ArticleGenome research2023
A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 42 citations in OpenAlex.
- Genome-wide variation landscape reveals temperature adaptation in Chinese indigenous cattle.Journal of animal science and biotechnology · 2026Article
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- Deciphering the Evolution Pattern of Structural Variations Overlapped With Repetitive Sequence During Cattle Evolution.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Large-Scale Comparative Genomics of European and Chinese Cattle Breeds Reveals Population Structure, Breeding History, and Adaptive Divergence.Animals : an open access journal from MDPI · 2026Article
- Genetic Diversification and Population Admixture Signatures in Yunnan Native Cattle.Animals : an open access journal from MDPI · 2026Article
- Assembly of a pangenome uncovers novel non-reference unique insertion sequences in cattle highlighting their genetic diversity.Journal of animal science and biotechnology · 2026Article
- The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution.Animals : an open access journal from MDPI · 2026Review
- Genomic Insights into the Origins, Population Structure, and Local Adaptation of Philippine Visayan Native Cattle.Animals : an open access journal from MDPI · 2026Article
- De Novo Assembly of Eight Commercial Crossbred Pig Genomes Provides Insights into the Potential Functional Impact of Structural Variation Hotspots.Biomolecules · 2026Article
- The chromosome-level genome of Chinese indicine cattle breed provides insights into bovine adaptation and immunity.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.Journal of advanced research · 2026Article
- Genome assemblies of IndianNAR genomics and bioinformatics · 2025Article
- Insights into natural neocentromere evolution from a cattle T2T X chromosome.Nature communications · 2025Article
- Genome assembly and structural variations of Guyuan cattle.Scientific data · 2025Article
- Exploring cattle structural variation in the era of long reads, pangenome graphs, and near-complete assemblies.Journal of animal science and biotechnology · 2025Review
- Current State of Fish Reference Genome and Pangenome: Methodologies, Sampling Strategies, Quality Assessment and Future Perspectives to Aquaculture Breeding.Marine biotechnology (New York, N.Y.) · 2025Review
- Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes.Genetics, selection, evolution : GSE · 2025Article
- A Strategy for Single-Run Sequencing of the Water Buffalo Genome: (II) Fast One-Step Assembly of Highly Continuous Chromosome Sequences.Animals : an open access journal from MDPI · 2025Article
- The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression.Nature communications · 2025Article
- Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
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Authors and funding
20 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern China, we assembled 20 high-quality partially phased genomes and integrated them into a multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) and 206 SV hotspots spanning ∼195 Mb of gene-rich sequence. We detected 34,249 archaic introgressed fragments in Chinese indicine cattle covering 1.93 Gb (73.3%) of the genome. We inferred an average of 3.8%, 3.2%, 1.4%, and 0.5% of introgressed sequence originating, respectively, from banteng-like, kouprey-like, gayal-like, and gaur-like
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.