086574 PUBMED: 24498277 info:eu-repo/semantics/OpenAccess ISSN: 1932-6203 EISSN: 1932-6203 PLoS ONE https://hal.sorbonne-universite.fr/hal-01002409 PLoS ONE, 2014, 9 (2), pp.e86574. ⟨10.1371/journal.pone.0086574⟩ [SDV]Life Sciences [q-bio] info:eu-repo/semantics/article Journal articles 2014 ftsorbonneuniv https://doi.org/10.1371/journal.pone.0086574 2023-05-30T01:09:54Z International audience Chondrus crispus is a common red macroalga living on the rocky shores of the North Atlantic Ocean. It has a long research history, being a major source of carrageenan, a thickener widely used in the food industry, but also for physiological and ecological studies. To establish it as a model for red algae, its genome has been sequenced, allowing the development of molecular tools such as quantification of gene expression, including RNAseq and RT-qPCR. To determine appropriate genes for RT-qPCR normalization, the expression of 14 genes was monitored in 18 conditions using two sets of algal samples: samples from the sequenced strain, cultured and stressed in laboratory conditions and C. crispus collected on the shore and stressed in situ. The expression stability of the genes between the samples was evaluated by comparing the Ct range and using the programs geNorm and NormFinder. The candidate genes encoded translation related proteins (initiation factors IF4A-1 and IF4A-2, elongation factor EF1α and eRF3, an eukaryotic polypeptide chain release factor), cytoskeleton proteins (two β-tubulins, α-tubulin and actin), enzymes involved in the pentose phosphate pathway (glucose 6-phosphate deshydrogenase), protein recycling process (ubiquitin and ubiquitin-conjugating enzyme) and glycolysis (isocitrate dehydrogenase). The two sets of samples showed different expression patterns. Most of the genes were stable in the algae cultivated in the laboratory, whereas environmental samples showed a more important variation in gene expression. When analyzing the two sets separately, the ranking of the most stables genes were different from one method to another. When considering all samples, the two statistical methods were concordant, revealing translation initiation factor 4A-2 and eukaryotic polypeptide chain release factor 3 as pertinent normalization genes. This study highlights thus the importance of testing reference genes according to the experiments as well as the genetic and physiological ... Article in Journal/Newspaper North Atlantic HAL Sorbonne Université PLoS ONE 9 2 e86574 |
institution |
Open Polar |
collection |
HAL Sorbonne Université |
op_collection_id |
ftsorbonneuniv |
language |
English |
topic |
[SDV]Life Sciences [q-bio] |
spellingShingle |
[SDV]Life Sciences [q-bio] Kowalczyk, Nathalie Rousvoal, Sylvie Hervé, Cécile Boyen, Catherine Collén, Jonas RT-qPCR normalization genes in the red alga Chondrus crispus. |
topic_facet |
[SDV]Life Sciences [q-bio] |
description |
International audience Chondrus crispus is a common red macroalga living on the rocky shores of the North Atlantic Ocean. It has a long research history, being a major source of carrageenan, a thickener widely used in the food industry, but also for physiological and ecological studies. To establish it as a model for red algae, its genome has been sequenced, allowing the development of molecular tools such as quantification of gene expression, including RNAseq and RT-qPCR. To determine appropriate genes for RT-qPCR normalization, the expression of 14 genes was monitored in 18 conditions using two sets of algal samples: samples from the sequenced strain, cultured and stressed in laboratory conditions and C. crispus collected on the shore and stressed in situ. The expression stability of the genes between the samples was evaluated by comparing the Ct range and using the programs geNorm and NormFinder. The candidate genes encoded translation related proteins (initiation factors IF4A-1 and IF4A-2, elongation factor EF1α and eRF3, an eukaryotic polypeptide chain release factor), cytoskeleton proteins (two β-tubulins, α-tubulin and actin), enzymes involved in the pentose phosphate pathway (glucose 6-phosphate deshydrogenase), protein recycling process (ubiquitin and ubiquitin-conjugating enzyme) and glycolysis (isocitrate dehydrogenase). The two sets of samples showed different expression patterns. Most of the genes were stable in the algae cultivated in the laboratory, whereas environmental samples showed a more important variation in gene expression. When analyzing the two sets separately, the ranking of the most stables genes were different from one method to another. When considering all samples, the two statistical methods were concordant, revealing translation initiation factor 4A-2 and eukaryotic polypeptide chain release factor 3 as pertinent normalization genes. This study highlights thus the importance of testing reference genes according to the experiments as well as the genetic and physiological ... |
author2 |
Végétaux marins et biomolécules Station biologique de Roscoff Roscoff (SBR) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS) Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M) Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS) |
format |
Article in Journal/Newspaper |
author |
Kowalczyk, Nathalie Rousvoal, Sylvie Hervé, Cécile Boyen, Catherine Collén, Jonas |
author_facet |
Kowalczyk, Nathalie Rousvoal, Sylvie Hervé, Cécile Boyen, Catherine Collén, Jonas |
author_sort |
Kowalczyk, Nathalie |
title |
RT-qPCR normalization genes in the red alga Chondrus crispus. |
title_short |
RT-qPCR normalization genes in the red alga Chondrus crispus. |
title_full |
RT-qPCR normalization genes in the red alga Chondrus crispus. |
title_fullStr |
RT-qPCR normalization genes in the red alga Chondrus crispus. |
title_full_unstemmed |
RT-qPCR normalization genes in the red alga Chondrus crispus. |
title_sort |
rt-qpcr normalization genes in the red alga chondrus crispus. |
publisher |
HAL CCSD |
publishDate |
2014 |
url |
https://hal.sorbonne-universite.fr/hal-01002409 https://hal.sorbonne-universite.fr/hal-01002409/document https://hal.sorbonne-universite.fr/hal-01002409/file/fetchObject.pdf https://doi.org/10.1371/journal.pone.0086574 |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_source |
ISSN: 1932-6203 EISSN: 1932-6203 PLoS ONE https://hal.sorbonne-universite.fr/hal-01002409 PLoS ONE, 2014, 9 (2), pp.e86574. ⟨10.1371/journal.pone.0086574⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0086574 info:eu-repo/semantics/altIdentifier/pmid/24498277 hal-01002409 https://hal.sorbonne-universite.fr/hal-01002409 https://hal.sorbonne-universite.fr/hal-01002409/document https://hal.sorbonne-universite.fr/hal-01002409/file/fetchObject.pdf doi:10.1371/journal.pone.0086574 PUBMED: 24498277 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1371/journal.pone.0086574 |
container_title |
PLoS ONE |
container_volume |
9 |
container_issue |
2 |
container_start_page |
e86574 |
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