A5008789966- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Genetic diversity and population structure
- Livestock and Poultry Management
- Land Use and Ecosystem Services
- Chromosomal and Genetic Variations
- Urban Green Space and Health
- Cancer-related molecular mechanisms research
- Animal Genetics and Reproduction
- Machine Learning in Bioinformatics
- Genetic Mapping and Diversity in Plants and Animals
- Glycosylation and Glycoproteins Research
- RNA and protein synthesis mechanisms
- Evolution and Paleontology Studies
- Plant responses to water stress
- Urban Agriculture and Sustainability
- Molecular Biology Techniques and Applications
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Biomedical Text Mining and Ontologies
- Animal Nutrition and Physiology
- Ecology and Vegetation Dynamics Studies
- Galectins and Cancer Biology
Northwest A&F University
2020-2025
Beijing Forestry University
2023
State Forestry and Grassland Administration
2023
Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence functions in domestic animals largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, 14,707...
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 across southern China, we assembled 20 high-quality partially phased genomes and integrated them into multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) 206 SV hotspots spanning ∼195 gene-rich detected 34,249...
Using ancestral recombination graphs, we investigated recent selection signatures in European beef cattle breeds, pinpointing sweep-driving variants the LCORL and STC2 loci with notable effects on body size growth rate. The ACT-to-A frameshift mutation occurs mainly central-European cattle, stimulates growth. Remarkably, similar truncating mutations were found seven of other most important domesticated species, but not populations wild relatives. In locus, identified a missense C-to-G...
Structural variations (SVs) are diverse forms of genetic alterations and drive a wide range human diseases. Accurately genotyping SVs, particularly occurring at repetitive genomic regions, from short-read sequencing data remains challenging. Here, we introduce SVLearn, machine-learning approach for bi-allelic SVs. It exploits dual-reference strategy to engineer curated set genomic, alignment, features based on reference genome in concert with an allele-based alternative genome. Using 38,613...
Eimeria are obligate protozoan parasites, and more than 1,500 species have been reported. However, genomes lag behind many other eukaryotes since obtaining oocysts is difficult due to a lack of sustainable in vitro culture, highly repetitive sequences, mixed infections. To address this challenge, we used whole-genome amplification single oocyst followed by long-read sequencing obtained chromosome-level genome tenella. The assembled was 52.13 Mb long, encompassing 15 chromosomes 46.94% repeat...
Abstracts Natural variants can significantly improve growth traits in livestock and serve as safe targets for gene editing, thus being applied animal molecular designed breeding. However, such large-effect mutations are severely lacking. Using ancestral recombination graphs, we investigated recent selection signatures beef cattle breeds, pinpointing sweep-driving the LCORL STC2 loci with notable effects on body size rate. The ACT-to-A frameshift mutation occurs mainly central-European...
Abstract Low‐coverage whole genome sequencing (lcWGS) has great potential to effectively genotype large‐scale population and provide solid data for imputation; however, the time imputation needs be optimized. There is also no publicly available reference panel selection in cattle. Here, we proposed a combination of Beagle v5.4 phasing GLIMPSE2 imputation, which fast accurate cattle lcWGS data. Furthermore, established multi‐breed with 61.8 million SNPs based on 2976 worldwide cattle, 1766...
Abstract The takin ( Budorcas taxicolor ) is one of the largest bovid herbivores in subfamily Caprinae. at high risk extinction, but its taxonomic status and genetic diversity remain unclear. In this study, we constructed first reference genome Bu . using PacBio long High‐Fidelity reads Hi‐C technology. assembled ~2.95 Gb with a contig N50 68.05 Mb, which were anchored onto 25+XY chromosomes. We found that was more closely related to muskox than other Caprinae species. Compared common...
Climate change, especially weather extremes like extreme cold or hot, is a major challenge for global livestock. One of the animal breeding goals sustainable livestock production should be to breed animals with excellent climate adaptability. Indigenous and poultry are well adapted local climate, they good resources study genetic footprints mechanism resilience extremes. In order identify selection signatures genes that might involved in hot adaptation indigenous chickens from different...
Chinese serow (
<title>Abstract</title> Structural variations (SVs) are diverse forms of genetic alterations and drive a wide range human diseases. Accurately genotyping SVs, particularly occurring at repetitive genomic regions, from short-read sequencing data remains challenging. Here, we introduce SVLearn, machine-learning approach for bi-allelic SVs. It exploits dual-reference strategy to engineer curated set genomic, alignment, features based on reference genome in concert with an allele-based...
Abstract Pangenomes can facilitate a deeper understanding of genome complexity. Using de novo phased long-read assemblies eight representative goat breeds, we constructed graph-based pangenome goats (Capra hircus) and discovered 113 Mb autosomal novel sequences. Combining this multi-assembly with low-coverage PacBio HiFi sequences, structural variations (SVs) database containing 59,325 SV deletions, 84,910 insertions 24,954 other complex alleles. This resource allowed reliable genotyping...
The takin (Budorcas taxicolor) is one of the largest bovid herbivores across caprinae subfamily. at high risk extinction, however, its taxonomic status still unclear. In this study, we constructed first reference genome B. taxicolor using PacBio long High-Fidelity reads and Hi-C technology. assembled ~2.95 Gb with a contig N50 68.05 Mb scaffold 101.27 Mb, which were anchored onto 25+XY chromosomes. Compared to common ancestral karyotype bovidae (2n=60), found (2n=52) experienced four...