RNA-assisted assembly of Physaria fendleri genome

Advances in assembly algorithms have allowed diverse strategies of genome construction to become available. The use of a hybrid assembler (run with paired-end short read data and short read-derived super-reads) can provide a starting set of contigs from which a high quality assembly can be made, however short read genomic DNA reads do not often give the coverage to assemble contigs large enough for accurate scaffolding and eventual super-scaffolding. This becomes an even bigger challenge when working with highly heterozygous species, as haplotigs contaminate the already-limited template pool that can be used for scaffolding and gap-filling. This project's goal is to use an original strand-specific RNA seq data set to improve a meta-assembly of alternative oilseed crop Physaria fendleri, addressing issues with heterozygosity and taking advantage of reference-based methods. This processed assembly will then be used for analysis of a transcriptomics experiment looking at the effect of inhibiting fatty acid elongation on central carbon metabolism.