Galbase: a comprehensive repository for integrating chicken multi-omics data

Abstract

Background: Multi-omics data can provide a stereoscopic view to explore potential causal variations and genes, as well as underlying genetic mechanisms of complex traits. However, for many non-mammalian species, including chickens, these resources are poorly integrated and reused, greatly limiting genetic research and breeding processes of the species.

Results: Here, we constructed Galbase, an easily accessible repository that integrates public chicken multi-omics data from 928 re-sequenced genomes, 429 transcriptomes, 379 epigenomes, 15,275 QTL entries, and 7,526 associations. A total of 21.67 million SNPs, 2.71 million InDels, and 488,583 cis-regulatory elements were included. Galbase allows users to retrieve genomic variations in geographical maps, gene expression profiling in heatmaps, and epigenomic signals in peak patterns. It also provides modules for batch annotation of genes, regions, and loci based on multi-layered omics data. Additionally, a series of convenient tools, including the UCSC Genome Browser, WashU Epigenome Browser, BLAT, BLAST, and LiftOver, were also integrated to facilitate search, visualization, and analysis of sequence features.

Conclusion: Galbase grants new opportunities to research communities to undertake in-depth functional genomic studies on chicken. All features of Galbase make it a useful resource to identify genetic variations responsible for chicken complex traits. Galbase is publicly available at http://animal.nwsuaf.edu.cn/ChickenVar .

Keywords: Chicken; Complex traits; Database; Omics data.

Fig. 1

The database structure and processing pipeline of Galbase

Fig. 2

Statistics of population genomic diversity based on random sampling of each group (To avoid the bias due to sample size variation, we reduced the sample size of each group down to five, following random sampling for 10 times.). a Genome-wide distribution of nucleotide diversity in each chicken group. b Distribution of F_ROH estimate in each chicken group

Fig. 3

Features of Galbase variation module. a Basic search interface includes filtering of variation rsID, gene symbol, and chromosomal location of both GRCg6a and GRCg7b assemblies. b Advanced search interface includes filtering of minor allele frequency and consequence type. c An example shows the chr5:41,020,238 locus at the TSHR gene and its allele frequency distribution of five RJF subspecies and 47 domestic chicken breeds. d An example shows the chr3:67,850,419 locus at the PDSS2 gene and its allele frequency distribution. The maps were created by using ECharts (https://github.com/apache/echarts) [43], an open-sourced and web-based framework based on JavaScript

Fig. 4

Features of Galbase expression module. a Screenshots of gene expression function and the result for one example. (The chicken illustration is processed from a chicken photo taken by Weiwei Fu, one of the authors of this article.) b Display of transcriptome expression histogram in Genome Browser. c A boxplot showing the range of expression levels across all chicken samples by clicking the gene symbol in Fig. 4b. Different colors represent different organ systems. d Display of the coverage depth of transcriptome reads in Genome Browser

Fig. 5

Presentation of multi-omics data for silky-feather trait. a Genotype pattern of the silky-feather fixed region (chr3:67,832,192–67,850,863). Only the chr3:67,850,419 locus conforms to a single gene recessive inheritance mode. b Display of epigenomics metadata in local WashU Epigenome Browser. c Display of epigenomics peaks and read coverage in local UCSC Genome Browser