Additional Data for Gene co-expression network analysis facilitates identification of novel important genes for the moulting process of the Atlantic salmon louse Lepeophtheirus salmonis

• Main Authors: Zhaoran Zhou, Eichner, Christiane, Nilsen, Frank, Jonassen, Inge, Dondrup, Michael
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: figshare 2021
• Subjects: Computational Biology; Atlantic salmon
• Online Access: https://dx.doi.org/10.6084/m9.figshare.c.5375315; https://figshare.com/collections/Additional_Data_for_Gene_co-expression_network_analysis_facilitates_identification_of_novel_important_genes_for_the_moulting_process_of_the_Atlantic_salmon_louse_Lepeophtheirus_salmonis/5375315

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 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 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 visible 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 the RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. The FOXO-like gene obtained highest scores in the regulatory impact factor calculation. Conclusions: We proposed 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 confirmed the effectiveness of our approach and demonstrated the indispensable role of RAB1A-like gene in the development of salmon louse. In addition to salmon louse, this approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.