Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
Low, W. Y.; Tearle, R.; Liu, C.; Koren, S.; Rhie, A.; Bickhart, D. M.; Rosen, B. D.; Kroneberg, Z. N.; Kingan, S. B.; Tseng, E.; Thibaud-Nissen, F.; Martin, F. J.; Billis, K.; Ghurye, J.; Hastie, A. R.; Lee, J.; Pang, A.; Heaton, M. P.; Phillippy, A. M.; Hiendleder, S.; Smith, T. P.; Williams, J. L.
Show abstract
We present high quality, phased genome assemblies representative of taurine and indicine cattle, subspecies that differ markedly in productivity-related traits and environmental adaptation. We report a new haplotype-aware scaffolding and polishing pipeline using contigs generated by the trio binning method to produce haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle breeds. These assemblies were used to identify structural and copy number variants that differentiate the subspecies and we found variant detection was sensitive to the specific reference genome chosen. Six gene families with immune related functions are expanded in the indicine lineage. Assembly of the genomes of both subspecies from a single individual enabled transcripts to be phased to detect allele-specific expression, and to study genome-wide selective sweeps. An indicus-specific extra copy of fatty acid desaturase is under positive selection and may contribute to indicine adaptation to heat and drought.
Matching journals
The top 3 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- Autosomal recessive loci contribute significantly to quantitative variation of male fertility in a dairy cattle population 94%
- Optimizing Cost-Effective Gene Expression Phenotyping Approaches in Cattle Using 3' mRNA Sequencing 94%
- Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome 93%
Similar papers in this journal
- Analysis of ovarian transcriptomes reveals thousands of novel genes in the insect vector Rhodnius prolixus 94%
- Phenogenomic resources immortalized in a panel of wild-derived strains of five species of house mice 93%
- Taxonomic assessment of two wild house mouse subspecies using whole genome sequencing 93%
Similar papers in this journal
- Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle 95%
- Pangenome genotyped structural variation improves molecular phenotype mapping in cattle 95%
- Inference of Selective Force on House Mouse Genomes during Secondary Contact in East Asia 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.