Haplotype-resolved chromosome-level genome assembly of four European white oak species

European white oaks, belonging to the Quercus section Quercus, hold significant ecological and economic value in forest ecosystems. These trees are known for their extensive genetic similarity and past gene exchange between species. However, existing genomic resources are unevenly distributed among the various species, hindering comparative studies and the development of pangenome frameworks.

To address this issue, researchers have now unveiled complete, chromosome-scale genome assemblies and annotations for four prominent European white oak species: Quercus robur, Q. petraea, Q. pubescens, and Q. frainetto. The assemblies were produced using advanced PacBio HiFi sequencing technology, and they encompass both phased haplotypes specific to each species.

These genome maps range in size from 779 to 817 megabases, with each one meticulously organized into 12 chromosome-scale pseudomolecules. The high level of completeness and contiguity achieved in these assemblies surpasses previous benchmarks. Additionally, the study provides specialized repeat annotations, complete sets of functionally annotated protein-coding genes, and fully sequenced organellar genomes for each species.

Notably, this resource marks the first-ever reference genomes for Q. pubescens and Q. frainetto, complementing the improved assemblies for Q. robur and Q. petraea, which were generated using a uniform sequencing and analysis protocol. With these comprehensive genome resources at hand, scientists now possess a standardized platform for conducting a wide array of comparative analyses, including pangenome construction, genome evolution investigations, and the exploration of adaptive mechanisms and interspecies gene flow in the context of European white oaks.