A highly contiguous reference genome assembly for pathotype 08 causing red rot disease in sugarcane.

UNLABELLED

Among the biotic factors, which affect the productivity and quality of sugarcane, red rot disease caused by the fungal pathogen, is the most devastating that cause enormous loss to millers as well as cane growers. We present a highly contiguous genome assembly of pathotype 08 which is virulent to popular sugarcane varieties grown in more than 3 million hectares in sub-tropical India. By performing long read sequencing on PacBio RSII system, 56.06 Mb assemblies with 238 contigs having N50 of 0.51 Mb and L50 of 34 was produced. A BUSCO completeness score of 97.24% (including 4.1% fragmented) of the entire 08 nuclear genome, greatly improved contiguity compared to an existing highly fragmented draft of 671 genome (48.13 Mb) was obtained. This 08 assembly had 54.14% GC content and possessed < 1% repetitive elements. A total of 18,635 protein-coding genes were predicted compared with 12,270 for 671. Among 617 CAZymes predicted, glycoside hydrolases were the predominant (298), and among 7264 genes associated with pathogenicity/virulence, 77 genes having effector functions were identified. The assembled genome showed its similarity with the genome of and the causal organisms of anthracnose in maize and in members of Brassicaceae, respectively. A total of 94 large sequences (> 100 kb) of 08 were mapped over 10 of 12 chromosomes with 106 synteny blocks. Results discussed here would provide an important tool for future studies of evolutionary and functional genomics in .

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02695-x.