A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)

Abstract Background The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to...

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Autores principales:	Zhaoran Zhou, Christiane Eichner, Frank Nilsen, Inge Jonassen, Michael Dondrup
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Gene co-expression network analysis Regularized logistic regression Differential co-expression analysis Regulatory impact factor Transcriptome Salmon louse Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/19a8058c79af41a89aa44a6f08440baf
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spelling	oai:doaj.org-article:19a8058c79af41a89aa44a6f08440baf2021-11-21T12:26:33ZA novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)10.1186/s12864-021-08054-71471-2164https://doaj.org/article/19a8058c79af41a89aa44a6f08440baf2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08054-7https://doaj.org/toc/1471-2164Abstract Background The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. Methods Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. Results Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with a RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like transcription factor obtained highest scores in the regulatory impact factor calculation. Conclusions We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirm the effectiveness of our approach and demonstrated the indispensable role of a RAB1A-like gene in the development of the salmon louse. We propose that our approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.Zhaoran ZhouChristiane EichnerFrank NilsenInge JonassenMichael DondrupBMCarticleGene co-expression network analysisRegularized logistic regressionDifferential co-expression analysisRegulatory impact factorTranscriptomeSalmon louseBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-25 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Gene co-expression network analysis Regularized logistic regression Differential co-expression analysis Regulatory impact factor Transcriptome Salmon louse Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Gene co-expression network analysis Regularized logistic regression Differential co-expression analysis Regulatory impact factor Transcriptome Salmon louse Biotechnology TP248.13-248.65 Genetics QH426-470 Zhaoran Zhou Christiane Eichner Frank Nilsen Inge Jonassen Michael Dondrup A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)
description	Abstract Background The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. Methods Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. Results Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with a RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like transcription factor obtained highest scores in the regulatory impact factor calculation. Conclusions We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirm the effectiveness of our approach and demonstrated the indispensable role of a RAB1A-like gene in the development of the salmon louse. We propose that our approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.
format	article
author	Zhaoran Zhou Christiane Eichner Frank Nilsen Inge Jonassen Michael Dondrup
author_facet	Zhaoran Zhou Christiane Eichner Frank Nilsen Inge Jonassen Michael Dondrup
author_sort	Zhaoran Zhou
title	A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)
title_short	A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)
title_full	A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)
title_fullStr	A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)
title_full_unstemmed	A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)
title_sort	novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the atlantic salmon louse (lepeophtheirus salmonis)
publisher	BMC
publishDate	2021
url	https://doaj.org/article/19a8058c79af41a89aa44a6f08440baf
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A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)

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