A Microarray study of Carpet-Shell Clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression Differences in gills and digestive gland
Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of th...
Published in: | Frontiers in Physiology |
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Online Access: | http://hdl.handle.net/10400.1/11758 https://doi.org/10.3389/fphys.2017.00943 |
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ftunivalgarve:oai:sapientia.ualg.pt:10400.1/11758 2023-05-15T15:59:09+02:00 A Microarray study of Carpet-Shell Clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression Differences in gills and digestive gland Saavedra, Carlos Milan, Massimo Leite, Ricardo B. Cordero, David Patarnello, Tomaso Leonor Cancela, M. Bargelloni, Luca 2017-11 http://hdl.handle.net/10400.1/11758 https://doi.org/10.3389/fphys.2017.00943 eng eng Frontiers Media Sa info:eu-repo/grantAgreement/FCT/5876/147257/PT 1664-042X http://hdl.handle.net/10400.1/11758 doi:10.3389/fphys.2017.00943 openAccess http://creativecommons.org/licenses/by/4.0/ CC-BY Oyster Crassostrea-Gigas Insulin-related peptide Pacific oyster Rna-seq Indeterminate growth Protein-metabolism Anodonta-Cygnea Pinctada-Fucata Mytilus-Edulis Myostatin gene article 2017 ftunivalgarve https://doi.org/10.3389/fphys.2017.00943 2022-05-30T08:48:23Z Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes. A total of 356 differentially expressed genes (DEG) were found. We tested the hypothesis that differential expression might be concentrated at the growth control gene core (GCGC), i. e., the set of genes that underlie the molecular mechanisms of genetic control of tissue and organ growth and body size, as demonstrated in model organisms. The GCGC includes the genes coding for enzymes of the insulin/ insulin-like growth factor signaling pathway (IIS), enzymes of four additional signaling pathways (Raf/ Ras/ Mapk, Jnk, TOR, and Hippo), and transcription factors acting at the end of those pathways. Only two out of 97 GCGC genes present in themicroarray showed differential expression, indicating a very little contribution of GCGC genes to growth-related differential gene expression. Forty eight DEGs were shared by both organs, with gene ontology (GO) annotations corresponding to transcription regulation, RNA splicing, sugar metabolism, protein catabolism, immunity, defense against pathogens, and fatty acid biosynthesis. GO termenrichment tests indicated that genes related to growth regulation, development and morphogenesis, extracellular matrix proteins, and proteolysis were overrepresented in the gills. In the digestive gland overrepresented GO terms referred to gene expression control through chromatin rearrangement, RAS-related small GTPases, glucolysis, and energy metabolism. These analyses suggest a relevant role of, among others, some genes related to the IIS, such as the ParaHox gene Xlox, ... Article in Journal/Newspaper Crassostrea gigas Pacific oyster Universidade do Algarve: Sapienta Pacific Frontiers in Physiology 8 |
institution |
Open Polar |
collection |
Universidade do Algarve: Sapienta |
op_collection_id |
ftunivalgarve |
language |
English |
topic |
Oyster Crassostrea-Gigas Insulin-related peptide Pacific oyster Rna-seq Indeterminate growth Protein-metabolism Anodonta-Cygnea Pinctada-Fucata Mytilus-Edulis Myostatin gene |
spellingShingle |
Oyster Crassostrea-Gigas Insulin-related peptide Pacific oyster Rna-seq Indeterminate growth Protein-metabolism Anodonta-Cygnea Pinctada-Fucata Mytilus-Edulis Myostatin gene Saavedra, Carlos Milan, Massimo Leite, Ricardo B. Cordero, David Patarnello, Tomaso Leonor Cancela, M. Bargelloni, Luca A Microarray study of Carpet-Shell Clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression Differences in gills and digestive gland |
topic_facet |
Oyster Crassostrea-Gigas Insulin-related peptide Pacific oyster Rna-seq Indeterminate growth Protein-metabolism Anodonta-Cygnea Pinctada-Fucata Mytilus-Edulis Myostatin gene |
description |
Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes. A total of 356 differentially expressed genes (DEG) were found. We tested the hypothesis that differential expression might be concentrated at the growth control gene core (GCGC), i. e., the set of genes that underlie the molecular mechanisms of genetic control of tissue and organ growth and body size, as demonstrated in model organisms. The GCGC includes the genes coding for enzymes of the insulin/ insulin-like growth factor signaling pathway (IIS), enzymes of four additional signaling pathways (Raf/ Ras/ Mapk, Jnk, TOR, and Hippo), and transcription factors acting at the end of those pathways. Only two out of 97 GCGC genes present in themicroarray showed differential expression, indicating a very little contribution of GCGC genes to growth-related differential gene expression. Forty eight DEGs were shared by both organs, with gene ontology (GO) annotations corresponding to transcription regulation, RNA splicing, sugar metabolism, protein catabolism, immunity, defense against pathogens, and fatty acid biosynthesis. GO termenrichment tests indicated that genes related to growth regulation, development and morphogenesis, extracellular matrix proteins, and proteolysis were overrepresented in the gills. In the digestive gland overrepresented GO terms referred to gene expression control through chromatin rearrangement, RAS-related small GTPases, glucolysis, and energy metabolism. These analyses suggest a relevant role of, among others, some genes related to the IIS, such as the ParaHox gene Xlox, ... |
format |
Article in Journal/Newspaper |
author |
Saavedra, Carlos Milan, Massimo Leite, Ricardo B. Cordero, David Patarnello, Tomaso Leonor Cancela, M. Bargelloni, Luca |
author_facet |
Saavedra, Carlos Milan, Massimo Leite, Ricardo B. Cordero, David Patarnello, Tomaso Leonor Cancela, M. Bargelloni, Luca |
author_sort |
Saavedra, Carlos |
title |
A Microarray study of Carpet-Shell Clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression Differences in gills and digestive gland |
title_short |
A Microarray study of Carpet-Shell Clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression Differences in gills and digestive gland |
title_full |
A Microarray study of Carpet-Shell Clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression Differences in gills and digestive gland |
title_fullStr |
A Microarray study of Carpet-Shell Clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression Differences in gills and digestive gland |
title_full_unstemmed |
A Microarray study of Carpet-Shell Clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression Differences in gills and digestive gland |
title_sort |
microarray study of carpet-shell clam (ruditapes decussatus) shows common and organ-specific growth-related gene expression differences in gills and digestive gland |
publisher |
Frontiers Media Sa |
publishDate |
2017 |
url |
http://hdl.handle.net/10400.1/11758 https://doi.org/10.3389/fphys.2017.00943 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
info:eu-repo/grantAgreement/FCT/5876/147257/PT 1664-042X http://hdl.handle.net/10400.1/11758 doi:10.3389/fphys.2017.00943 |
op_rights |
openAccess http://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fphys.2017.00943 |
container_title |
Frontiers in Physiology |
container_volume |
8 |
_version_ |
1766394942017503232 |