Bioproject ID: PRJNA351886

bioproject id PRJNA351886      to NCBI
key word baseline;RNA-SEQ DATA;WILD;GROWTH;ADAPTATION;ANNOTATION;ALIGNMENT;GENETICS;GENOMICS;ANIMALS;BIOLOGY
experiment type domestication
publication Chen, X. , et al. "Domestication drive the changes of immune and digestive system of Eurasian perch (Perca fluviatilis)." PLoS ONE 12.3(2017):e0172903.
description Comparative transcriptome between wild and domesticated Eurasian perch
abstract Domestication has altered a variety of traits within the Eurasian perch (Perca fluviatilis), including phenotypic, physiological and behavioral traits of Eurasian perch (Perca fluviatilis). Little is known, however, about the genetic changes between domesticated and wild Eurasian perch. In this study, we assembled a high-quality de novo reference transcriptome and identified differentially expressed genes between wild and domesticated Eurasian perch. A total of 113,709 transcripts were assembled, and 58,380 transcripts were annotated. Transcriptomic comparison revealed 630 differentially expressed genes between domesticated and wild Eurasian perch. Within domesticated Eurasian perch there were 412 genes that were up-regulated including MHCI, MHCII, chia, ighm within immune system development. There were 218 genes including try1, ctrl, ctrb, cela3b, cpa1 and cpb1, which were down-regulated that were associated with digestive processes. Our results indicated domestication drives the changes of immune and digestive system of Eurasian perch. Our study not only provide valuable genetic resources for further studies in Eurasian perch, but also provide novel insights into the genetic basis of physiological changes in Eurasian perch during domestication process.

Sample Information

sample id sample name tissue strain treatment description
1. SRR4787434 Eurasian perch fresh brain, heart, gill, liver, muscle, kidney, and pancreas nan domesticate Two groups (wild and domesticated) of fish were collected within the Xin Jiang Province of China. Two biological replicates were collected for wild and domesticated groups. Following anaesthetization (in tricaine methanesulfonate (MS222) at a concentration of 1:18000), each individual was weighed, and then fresh brain, heart, gill, liver, muscle, kidney, and pancreas tissues were quickly collected and immediately stored in liquid nitrogen for RNA isolation. After RNA extraction, RNA from each tissue type were diluted to equal concentrations and then pooled together for each fish individual for RNA-Seq sequencing.