Single-library chromosome-scale diploid assemblies of vole genomes resolve a species-specific duplication implicated in pair bonding

Abuelanin, Mohamed, Kaya, Gulhan, Lake, Juniper A, Lambert, Christine, Wu, Melody V, Berendzen, Kristen M, Krasheninnikova, Ksenia, Wood, Jonathan MD, Solomon, Nancy G, Donaldson, Zoe R, Bales, Karen L, Howe, Kerstin, Korlach, Jonas, Manoli, Devanand, Tollkuhn, Jessica, Dennis, Megan Y (March 2026) Single-library chromosome-scale diploid assemblies of vole genomes resolve a species-specific duplication implicated in pair bonding. bioRxiv. ISSN 2692-8205 (Submitted)

PDF 10.64898.2026.03.13.711624.pdf - Submitted Version Available under License Creative Commons Attribution Non-commercial. Download (5MB)

Abstract

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~62, and 99.3% BUSCO completeness. Comparing the two new genomes identifies complex structural changes impacting Avpr1a, previously implicated in pair bonding, including a species-specific duplication missing from the existing prairie vole reference genome. These divergent genomic features offer new avenues of investigation related to behavioral divergence between prairie and meadow voles. This single-library approach facilitates a simplified and more affordable assembly workflow, producing near-complete genomes of diverse species using one sequencing platform.

Item Type:	Paper
Subjects:	Investigative techniques and equipment organism description > animal behavior Investigative techniques and equipment > assays Investigative techniques and equipment > assays > long-read sequencing
CSHL Authors:	Wu, Melody Tollkuhn, Jessica
Communities:	CSHL labs > Tollkuhn lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	17 March 2026
Date Deposited:	07 Apr 2026 19:29
Last Modified:	07 Apr 2026 19:29
PMCID:	PMC13015472
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/42147

Actions (login required)

Administrator's edit/view item