Toward a contig reduction in genomic assembly of Puccinia striiformis f. sp. tritici isolate SWS484

Puccinia striiformis f. sp. tritici (Pst) causal agent of stripe (yellow) rust of wheat elicits significant losses due to decreases in yield and quality in susceptible lines worldwide. Since 2000, new and highly virulent isolates have evolved, and for these, limited host resistance is available. This has created a serious threat to the North American wheat production and global food production. The genome size of Pst is ≈117 Mb. Illumina paired-ends and mate pairs sequencing and PacBio analyses were carried out to characterize isolate SWS484. Last year, we obtained a genomic assembly of 15,289 contigs using a 56x PacBio genome size coverage. Increasing the coverage to 85x led to a decrease of contig numbers by a factor of 8.5 to 1,808 contigs. As expected N25, N50, N75 and N90 statistics were improved in this novel assembly. The quality of assembly was substantially increased as all unknown nucleotides N were resolved. The size of the assembled sequences decreased by 23% to 129,707,087 bp, a value closer to the estimated genome size. Our new contig assembly of isolate SWS484 appears to be complete and representative of Pst isolate genomes as transcripts of reference Pst78 isolate were mapped against all genomic contigs but six.