title: Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane.
abstract: Sporisorium scitamineum is a biotrophic fungus responsible for the sugarcane smut, a worldwide spread disease. This study provides the complete sequence of individual chromosomes of S. scitamineum from telomere to telomere achieved by a combination of PacBio long reads and Illumina short reads sequence data, as well as a draft sequence of a second fungal strain. Comparative analysis to previous available sequences of another strain detected few polymorphisms among the three genomes. The novel complete sequence described herein allowed us to identify and annotate extended subtelomeric regions, repetitive elements and the mitochondrial DNA sequence. The genome comprises 19,979,571 bases, 6,677 genes encoding proteins, 111 tRNAs and 3 assembled copies of rDNA, out of our estimated number of copies as 130. Chromosomal reorganizations were detected when comparing to sequences of S. reilianum, the closest smut relative, potentially influenced by repeats of transposable elements. Repetitive elements may have also directed the linkage of the two mating-type loci. The fungal transcriptome profiling from in vitro and from interaction with sugarcane at two time points (early infection and whip emergence) revealed that 13.5% of the genes were differentially expressed in planta and particular to each developmental stage. Among them are plant cell wall degrading enzymes, proteases, lipases, chitin modification and lignin degradation enzymes, sugar transporters and transcriptional factors. The fungus also modulates transcription of genes related to surviving against reactive oxygen species and other toxic metabolites produced by the plant. Previously described effectors in smut/plant interactions were detected but some new candidates are proposed. Ten genomic islands harboring some of the candidate genes unique to S. scitamineum were expressed only in planta. RNAseq data was also used to reassure gene predictions.
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Lucas M
authors.initials: LM
authors.lastname: Taniguti
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Patricia D C
authors.initials: PD
authors.lastname: Schaker
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Juliana
authors.initials: J
authors.lastname: Benevenuto
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Leila P
authors.initials: LP
authors.lastname: Peters
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Giselle
authors.initials: G
authors.lastname: Carvalho
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Palhares
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Maria C
authors.initials: MC
authors.lastname: Quecine
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Filipe R S
authors.initials: FR
authors.lastname: Nunes
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Maria C P
authors.initials: MC
authors.lastname: Kmit
authors.affiliation: Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3T 2N2.
authors.forename: Alvan
authors.initials: A
authors.lastname: Wai
authors.affiliation: Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada, R3T 2N2.
authors.forename: Georg
authors.initials: G
authors.lastname: Hausner
authors.affiliation: CSIRO Agriculture, Flagship, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
authors.forename: Karen S
authors.initials: KS
authors.lastname: Aitken
authors.affiliation: CSIRO Agriculture, Flagship, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Berkman
authors.affiliation: Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
authors.forename: James A
authors.initials: JA
authors.lastname: Fraser
authors.affiliation: Centre for Comparative Genomics, Murdoch University, Perth, Australia.
authors.forename: Paula M
authors.initials: PM
authors.lastname: Moolhuijzen
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Luiz L
authors.initials: LL
authors.lastname: Coutinho
authors.affiliation: Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana-IAC/Apta Ribeirão Preto, São Paulo, Brazil.
authors.forename: Silvana
authors.initials: S
authors.lastname: Creste
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Maria L C
authors.initials: ML
authors.lastname: Vieira
authors.affiliation: Mendelics Análise Genômica, Rua Cubatão 86, Cj. 1602, 04013-000, São Paulo, SP, Brazil.
authors.forename: João P
authors.initials: JP
authors.lastname: Kitajima
authors.affiliation: College of Agriculture "Luiz de Queiroz", University of São Paulo, Av. Pádua Dias 11, PO BOX 9, 13400-970, Piracicaba, São Paulo, Brazil.
authors.forename: Claudia B
authors.initials: CB
authors.lastname: Monteiro-Vitorello
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D016681:Genome, Fungal; D054884:Host-Pathogen Interactions / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D031786:Saccharum / Q000382:microbiology; D059467:Transcriptome; D014587:Ustilaginales / Q000235:genetics* / Q000472:pathogenicity; D014774:Virulence / Q000235:genetics