# A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana

## TL;DR

This paper presents a detailed genome assembly for southern live oak, aiding in the study of oak evolution, hybridization, and centromere structure.

## Contribution

The first chromosome-scale, haplotype-resolved genome assembly for Quercus virginiana and section Virentes.

## Key findings

- The genome assembly reveals syntenic relationships among major oak sections.
- Putative centromeric regions show a patchwork satellite architecture.
- The assembly supports future comparative and population genetic studies in Quercus.

## Abstract

Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here, we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes program. Originating from a clone of Auburn University's historic “Toomer's Oak,” this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana genome will support research into the evolution and adaptation of the Quercus genus.

Aközbek et al. present a chromosome-scale genome assembly for southern live oak (Quercus virginiana), the first reference for section Virentes. This reference enables other researchers studying Quercus evolution and genetics to conduct further comparative genomics and population genetic studies. Comparative analyses within the genus reinforce previous research that the major oak sections are highly syntenic. Additionally, this assembly provides a detailed characterization of putative centromeric regions in Quercus, revealing a “patchwork” satellite architecture that warrants functional investigation. This assembly adds to the growing resources available in oak genomics, thus improving our ability to investigate evolutionary dynamics, adaptation, and hybridization potential within Quercus.