PacBio Sequencing and Genome Annotation of Sporisorium scitamineum

S. scitamineum is a pathogen causing sugarcane smut disease. The complete genome of a Brazilian isolate was sequenced using PacBio technology in concert with Illumina paired end reads. A BAC library was also used to confirm regions of interest in a strain with opposite mating type. 738,568 PacBio reads with average length of 3,047 bp were assembled using HGAP package, resulting in 22 chromosomes ranging from 475,902 to 2,009,762 bp (PacBio coverage 112x) and other four contigs of around 100 kbp encompassing mostly repetitive regions. Eight S. scitamineum chromosomes were rearranged compared to the 23 chromosomes of S. reilianum.  Illumina reads of 620x coverage were used to confirm assembly and sequence. The genome size is 19,95 Mbp. Gene prediction was accomplished by using the Ustilago maydis gene model calculated by the Augustus software integrating RNAseq paired-end reads. The genome have 6,677 ORFs, and 3,262 of them have introns. Transcripts covered 97% of all predicted genes. Comparative analysis to predicted proteins of other smut fungi using BLASTp (e-value < 10e-14) resulted in 178 specific ORFs of S. scitamineum, of these, 140 have at least 25% of the sequence covered by RNAseq reads. BLASTp analysis also showed that the predicted proteins of S. scitamineum have around 82, 75 and 72% with S. reilianum, Ustilago maydis and U. hordei proteins, respectively.