Dataset for brain transcriptome and whole-genome resequencing of mandarin fish (Siniperca chuatsi) with contrasting feed domestication performance

Description

This dataset contains raw sequencing data from a study investigating the genetic basis of feed domestication difficulty in mandarin fish (Siniperca chuatsi). Two groups were established based on feeding performance during a standardized three-phase domestication protocol: easily domesticable fish (group T, feed-accepting) and difficult-to-domesticate fish (group W, feed-resistant). Brain tissues from 15 individuals per group were used for transcriptome sequencing (RNA-seq), and fin clip tissues from 30 individuals per group were used for whole-genome resequencing (WGS). RNA-seq libraries were sequenced on the Illumina NovaSeq X Plus platform (PE150), and WGS libraries were sequenced on the Illumina NovaSeq platform (PE150) at an average depth of ≥10×. All reads were generated from Siniperca chuatsi and can be aligned to the reference genome ASM2008510v1 (GCF_020085105.1). The dataset includes raw FASTQ files for both RNA-seq and WGS, along with sample metadata describing group assignment, tissue type, and sequencing platform. These data can be used to reproduce the analyses in the associated manuscript, including differential gene expression analysis, gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), SNP calling, and intergroup differential SNP identification. Users can process the raw reads with standard pipelines (e.g., fastp, HISAT2, featureCounts, DESeq2, Sentieon/GATK) to explore molecular mechanisms underlying feed domestication and to develop molecular markers for breeding easily domesticable mandarin fish.

Institutions

• Shanghai Ocean University

  Shanghai, Shanghai

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