de novo Assembly of a Complex Panicoid Grass Genome Using Ultra-Long PacBio Reads with P6C4 Chemistry

Drought is responsible for much of global losses in crop yields and understanding how plants naturally cope with drought stress is essential for breeding and engineering crops for the changing climate. Oropetium thomaeum (Oro) has the smallest known genome (250 Mb) among the grasses and has the unusual characteristic of also being a resurrection plant. Resurrection plants desiccate to complete dryness during times of drought, then "come back to life" once water is available. The genome sequence features complex repeat structures such as telomeres, centromeres, and ribosomal gene cassettes that play a role in how Oro maintains its genome structure during the desiccation process. These repetitive, difficult to sequence features rendered a low quality, highly fragmented Illumina based assembly. Ultra-long PacBio reads using the new P6C4 chemistry and the latest 15kb Blue Pippin shearing protocol have an average read length of 14kb providing 80X coverage and 10X of reads over 20kb. The preliminary assembly has a contig N50 of 428kb and total size of 230Mb (92% of the genome), making it one of the best assembled plant genomes to date. The Oro genome shows unique gene family expansions that contribute to its unique desiccation properties and augment comparative genomics in the grasses. Understanding the genomic mechanisms by which a resurrection plant such as Oro achieves such remarkable tolerance to extreme desiccation will provide insights for engineering and intelligent breeding of improved food, fuel, and fiber crops.