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Complete genome sequence of Sporisorium scitamineum and biotrophic interaction transcriptome with sugarcane

Abstract

Sporisorium scitamineum is a biotrophic fungi responsible for the sugarcane smut, aworldwide spread disease. This study provides the complete sequence of individualchromosomes of S. scitamineum from telomere to telomere achieved by a combination ofPacBio long reads and Illumina short reads sequence data, as well as a draft sequence ofa second fungal strain. Comparative analysis to previous available sequences of anotherstrain detected few polymorphisms among the three genomes. The novel completesequence described herein allowed us to identify and annotate extended subtelomericregions, repetitive elements and the mitochondrial DNA sequence. The genomecomprises 19,979,571 bases, 6,677 genes encoding proteins, 111 tRNAs and 3 assembledcopies of rDNA, out of our estimated number of copies as 130. Chromosomalreorganizations were detected when comparing to sequences of S. reilianum, the closestsmut relative, potentially influenced by repeats of transposable elements. Repetitiveelements may have also directed the linkage of the two mating-type loci. The fungaltranscriptome profiling from in vitro and from interaction with sugarcane at two timepoints (early infection and whip emergence) revealed that 13.5% of the genes weredifferentially expressed in planta and particular to each developmental stage. Amongthem are plant cell wall degrading enzymes, proteases, lipases, chitin modification andlignin degradation enzymes, sugar transporters and transcriptional factors. The fungus also modulates transcription of genes related to surviving against reactive oxygen speciesand other toxic metabolites produced by the plant. Previously described effectors insmut/plant interactions were detected but some new candidates are proposed. Tengenomic islands harboring some of the candidate genes unique to S. scitamineum wereexpressed only in planta. RNAseq data was also used to reassure gene predictions. (AU)

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