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 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.
| Original language | English |
|---|---|
| Article number | jkad209 |
| Journal | G3: Genes, Genomes, Genetics |
| Volume | 13 |
| Issue number | 11 |
| DOIs | |
| State | Published - 2023 |
Funding
We acknowledge the Penn State Genomics Core Facility, University Park, PA, for conducting the Illumina and PacBio genomic DNA sequencing and Istvan Albert and Aswathy Sebastian of The Huck Institute of Life Sciences at Penn State for initial de novo genome sequence assemblies and read mapping to assess data quality. We thank Albert Abbott, Andrew Hipp, James McKenna, Nicole Zembower, Maureen Mailander, Lianna Johnson, Claire Lorts, Xin Chen, and Grant Smith for assistance with sample collecting and analyses. We highly appreciate Matthew Huff and Zane Smith for their valuable review of the manuscript. Funding was provided by USDA McIntire-Stennis capacity grant #NI20MSCFRXXXG043 to JC; by the USDA McIntire-Stennis program accession no. 1017893 to CK; by the USDA National Institute of Food and Agriculture Federal Appropriations project PEN04532 to JC; by a seed grant (accession no. 1000326) from The Penn State Institutes of Energy and the Environment to LL, JC, and JRL; by Deutsche Forschungsgemeinschaft [DFG, German Research Foundation, reference number 429696097 (GA 714/7-1)] to OG; by the National Science Foundation grant #DEB-1927009 to JRL; and the University of Missouri Center for Agroforestry and the USDA/ARS Dale Bumpers Small Farm Research Center, agreement numbers 58-6020-6-001 and 58–6020-0-007 from the USDA Agricultural Research Service. Funding was provided by USDA McIntire-Stennis capacity grant #NI20MSCFRXXXG043 to JC; by the USDA McIntire-Stennis program accession no. 1017893 to CK; by the USDA National Institute of Food and Agriculture Federal Appropriations project PEN04532 to JC; by a seed grant (accession no. 1000326) from The Penn State Institutes of Energy and the Environment to LL, JC, and JRL; by Deutsche Forschungsgemeinschaft [DFG, German Research Foundation, reference number 429696097 (GA 714/7-1)] to OG; by the National Science Foundation grant #DEB-1927009 to JRL; and the University of Missouri Center for Agroforestry and the USDA/ARS Dale Bumpers Small Farm Research Center, agreement numbers 58-6020-6-001 and 58–6020-0-007 from the USDA Agricultural Research Service.
Keywords
- bud break
- common garden
- disease resistance genes
- environmental adaptation
- genome
- Genomics
- IGT/LAZY
- marcescence
- northern red oak
- plant disease resistance genes
- Plant Genetics
- quantitative trait loci
- Quercus rubra
- rRNA
- terpene synthase genes