Galbase: a comprehensive repository for integrating chicken multi-omics data
Weiwei Fu,
Rui Wang,
Naiyi Xu,
Jinxin Wang,
Ran Li,
Hojjat Asadollahpour Nanaei,
Qinghua Nie,
Xin Zhao,
Jianlin Han,
Ning Yang,
Yu Jiang
Affiliations
Weiwei Fu
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
Rui Wang
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
Naiyi Xu
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
Jinxin Wang
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
Ran Li
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
Hojjat Asadollahpour Nanaei
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
Qinghua Nie
Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University
Xin Zhao
Department of Animal Science, McGill University
Jianlin Han
CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS)
Ning Yang
National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University
Yu Jiang
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University
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 .
