News & Events
New publication: The intronic branch point sequence is under strong evolutionary constraint in the bovine and human genome
Pre-mRNA splicing by the spliceosomal complex requires several cis-acting intronic features including the splice acceptor and donor sites, polypyrimidine tract and the branch point sequence. We herein, for the first time, computationally predict branch point sequences in 179,476 bovine introns and investigate their variability at nucleotide resolution. We show that the conserved residues of the branch point sequence are targets of extreme purifying selection, harbouring less variants than coding sequences suggesting extreme purifying selection. Further we provide evidence that mutations in evolutionarily conserved residues lead to alternative splicing.
DOI: external pagehttps://doi.org/10.1038/s42003-021-02725-7call_made
Kadri et al. The intronic branch point sequence is under strong evolutionary constraint in the bovine and human genome. external pagehttps://www.nature.com/articles/s42003-021-02725-7call_made
New publication: Genome-wide SNP data unravel the ancestry and signatures of divergent selection in Ghurrah pigs of India
Despite India’s rich biodiversity and proximity to the geographical origins of the domestic pig, the place of Indian pigs in the global phylogeny is unclear. Using microarray-derived (porcine 60K SNP chip) genotypes of 11 Ghurrah pigs from North-Western India and a public dataset comprising 146 breeds, we determined the genomic ancestry of Ghurrah pigs and compared their genetic constitution to European and Asian breeds to ascertain signatures of divergent selection.
Results showed that Ghurrah pigs contain genes of Asian and European ancestry with signs of inter-species introgression. Using Admixture LD – decay statistics, the European admixture event was dated to the recent past, coinciding with the start of cross-breeding efforts in India. The complex Asian ancestry pattern of the breed resembled that of Asian wild boars, suggesting introgression from an Indian wild boar relative. Our results presented the first genomic characterization of an Indian pig breed using dense microarray-derived genotypes and highlighted the importance of further genomic characterization of Indian domestic and wild pigs.
DOI: external pagehttps://doi.org/10.1016/j.livsci.2021.104587call_made
Mehrotra et al. Genome-wide SNP data unravel the ancestry and signatures of divergent selection in Ghurrah pigs of India. external pagehttps://www.sciencedirect.com/science/article/pii/S1871141321001955?via%3Dihubcall_made
New publication: Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
Reference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely accepted bovine reference genome. Haplotype-resolved genomes that exceed the current bovine reference genome in quality and continuity have been assembled for different breeds of cattle. Using whole genome sequencing data of 161 Brown Swiss cattle, we compared the accuracy of read mapping and sequence variant genotyping as well as downstream genomic analyses between the bovine reference genome (ARS-UCD1.2) and a highly continuous Angus-based assembly (UOA_Angus_1).
DOI: external pagehttps://doi.org/10.1186/s12864-021-07554-wcall_made
Lloret-Villas et al. Investigating the impact of reference assembly choice on genomic analyses in a cattle breed. external pagehttps://rdcu.be/ckXgucall_made
New publication: Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs from Nosková et al.
Sequencing haplotypes of key ancestor animals of two pig lines from Swiss Large White breed facilitated genotyping by low-pass sequencing.
We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses of principal component, admixture and fixation index (FST) analyses indicated considerable genetic differentiation, even though the split into two populations occurred only few generations ago. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line. Two complementary approaches for detecting signatures of selection showed only minor overlap between the lines. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.
DOI: external pagehttps://doi.org/10.1186/s12864-021-07610-5call_made
Nosková et al. Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs. external pagehttps://rdcu.be/ci8PMcall_made