Table_1_Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis.xlsx
Piscirickettsia salmonis is the etiologic agent of salmon rickettsial syndrome (SRS) and is responsible for considerable economic losses in salmon aquaculture. The bacterium affects coho salmon (CS; Oncorhynchus kisutch), Atlantic salmon (AS; Salmo salar), and rainbow trout (RT; Oncorhynchus mykiss)...
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Online Access: | https://doi.org/10.3389/fgene.2019.00665.s004 https://figshare.com/articles/Table_1_Comparative_Genomic_Analysis_of_Three_Salmonid_Species_Identifies_Functional_Candidate_Genes_Involved_in_Resistance_to_the_Intracellular_Bacterium_Piscirickettsia_salmonis_xlsx/9250097 |
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ftfrontimediafig:oai:figshare.com:article/9250097 2023-05-15T15:32:16+02:00 Table_1_Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis.xlsx José M. Yáñez Grazyella M. Yoshida Ángel Parra Katharina Correa Agustín Barría Liane N. Bassini Kris A. Christensen Maria E. López Roberto Carvalheiro Jean P. Lhorente Rodrigo Pulgar 2019-08-05T11:59:20Z https://doi.org/10.3389/fgene.2019.00665.s004 https://figshare.com/articles/Table_1_Comparative_Genomic_Analysis_of_Three_Salmonid_Species_Identifies_Functional_Candidate_Genes_Involved_in_Resistance_to_the_Intracellular_Bacterium_Piscirickettsia_salmonis_xlsx/9250097 unknown doi:10.3389/fgene.2019.00665.s004 https://figshare.com/articles/Table_1_Comparative_Genomic_Analysis_of_Three_Salmonid_Species_Identifies_Functional_Candidate_Genes_Involved_in_Resistance_to_the_Intracellular_Bacterium_Piscirickettsia_salmonis_xlsx/9250097 CC BY 4.0 CC-BY Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy coho salmon rainbow trout Atlantic salmon Piscirickettsia salmonis genome-wide association study comparative genomics piscirickettsiosis Dataset 2019 ftfrontimediafig https://doi.org/10.3389/fgene.2019.00665.s004 2019-08-07T22:59:47Z Piscirickettsia salmonis is the etiologic agent of salmon rickettsial syndrome (SRS) and is responsible for considerable economic losses in salmon aquaculture. The bacterium affects coho salmon (CS; Oncorhynchus kisutch), Atlantic salmon (AS; Salmo salar), and rainbow trout (RT; Oncorhynchus mykiss) in several countries, including Norway, Canada, Scotland, Ireland, and Chile. We used Bayesian genome-wide association study analyses to investigate the genetic architecture of resistance to P. salmonis in farmed populations of these species. Resistance to SRS was defined as the number of days to death and as binary survival (BS). A total of 828 CS, 2130 RT, and 2601 AS individuals were phenotyped and then genotyped using double-digest restriction site-associated DNA sequencing and 57K and 50K Affymetrix® Axiom® single nucleotide polymorphism (SNP) panels, respectively. Both traits of SRS resistance in CS and RT appeared to be under oligogenic control. In AS, there was evidence of polygenic control of SRS resistance. To identify candidate genes associated with resistance, we applied a comparative genomics approach in which we systematically explored the complete set of genes adjacent to SNPs, which explained more than 1% of the genetic variance of resistance in each salmonid species (533 genes in total). Thus, genes were classified based on the following criteria: i) shared function of their protein domains among species, ii) shared orthology among species, iii) proximity to the SNP explaining the highest proportion of the genetic variance, and iv) presence in more than one genomic region explaining more than 1% of the genetic variance within species. Our results allowed us to identify 120 candidate genes belonging to at least one of the four criteria described above. Of these, 21 of them were part of at least two of the criteria defined above and are suggested to be strong functional candidates influencing P. salmonis resistance. These genes are related to diverse biological processes, such as kinase activity, GTP ... Dataset Atlantic salmon Salmo salar Frontiers: Figshare Canada Norway |
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Frontiers: Figshare |
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ftfrontimediafig |
language |
unknown |
topic |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy coho salmon rainbow trout Atlantic salmon Piscirickettsia salmonis genome-wide association study comparative genomics piscirickettsiosis |
spellingShingle |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy coho salmon rainbow trout Atlantic salmon Piscirickettsia salmonis genome-wide association study comparative genomics piscirickettsiosis José M. Yáñez Grazyella M. Yoshida Ángel Parra Katharina Correa Agustín Barría Liane N. Bassini Kris A. Christensen Maria E. López Roberto Carvalheiro Jean P. Lhorente Rodrigo Pulgar Table_1_Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis.xlsx |
topic_facet |
Genetics Genetic Engineering Biomarkers Developmental Genetics (incl. Sex Determination) Epigenetics (incl. Genome Methylation and Epigenomics) Gene Expression (incl. Microarray and other genome-wide approaches) Genome Structure and Regulation Genomics Genetically Modified Animals Livestock Cloning Gene and Molecular Therapy coho salmon rainbow trout Atlantic salmon Piscirickettsia salmonis genome-wide association study comparative genomics piscirickettsiosis |
description |
Piscirickettsia salmonis is the etiologic agent of salmon rickettsial syndrome (SRS) and is responsible for considerable economic losses in salmon aquaculture. The bacterium affects coho salmon (CS; Oncorhynchus kisutch), Atlantic salmon (AS; Salmo salar), and rainbow trout (RT; Oncorhynchus mykiss) in several countries, including Norway, Canada, Scotland, Ireland, and Chile. We used Bayesian genome-wide association study analyses to investigate the genetic architecture of resistance to P. salmonis in farmed populations of these species. Resistance to SRS was defined as the number of days to death and as binary survival (BS). A total of 828 CS, 2130 RT, and 2601 AS individuals were phenotyped and then genotyped using double-digest restriction site-associated DNA sequencing and 57K and 50K Affymetrix® Axiom® single nucleotide polymorphism (SNP) panels, respectively. Both traits of SRS resistance in CS and RT appeared to be under oligogenic control. In AS, there was evidence of polygenic control of SRS resistance. To identify candidate genes associated with resistance, we applied a comparative genomics approach in which we systematically explored the complete set of genes adjacent to SNPs, which explained more than 1% of the genetic variance of resistance in each salmonid species (533 genes in total). Thus, genes were classified based on the following criteria: i) shared function of their protein domains among species, ii) shared orthology among species, iii) proximity to the SNP explaining the highest proportion of the genetic variance, and iv) presence in more than one genomic region explaining more than 1% of the genetic variance within species. Our results allowed us to identify 120 candidate genes belonging to at least one of the four criteria described above. Of these, 21 of them were part of at least two of the criteria defined above and are suggested to be strong functional candidates influencing P. salmonis resistance. These genes are related to diverse biological processes, such as kinase activity, GTP ... |
format |
Dataset |
author |
José M. Yáñez Grazyella M. Yoshida Ángel Parra Katharina Correa Agustín Barría Liane N. Bassini Kris A. Christensen Maria E. López Roberto Carvalheiro Jean P. Lhorente Rodrigo Pulgar |
author_facet |
José M. Yáñez Grazyella M. Yoshida Ángel Parra Katharina Correa Agustín Barría Liane N. Bassini Kris A. Christensen Maria E. López Roberto Carvalheiro Jean P. Lhorente Rodrigo Pulgar |
author_sort |
José M. Yáñez |
title |
Table_1_Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis.xlsx |
title_short |
Table_1_Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis.xlsx |
title_full |
Table_1_Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis.xlsx |
title_fullStr |
Table_1_Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis.xlsx |
title_full_unstemmed |
Table_1_Comparative Genomic Analysis of Three Salmonid Species Identifies Functional Candidate Genes Involved in Resistance to the Intracellular Bacterium Piscirickettsia salmonis.xlsx |
title_sort |
table_1_comparative genomic analysis of three salmonid species identifies functional candidate genes involved in resistance to the intracellular bacterium piscirickettsia salmonis.xlsx |
publishDate |
2019 |
url |
https://doi.org/10.3389/fgene.2019.00665.s004 https://figshare.com/articles/Table_1_Comparative_Genomic_Analysis_of_Three_Salmonid_Species_Identifies_Functional_Candidate_Genes_Involved_in_Resistance_to_the_Intracellular_Bacterium_Piscirickettsia_salmonis_xlsx/9250097 |
geographic |
Canada Norway |
geographic_facet |
Canada Norway |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
doi:10.3389/fgene.2019.00665.s004 https://figshare.com/articles/Table_1_Comparative_Genomic_Analysis_of_Three_Salmonid_Species_Identifies_Functional_Candidate_Genes_Involved_in_Resistance_to_the_Intracellular_Bacterium_Piscirickettsia_salmonis_xlsx/9250097 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fgene.2019.00665.s004 |
_version_ |
1766362777945899008 |