ArticleCommunications biology2025
Constructing a draft Indian cattle pangenome using short-read sequencing.
Article in Communications biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- The Pan-Genome of 1107 Spotted Sea Bass Accessions Reveals Gene Evolution Patterns During Domestication Selection.Molecular ecology resources · 2026Article
- Immune responses of Bos indicus versus Bos taurus cattle towards Bluetongue virus or Schmallenberg virus differ significantly.Communications biology · 2026Article
- The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution.Animals : an open access journal from MDPI · 2026Review
- Omics in mini-livestock: a genomic perspective on the future of sustainable food systems.Frontiers in genetics · 2025Review
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Indian desi cattle, known for their adaptability and phenotypic diversity, represent a valuable genetic resource. However, a single reference genome often fails to capture the full extent of their genetic variation. To address this, we construct a pangenome for desi cattle by identifying and characterizing non-reference novel sequences (NRNS). We sequence 68 genomes from seven breeds, generating 48.35 billion short reads. Using the PanGenome Analysis (PanGA) pipeline, we identify 13,065 NRNS (~41 Mbp), with substantial variation across the population. Most NRNS were unique to desi cattle, with minimal overlap (4.1%) with the Chinese indicine pangenome. Approximately 40% of NRNS exhibited ancestral origins within the Bos genus and were enriched in genic regions, suggesting functional roles. These sequences are linked to quantitative trait loci for traits such as milk production. The pangenome approach enhances read mapping accuracy, reduces spurious single nucleotide polymorphism calls, and uncovers novel genetic variants, offering a deeper understanding of desi cattle genomics.
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