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Description
Global Climate Change and the associated debilitating effects of heat and drought stress will generate extensive losses in worldwide agricultural production. The generation of crop plants that are resistant to heat and drought stress requires a much more detailed understanding of plant thermotolerance and drought tolerance. Towards this end, studies have been conducted with the genus Boechera (Brassicaceae) to explore how plants have naturally acquired thermotolerance. Boechera depauperata, an allotriploid species that is closely related to the model plant Arabidopsis thaliana, exhibits high resistance to heat and drought stress. The goals of this study are to assemble a high-quality genome assembly that can assist in understanding the genetic traits that underlie Boechera’s high tolerance to abiotic stress. Two de novo assemblies of the B. depauperata genome were constructed using short Illumina reads and long PacBio reads in collaboration with the Department of Energy Joint Genome Institute. The Joint Genome Institute used the MECAT assembler and constructed a diploid a genome that was 232 Mb in size with an N50 of 8.1 Mb. I constructed a second assembly using the Canu assembler which produced a genome that was 642 Mb in size before polishing and size reduction with an N50 of 1.7 Mb. Evidence-based and de novo methods were used on the MECAT assembly to identify 21,724 protein-coding genes. Repeat regions and long terminal repeat retrotransposons were also annotated. The identified protein-coding genes were cross-referenced with known upregulated gene families during heat stress to find similarities between the two. Keywords: Boechera; Brassicaceae; genome; assembly; annotation; polyploidy
