Oryza australiensis genome sequencing

The goal of this study is to sequence and assemble to genome of an extremophile wild species of rice, Oryza australiensis. This genome has previously been challenging to assemble using short read technologies due to its high LTR content. Here, we used ONT reads to bridge seqeunces between LTR elements to assemble the most contiguous assembly for O. australiensis to date. We use short reads (Illumina) and the long reads to polish the assembly, and PacBio Iso-Seq reads from 5 tissues to assist in annotation. We also collected long read data from three other populations (i.e. one individual per population) of O. australiensis for the purpose of identifying genomic variation associated with salt tolerance differences reported by Yichie et al. (2019).