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

Abstract

SummaryWhite oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important.We report the first haplotype-resolved chromosome-scale genome assembly ofQ. albaand conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. In addition, we probe the genetic diversity of this widespread species and investigate its phylogenetic relationships with other oaks using whole-genome data.Our genome assembly comprises two haplotypes each consisting of 12 chromosomes. We found that the species has high genetic diversity, much of which predates the divergence ofQ. albafrom other oak species and likely impacts divergence time estimation inQuercus. Our phylogenetic results highlight phylogenetic discordance across the genus and suggest different relationships among North American oaks than have been reported previously. Despite a high preservation of chromosome synteny and genome size across theQuercusphylogeny, certain gene families have undergone rapid changes in size including resistance genes (R genes).The white oak genome represents a major new resource for studying genome diversity and evolution inQuercusand forest trees more generally. Future research will continue to reveal the full scope of genomic diversity across the white oak clade.