ArticleNucleic acids research2022
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
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- Adoption of Standard Reference SNP Identifiers in Agricultural Genomics for Interoperability and Data Reuse.Scientific data · 2026Article
- Whole genome sequencing revealed genetic diversity, population structure, and selective signature of Tianhua mutton sheep.BMC genomics · 2026Article
- Genetic admixture and adaptive signatures of Guanling cattle revealed by whole-genome sequence.BMC genomics · 2026Article
- Population genomics of Nigerian goat breeds and neighbouring populations in the West Africa-Cameroon transboundary livestock corridor.PloS one · 2026Article
- Whole-Genome Resequencing Analysis Reveals the Local Ancestry and Selection of Kongshan Cattle.Biology · 2025Article
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- The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression.Nature communications · 2025Article
- Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle.Genomics, proteomics & bioinformatics · 2025Article
- Genomic insights into the convergent evolution of desert adaptation in camels and antelopes.Zoological research · 2025Article
- LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals.Genomics, proteomics & bioinformatics · 2025Article
- A comparative review of short genetic variant databases across humans and animal species.Briefings in bioinformatics · 2025Review
- Genetic basis and origin of coat color in Leiqiong cattle.Zoological research · 2025Article
- Admixture and selection offer insights for the conservation and breeding of Guyuan cattle.BMC biology · 2025Article
- BbGSD: Black-boned Sheep Genome SNP Database.Database : the journal of biological databases and curation · 2025Article
- Deciphering the Population Characteristics of Leiqiong Cattle Using Whole-Genome Sequencing Data.Animals : an open access journal from MDPI · 2025Article
- ZNF280AY: a pseudogene on the ovine Y chromosome and its copy number variation associated with testicular size in Hu sheep.Journal of animal science · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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