A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species

Abstract

Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra 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 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Q. 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. 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. Phylogenetic analysis also identified four subfamilies of the IGT/LAZY gene family in Q. rubra important for plant structure. 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 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 expedite comparative genomics and biological studies in Quercus species.

Ex situ conservation of two rare oak species using microsatellite and SNP markers

“…Genome sizes for each species are estimated to be ~750 Mb, similar to the sizes of reference genomes used (Plomion et al, 2018 for Q. robur;Kapoor et al, 2023 for Q. rubra; see below). More genotyping details for SNPs can be found in the Data S1: Section 1.4.2.…”

“…To generate reference alignment datasets, quality-filtered sequences were aligned using GSNAP (Wu & Nacu, 2010) to different reference genomes based on the section of the Quercus genus each sample species was found in. Q. acerifolia (section Lobatae, Quercus subgenus) samples were aligned to the red oak (Q. rubra) reference genome (Kapoor et al, 2023). Q. boyntonii (section Quercus, Quercus subgenus) samples were aligned to the English oak (Q. robur) reference genome (V2_2N, Plomion et al, 2018).…”

The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species

“…Future work using whole-genome resequencing data of Q. tomentella (generated as part of the CCGP) is necessary to validate this putative inversion and investigate whether it has evolutionary significance. Intraspecific variation in inversions between haplotypes has been found in an increasing number of species, including Q. rubra ( Kapoor et al 2023 ), and these chromosomal inversions may be involved in adaptation by reducing recombination within blocks of locally adapted alleles ( Huang and Rieseberg 2020 ).…”

“…Additionally, this genome assembly is the first for Quercus section Protobablanus , a small clade restricted to western North America ( Nixon 2002 ; Ortego et al 2018 ). The genome assembly described here expands the taxonomic coverage of currently available oak genomic resources, which already include several reference genomes ( Bodénès et al 2016 ; Plomion et al 2018 ; Ramos et al 2018 ; Ai et al 2022 ; Maldonado-Alconada et al 2022 ; Sork et al 2022 ; Kapoor et al 2023 ; O’Donnell et al unpublished data), expanding opportunities for further evolutionary studies using oaks as a model clade ( Cavender-Bares 2018 ).…”

A haplotype-resolved reference genome ofQuercus albasheds light on the evolutionary history of oaks

“…The first published oak genome was that of Quercus robur (Plomion et al, 2016a), the pedunculate oak, which is common throughout western Eurasia. To date, there have been at least nine Quercus species with published chromosome-scale genomes, including four annotated genomes from the white oak clade (Plomion et al, 2016a;Han et al, 2022;Liu et al, 2022;Sork et al, 2022;Zhou et al, 2022;Ai et al, 2022;Kapoor et al, 2023;Wang et al, 2023). This growing number of annotated genomes allows for comparative analyses of gene content and inferences of genome evolution across the oak phylogeny.…”