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

L.M. Taniguti; P.D.C. Schaker; J. Benevenuto; L.P. Peters; G. Carvalho; A. Palhares; M.C. Quecine; F.R.S. Nunes; M.C.P. Kmit; A. Wai; G. Hausner; K.S. Aitken; P.J. Berkman; J.A. Fraser; P.M. Moolhuijzen; L.L. Coutinho; S. Creste; M.L.C. Vieira; J.P. Kitajima; C.B. Monteiro-Vitorello

doi:10.1371/journal.pone.0129318

Back

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

Journal article

Open access

Peer reviewed

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

L.M. Taniguti, P.D.C. Schaker, J. Benevenuto, L.P. Peters, G. Carvalho, A. Palhares, M.C. Quecine, F.R.S. Nunes, M.C.P. Kmit, A. Wai, …

PloS one, Vol.10(6), e0129318

2015

DOI: https://doi.org/10.1371/journal.pone.0129318

Files and links (2)

pdf

sporisorium_scitamineum.pdfDownload View

Published (Version of Record) Open Access

url

Free to Read *No subscription requiredView

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.

Details

Title: Complete genome sequence of sporisorium scitamineum and biotrophic interaction transcriptome with sugarcane
Authors/Creators: L.M. Taniguti (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
P.D.C. Schaker (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
J. Benevenuto (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
L.P. Peters (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
G. Carvalho (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
A. Palhares (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
M.C. Quecine (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
F.R.S. Nunes (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
M.C.P. Kmit (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
A. Wai (Author/Creator) - University of Manitoba
G. Hausner (Author/Creator) - University of Manitoba
K.S. Aitken (Author/Creator) - Commonwealth Scientific and Industrial Research Organisation
P.J. Berkman (Author/Creator) - Commonwealth Scientific and Industrial Research Organisation
J.A. Fraser (Author/Creator) - The University of Queensland
P.M. Moolhuijzen (Author/Creator) - Murdoch University
L.L. Coutinho (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
S. Creste (Author/Creator) - Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana-IAC/Apta Ribeirão Preto, São Paulo, Brazil.
M.L.C. Vieira (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
J.P. Kitajima (Author/Creator) - Mendelics
C.B. Monteiro-Vitorello (Author/Creator) - Escola Superior de Agricultura Luiz de Queiroz
Publication Details: PloS one, Vol.10(6), e0129318
Publisher: Public Library of Science
Identifiers: 991005540043207891
Copyright: © 2015 Taniguti et al.
Murdoch Affiliation: Centre for Comparative Genomics
Language: English
Resource Type: Journal article

UN Sustainable Development Goals (SDGs)

This output has contributed to the advancement of the following goals:

Source: InCites

Metrics

154 File views/ downloads

123 Record Views

90 Times Cited - Web of Science

InCites Highlights

These are selected metrics from InCites Benchmarking & Analytics tool, related to this output

Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.419 Jasmonic Acid
Web Of Science research areas: Biochemistry & Molecular Biology
ESI research areas: Plant & Animal Science