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

Abstract

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.

Systematic identification of smORFs in domestic silkworm (Bombyx mori)

“…Like tissue-specific genes (called luxury genes), tissue-specific smORFs may also play a key role in specific physiological functions of their respective tissues ( Nguinkal et al, 2021 ; He et al, 2018 ). To explore the tissue-specific expression of smORFs in different tissues, TSPEX software was used to analyze the tissue specificity of all identified smORFs, and a TSI value was used to indelicate and filter the tissue-specificity.…”

Preclinical Repurposing of Sitagliptin as a Drug Candidate for Colorectal Cancer by Targeting CD24/CTNNB1/SOX4-Centered Signaling Hub

“…We used the HPA database (https://www.proteinatlas.org/ accessed on 28 May 2023) to retrieve the cell-type atlas showing the single-cell RNA sequencing (scRNA-seq) data of DPP4, CTNNB1, CD24, and SOX4 expression in colon tissue [61]. The expression of each gene in the specified cell types was explored using the interactive UMAP plots and bar chart [62].…”

The Discovery and Characterization of Conserved and Novel miRNAs in the Different Developmental Stages and Organs of Pikeperch (Sander lucioperca)

“…In addition to its growing commercial importance, research on the genetic and genomic composition of pikeperch has also gained momentum. With recent publications on its genome [ 45 , 46 ] and transcriptome [ 47 ], the systematic exploration of functional genomics is feasible in the context of, for instance, relevant commercial traits. So far, nobody has explored miRNA genes and their expression in pikeperch.…”