Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis .
Networks of co-expressed genes produce complex phenotypes associated with functional novelty. Sex differences in gene expression levels or in the structure of gene co-expression networks can cause sexual dimorphism and may resolve sexually antagonistic selection. Here we used RNA-sequencing in the s...
Published in: | G3 Genes|Genomes|Genetics |
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Oxford University Press (OUP)
2019
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Online Access: | http://livrepository.liverpool.ac.uk/3064050/ https://doi.org/10.1534/g3.118.200910 http://livrepository.liverpool.ac.uk/3064050/1/Sex-Specific%20Co-expression%20Networks%20and%20Sex-Biased%20Gene%20Expression%20in%20the%20Salmonid%20Brook%20Charr%20Salvelinus%20fontinalis.pdf |
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ftunivliverpool:oai:livrepository.liverpool.ac.uk:3064050 2023-05-15T14:30:12+02:00 Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis . Sutherland, Ben JG Prokkola, Jenni M Audet, Céline Bernatchez, Louis 2019-03 text http://livrepository.liverpool.ac.uk/3064050/ https://doi.org/10.1534/g3.118.200910 http://livrepository.liverpool.ac.uk/3064050/1/Sex-Specific%20Co-expression%20Networks%20and%20Sex-Biased%20Gene%20Expression%20in%20the%20Salmonid%20Brook%20Charr%20Salvelinus%20fontinalis.pdf en eng eng Oxford University Press (OUP) http://livrepository.liverpool.ac.uk/3064050/1/Sex-Specific%20Co-expression%20Networks%20and%20Sex-Biased%20Gene%20Expression%20in%20the%20Salmonid%20Brook%20Charr%20Salvelinus%20fontinalis.pdf Sutherland, Ben JG orcid:0000-0002-2029-9893 , Prokkola, Jenni M orcid:0000-0003-2987-4417 , Audet, Céline orcid:0000-0003-3366-210X and Bernatchez, Louis orcid:0000-0002-8085-9709 (2019) Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis . G3 (Bethesda, Md.), 9 (3). pp. 955-968. Article NonPeerReviewed 2019 ftunivliverpool https://doi.org/10.1534/g3.118.200910 2023-01-19T23:47:30Z Networks of co-expressed genes produce complex phenotypes associated with functional novelty. Sex differences in gene expression levels or in the structure of gene co-expression networks can cause sexual dimorphism and may resolve sexually antagonistic selection. Here we used RNA-sequencing in the salmonid Brook Charr Salvelinus fontinalis to characterize sex-specific co-expression networks in the liver of 47 female and 53 male offspring. In both networks, modules were characterized for functional enrichment, hub gene identification, and associations with 15 growth, reproduction, and stress-related phenotypes. Modules were then evaluated for preservation in the opposite sex, and in the congener Arctic Charr Salvelinus alpinus Overall, more transcripts were assigned to a module in the female network than in the male network, which coincided with higher inter-individual gene expression and phenotype variation in the females. Most modules were preserved between sexes and species, including those involved in conserved cellular processes ( e.g. , translation, immune pathways). However, two sex-specific male modules were identified, and these may contribute to sexual dimorphism. To compare with the network analysis, differentially expressed transcripts were identified between the sexes, revealing a total of 16% of expressed transcripts as sex-biased. For both sexes, there was no overrepresentation of sex-biased genes or sex-specific modules on the putative sex chromosome. Sex-biased transcripts were also not overrepresented in sex-specific modules, and in fact highly male-biased transcripts were enriched in preserved modules. Comparative network analysis and differential expression analyses identified different aspects of sex differences in gene expression, and both provided new insights on the genes underlying sexual dimorphism in the salmonid Brook Charr. Article in Journal/Newspaper Arctic charr Arctic Salvelinus alpinus The University of Liverpool Repository Arctic G3 Genes|Genomes|Genetics 9 3 955 968 |
institution |
Open Polar |
collection |
The University of Liverpool Repository |
op_collection_id |
ftunivliverpool |
language |
English |
description |
Networks of co-expressed genes produce complex phenotypes associated with functional novelty. Sex differences in gene expression levels or in the structure of gene co-expression networks can cause sexual dimorphism and may resolve sexually antagonistic selection. Here we used RNA-sequencing in the salmonid Brook Charr Salvelinus fontinalis to characterize sex-specific co-expression networks in the liver of 47 female and 53 male offspring. In both networks, modules were characterized for functional enrichment, hub gene identification, and associations with 15 growth, reproduction, and stress-related phenotypes. Modules were then evaluated for preservation in the opposite sex, and in the congener Arctic Charr Salvelinus alpinus Overall, more transcripts were assigned to a module in the female network than in the male network, which coincided with higher inter-individual gene expression and phenotype variation in the females. Most modules were preserved between sexes and species, including those involved in conserved cellular processes ( e.g. , translation, immune pathways). However, two sex-specific male modules were identified, and these may contribute to sexual dimorphism. To compare with the network analysis, differentially expressed transcripts were identified between the sexes, revealing a total of 16% of expressed transcripts as sex-biased. For both sexes, there was no overrepresentation of sex-biased genes or sex-specific modules on the putative sex chromosome. Sex-biased transcripts were also not overrepresented in sex-specific modules, and in fact highly male-biased transcripts were enriched in preserved modules. Comparative network analysis and differential expression analyses identified different aspects of sex differences in gene expression, and both provided new insights on the genes underlying sexual dimorphism in the salmonid Brook Charr. |
format |
Article in Journal/Newspaper |
author |
Sutherland, Ben JG Prokkola, Jenni M Audet, Céline Bernatchez, Louis |
spellingShingle |
Sutherland, Ben JG Prokkola, Jenni M Audet, Céline Bernatchez, Louis Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis . |
author_facet |
Sutherland, Ben JG Prokkola, Jenni M Audet, Céline Bernatchez, Louis |
author_sort |
Sutherland, Ben JG |
title |
Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis . |
title_short |
Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis . |
title_full |
Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis . |
title_fullStr |
Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis . |
title_full_unstemmed |
Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis . |
title_sort |
sex-specific co-expression networks and sex-biased gene expression in the salmonid brook charr salvelinus fontinalis . |
publisher |
Oxford University Press (OUP) |
publishDate |
2019 |
url |
http://livrepository.liverpool.ac.uk/3064050/ https://doi.org/10.1534/g3.118.200910 http://livrepository.liverpool.ac.uk/3064050/1/Sex-Specific%20Co-expression%20Networks%20and%20Sex-Biased%20Gene%20Expression%20in%20the%20Salmonid%20Brook%20Charr%20Salvelinus%20fontinalis.pdf |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic charr Arctic Salvelinus alpinus |
genre_facet |
Arctic charr Arctic Salvelinus alpinus |
op_relation |
http://livrepository.liverpool.ac.uk/3064050/1/Sex-Specific%20Co-expression%20Networks%20and%20Sex-Biased%20Gene%20Expression%20in%20the%20Salmonid%20Brook%20Charr%20Salvelinus%20fontinalis.pdf Sutherland, Ben JG orcid:0000-0002-2029-9893 , Prokkola, Jenni M orcid:0000-0003-2987-4417 , Audet, Céline orcid:0000-0003-3366-210X and Bernatchez, Louis orcid:0000-0002-8085-9709 (2019) Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis . G3 (Bethesda, Md.), 9 (3). pp. 955-968. |
op_doi |
https://doi.org/10.1534/g3.118.200910 |
container_title |
G3 Genes|Genomes|Genetics |
container_volume |
9 |
container_issue |
3 |
container_start_page |
955 |
op_container_end_page |
968 |
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1766304092908421120 |