Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to the northeastern United States. We present a chromosome-scale, haplotype-resolved genome of Q. rubra, a representative red oak species, generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Megabases (Mb) with 95.27% of the genome sequences scaffolded into 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Q. lobata and Q. mongolica reveal high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other oak and rosid tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the nine species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Q. robur. Single major QTL regions were identified for vegetative bud break and marcescence which contain candidate genes for further research, including a putative ortholog of the circadian clock constituent cryptochrome (CRY2) and a family of eight tandemly duplicated genes for serine protease inhibitors, respectively. Genome-environment associations across natural populations identified candidate abiotic stress tolerance genes and predicted performance in a common garden. This high-quality red oak genome represents an essential resource to the oak genomics community which will further supplement the knowledge of Quercus genomics.

Background. Symbioses between Geosmithia fungi and wood-boring and bark beetles seldom result in disease induction within the plant host. Yet exceptions exist such as Geosmithia morbida, the causal agent of Thousand Cankers Disease (TCD) of walnuts and wingnuts, and Geosmithia sp. 41, the causal agent of Foamy Bark Canker disease of oaks. Isolates of G. obscura were recovered from black walnut trees in eastern Tennessee and at least one isolate induced cankers following artificial inoculation. Due to the putative pathogenicity and lack of recovery of G. obscura from natural lesions, a molecular diagnostic screening tool was developed using microsatellite markers mined from the G. obscura genome. Results. A total of 3,256 candidate microsatellite markers were identified (2236, 789, 137 di-, tri-, and tetra- motifs were identified, respectively), with 2011, 703, 101 di-, tri-, and tetra- motifs containing markers with primers. From these, 75 microsatellite markers were randomly selected, screened, and optimized, resulting in 28 polymorphic markers that yielded single, consistently recovered bands which were used in downstream analyses. Five of these microsatellite markers were found to be specific to G. obscura and did not cross-amplify into other, closely related species. Although the remaining tested markers could be useful, they cross-amplified within different Geosmithia species, making them not reliable for G. obscura detection. Conclusion. Five novel microsatellite markers (GOBS9, GOBS10, GOBS41, GOBS43, GOBS50) were developed based on the G. obscura genome. These species-specific microsatellite markers are available as a tool for use in molecular diagnostics and can assist future surveillance studies.