RGD v2.0: a major update of the ruminant functional and evolutionary genomics database

Abstract

Ruminant Genome Database (RGD; http://animal.nwsuaf.edu.cn/RGD) provides visualization and analysis tools for ruminant comparative genomics and functional annotations. As more high-quality ruminant genome assemblies have become available, we have redesigned the user interface, integrated and expanded multi-omics data, and developed novel features to improve the database. The new version, RGD v2.0, houses 78 ruminant genomes; 110-species synteny alignments for major livestock (including cattle, sheep, goat) and wild ungulates; 21 012 orthologous gene clusters with Gene Ontology and pathway annotation; ∼8 600 000 conserved elements; and ∼1 000 000 cis-regulatory elements by utilizing 1053 epigenomic data sets. The transcriptome data in RGD v2.0 has nearly doubled, currently with 1936 RNA-seq data sets, and 155 174 phenotypic data sets have been newly added. New and updated features include: (i) The UCSC Genome Browser, BLAT, BLAST and Table Browser tools were updated for six available ruminant livestock species. (ii) The LiftOver tool was newly introduced into our browser to allow coordinate conversion between different ruminant assemblies. And (iii) tissue specificity index, tau, was calculated to facilitate batch screening of specifically expressed genes. The enhanced genome annotations and improved functionality in RGD v2.0 will be useful for study of genome evolution, environmental adaption, livestock breeding and biomedicine.

Figure 1.

The processing pipeline used to construct RGD v2.0. RGD v2.0 integrated comparative genomics, transcriptomics, epigenomics and phenotypic data. Users can search a gene symbol or a genomic region to get results in an interactive table and graph.

Figure 2.

An example of Cervidae-specific diverged sites in the 3’UTR of the NOVA1 gene. (A) NOVA1 gene structure and conserved elements in 100 vertebrates and 30 mammals. (B) Cervidae uniquely divergent sites present in NOVA1. We display the new tracks of 110-species alignments and conserved elements. And 29 genomes were assembled based on third-generation sequencing platform.

Figure 3.

Application of the regulatory data and multiple genome alignments to identify the key variations of PLAG1 gene. (A) The heat map on the left shows the emission probabilities of 15-chromatin state identified by ChromHMM based on the data of six epigenomic markers (H3K4me3, H3K27ac, H3K4me1, H3K27me3, CTCF and ATAC-seq) from nine bovine tissues. The heat maps in the middle and right show the overlap enrichment for various genomic annotations. (B) Two candidate variations, ss319607405 (14:23375648–23375650), and ss319607406 (14:23375692), were located in the active transcriptional start site (TSS) and promoter regions, and overlapped with a highly conserved element. (C) Detailed regulatory signals and multiple sequence alignments around these two variations.