Abstract Detail

Comparative Genomics/Transcriptomics

Kapoor, Beant [1], Jenkins, Jerry [2], Schmutz, Jeremy [3], Zhebentyayeva, Tetyana [4], Kulheim, Carsten [5], Lasky, Jesse [6], Leites, Laura [7], Schlarbaum, Scott [8], Carlson, John E. [4], Staton, Margaret [9], Coggeshall, Mark [10], Romero-Severson, Jeanne [11], Islam-Faridi, Nurul [12].

Exploring the structural variation and genome inheritance patterns using three generation red oak pedigree.

Northern red oak (Quercus rubra L.) is a diploid (2n = 2x = 12) monoecious, deciduous tree species belonging to the Fagaceae family in the Lobatae (red oaks) section of the Quercus genus. They are often dominant tree species, inhabiting a wide range of ecosystems in the eastern North America, and provide valuable ecological functions, including mast for wildlife, watershed health, and carbon sequestration. Northern red oaks are also economically important tree species as their wood is used for furniture, veneer, interior finishing, cabinets, flooring etc. Tree improvement and breeding programs for oaks focus on many traits for improved ecological and economic performance but must overcome long generation times and large space requirements. While recent genome sequencing studies have focused on the white oak group, section Quercus, genome resources for the red oak group still need to be developed. The reference tree chosen for genome sequencing in this project is an F2 progeny from an F1-intercross within a full-sib Q. rubra genetic mapping family. We generated a chromosome level haplotype-resolved genome assembly with primary assembly of length 739.58 Mb and scaffold N50 of 58.1Mb, an improvement in contiguity in comparison to reference genomes for pedunculate oak (Q. robur) (scaffold N50 = 1.35 Mb) and valley oak (Q. lobata). A total of 92.26% of the red oak primary assembly is contained in the 12 pseudo-chromosomes. BUSCO analysis indicated that 97.71% of the core eukaryotic genes are completely present in the red oak primary assembly. A total of 33,333 protein-coding genes and 47,780 protein-coding transcripts are predicted in the red oak primary genome assembly. Reference genome assemblies have also been produced for the original two parents of the F1 intercross family and the parents of the sequenced F2 plant. Extensive nucleotide and structural variation was observed among the three-generation tree pedigree genomes, not unexpected for an obligate outcrossing species. Using these five genomes and genotyping by sequencing of additional pseudo-F2 population members, this experimental design enables the exploration of the recombination and inheritance patterns of this variation. These resources will support ongoing oak genetic improvement efforts and provide insights into the evolution of Quercus and current standing species diversity.

1 - University of Tennessee, Knoxville, Entomology and Plant Pathology, 370 Plant Biotechnology Building, Knoxville, TN, 37996, USA
2 - Hudson Alpha Institute for Biotechnology, Huntsville, AL, 35806, USA
3 - Hudson Alpha Institute for Biotechnology, Huntsville, AL, 36806, USA
4 - Pennsylvania State University, Department of Ecosystem Science and Management, State College, PA, 16802, USA
5 - Michigan Tech University, College of Forest Resources and Environmental Science, Houghton, MI, 49931, USA
6 - 633 E Waring Ave, State College, PA, 16801, United States
7 - Pennsylvania State University, Department of Ecosystem Science and Management, University Park, PA, 16802, USA
8 - University of Tennessee, Entomology and Plant Pathology, 2505 EJ Champman Drive, Knoxville, TN, 37996, USA
9 - University Of Tennessee, Knoxville, 2505 EJ Chapman Drive, 370 PBB, 2505 EJ Chapman Drive, 370 PBB, Knoxville, TN, 37996, United States
10 - University of Missouri, School of Natural Resources, Columbia, MO, 65211, USA
11 - University of Notre Dame, Department of Biological Sciences, Notre Dame, IN, 46556, USA
12 - Texas A&M University, College Station, TX, 77843, USA

Northern red oak
Reference genome
Structural variation
Haplotype blocks
Recombination breakpoints.

Presentation Type: Oral Paper
Number: CGT2002
Abstract ID:673
Candidate for Awards:Margaret Menzel Award

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