Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA.
Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
G3 (Bethesda). 2023 Nov 1;13(11). doi: 10.1093/g3journal/jkad209.
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 Quercus lobata and Quercus 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 9 species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Quercus robur. Phylogenetic analysis also identified 4 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 8 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 genomic community, which will expedite comparative genomics and biological studies in Quercus species.
北方红栎（Quercus rubra L.）是一种生态和经济上都很重要的北美本土森林树种。我们通过 PacBio 序列和染色质构象捕获（Hi-C）支架的组合，生成了北方红栎的染色体水平基因组。这是红栎分支（节 Lobatae）的第一个参考基因组。北方红栎的组装跨度为 739Mb，基因组的 95.27%被组装到 12 条染色体中，包含 33,333 个蛋白质编码基因。与 Quercus lobata 和 Quercus mongolica 的基因组比较显示，存在高度的共线性，同时存在着染色体内结构变异。与其他树种的同源基因家族分析表明，与防御反应相关的基因家族在整个北方红栎基因组中同时扩张和收缩。在分析的 9 个物种中，北方红栎拥有最多的 CC-NBS-LRR 和 TIR-NBS-LRR 抗性基因。萜烯合酶基因家族的比较进一步揭示了 TPS-b 亚家族的串联基因复制，与 Quercus robur 相似。系统发育分析还鉴定了北方红栎中 IGT/LAZY 基因家族的 4 个子家族，这些家族对植物结构很重要。确定了营养芽休眠和枯梢的 4 个主要 QTL 区域，其中包含候选基因，进一步的研究，包括一个假定的生物钟成分隐花色素（CRY2）的同源基因和 8 个串联重复的丝氨酸蛋白酶抑制剂基因。对自然种群的全基因组与环境关联分析，鉴定了候选的非生物胁迫耐受基因，并预测了在普通花园中的表现。这个高质量的北方红栎基因组是栎属基因组社区的重要资源，将加速栎属物种的比较基因组学和生物学研究。
