Establishment and utilization of Quercus and Citrus genomic and pangenomic resources

In the past 50 years, climate change has significantly impacted host-pathogen interactions in both fruit trees and hardwood forests. Quercus rubra L. (Northern red oak) and Citrus spp. have been seriously impacted by fungal and bacterial diseases, respectively. Quercus rubra L. is an ecologically and economically important forest tree native to North America, which is severely impacted by oak wilt disease. Huanglongbing disease (HLB) is a severe citrus disease worldwide. Our overarching goals were to establish genomic resources for Q. rubra and a pangenome for Citrus spp. We generated a chromosome-scale genome of Q. rubra using the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (sectionLobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Q. mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubragenome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the 9 species analyzed. We utilized a three-generation Q. rubra pedigree to establish a truth set of structural variants (SVs) using three different long read SV callers. As expected, shorter variants (≤ 1 Kb) were more common than the longer ones (> 10 Kb). We found extensive structural variations present inside exons, genes, 5 Kb upstream and downstream regions. To our knowledge, this is the first study to characterize genome wide SVs in Q. rubra species. Finally, we generated a pangenome graph using three citrus cultivars that are susceptible to the HLB disease and three Citrus spp. that exhibited varying degree of tolerance to the HLB disease. The high-quality haplotype-resolved Q. rubra genome and Citrus pangenome represent essential resources to the oak genomic community and citrus breeding programs that will facilitate comparative genomics and biological studies in Quercus and Citrus species.