Single-library vole assemblies
High-quality reference genomes are essential to effectively characterize genomic drivers of speciation, phenotypic diversity, and disease causality. Larger complex genomes often require integration of long-read DNA sequencing with additional genomic data, such as chromosome conformation capture (Hi-C or CiFi) to generate phased chromosome-scale assemblies, however this requires multiple sequencing platforms (in the case of Hi-C) or the construction of multiple long-read sequencing libraries. Here, we devise a strategy that combines PacBio HiFi and CiFi sequencing in a single library and run to efficiently produce high-quality contiguous chromosome-scale diploid genome assemblies. We apply this approach to liver tissue from single individuals of prairie vole (Microtus ochrogaster) and meadow vole (Microtus pennsylvanicus), generating haplotype-resolved, chromosome-scale 2.3 Gbp genomes with QV>70, and 99.3% BUSCO completeness. Comparing the two new genomes resolves a prairie vole-specific duplication of AVPR1A, previously implicated in pair bonding but missing from the existing prairie vole reference genome, suggesting a possible driver of behavioral divergence from meadow voles. This single-library approach facilitates efficient and accurate genome assembly of diverse species using one sequencing platform.
High-quality reference genomes are essential to effectively characterize genomic drivers of speciation, phenotypic diversity, and disease causality. Larger complex genomes often require integration of long-read DNA sequencing with additional genomic data, such as chromosome conformation capture (Hi-C or CiFi) to generate phased chromosome-scale assemblies, however this requires multiple sequencing platforms (in the case of Hi-C) or the construction of multiple long-read sequencing libraries. Here, we devise a strategy that combines PacBio HiFi and CiFi sequencing in a single library and run to efficiently produce high-quality contiguous chromosome-scale diploid genome assemblies. We apply this approach to liver tissue from single individuals of prairie vole (Microtus ochrogaster) and meadow vole (Microtus pennsylvanicus), generating haplotype-resolved, chromosome-scale 2.3 Gbp genomes with QV>70, and 99.3% BUSCO completeness. Comparing the two new genomes resolves a prairie vole-specific duplication of AVPR1A, previously implicated in pair bonding but missing from the existing prairie vole reference genome, suggesting a possible driver of behavioral divergence from meadow voles. This single-library approach facilitates efficient and accurate genome assembly of diverse species using one sequencing platform.
UNIVERSITY OF CALIFORNIA - DAVIS