Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch

Cells

Arne Sahm¹  Saptarshi Bej²  Lidia de los Ríos-Pérez³  Marieke Verleih⁴  Julien Alban Nguinkal⁴  Ronald Marco Brunner⁴  Alexander Rebl⁴  Tom Goldammer⁴ 

[1] Computational Biology of Aging, Fritz Lipmann Institute (FLI)-Leibniz Institute on Aging, 07745 Jena, Germany;Department of Systems Biology and Bioinformatics, Faculty of Computer Science and Electrical Engineering, University of Rostock, 18057 Rostock, Germany;Institute of Genetics and Biometry, Research Institute for Farm Animals (FBN), 18196 Dummerstorf, Germany;Institute of Genome Biology, Research Institute for Farm Animals (FBN), 18196 Dummerstorf, Germany;

关键词: RNA-Seq;    tissue-specificity;    positive selection;    fish transcriptomics;    co-expression;   

DOI  :  10.3390/cells10092289

来源: DOAJ

【 摘 要 】

Promising efforts are ongoing to extend genomics resources for pikeperch (Sander lucioperca), a species of high interest for the sustainable European aquaculture sector. Although previous work, including reference genome assembly, transcriptome sequence, and single-nucleotide polymorphism genotyping, added a great wealth of genomic tools, a comprehensive characterization of gene expression across major tissues in pikeperch still remains an unmet research need. Here, we used deep RNA-Sequencing of ten vital tissues collected in eight animals to build a high-confident and annotated trancriptome atlas, to detect the tissue-specificity of gene expression and co-expression network modules, and to investigate genome-wide selective signatures in the Percidae fish family. Pathway enrichment and protein–protein interaction network analyses were performed to characterize the unique biological functions of tissue-specific genes and co-expression modules. We detected strong functional correlations and similarities of tissues with respect to their expression patterns—but also significant differences in the complexity and composition of their transcriptomes. Moreover, functional analyses revealed that tissue-specific genes essentially play key roles in the specific physiological functions of the respective tissues. Identified network modules were also functionally coherent with tissues’ main physiological functions. Although tissue specificity was not associated with positive selection, several genes under selection were found to be involved in hypoxia, immunity, and gene regulation processes, that are crucial for fish adaption and welfare. Overall, these new resources and insights will not only enhance the understanding of mechanisms of organ biology in pikeperch, but also complement the amount of genomic resources for this commercial species.

【 授权许可】

Unknown