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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane

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Author(s):
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Taniguti, Lucas M. [1] ; Schaker, Patricia D. C. [1] ; Benevenuto, Juliana [1] ; Peters, Leila P. [1] ; Carvalho, Giselle [1] ; Palhares, Alessandra [1] ; Quecine, Maria C. [1] ; Nunes, Filipe R. S. [1] ; Kmit, Maria C. P. [1] ; Wai, Alvan [2] ; Hausner, Georg [2] ; Aitken, Karen S. [3] ; Berkman, Paul J. [3] ; Fraser, James A. [4] ; Moolhuijzen, Paula M. [5] ; Coutinho, Luiz L. [1] ; Creste, Silvana [6] ; Vieira, Maria L. C. [1] ; Kitajima, Joao P. [7] ; Monteiro-Vitorello, Claudia B. [1]
Total Authors: 20
Affiliation:
[1] Univ Sao Paulo, Coll Agr Luiz de Queiroz, BR-13400970 Sao Paulo - Brazil
[2] Univ Manitoba, Dept Microbiol, Winnipeg, MB R3T 2N2 - Canada
[3] CSIRO Agr, Flagship, Queensland Biosci Precinct, St Lucia, Qld 4067 - Australia
[4] Univ Queensland, Sch Chem & Mol Biosci, Australian Infect Dis Res Ctr, Brisbane, Qld - Australia
[5] Murdoch Univ, Ctr Comparat Genom, Perth, WA - Australia
[6] Ctr Avancado Pesquisa Tecnol Agronegocio Cana IAC, Sao Paulo - Brazil
[7] Mendel Anal Genom, BR-04013000 Sao Paulo, SP - Brazil
Total Affiliations: 7
Document type: Journal article
Source: PLoS One; v. 10, n. 6 JUN 12 2015.
Web of Science Citations: 38
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 Sporisorium 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 Sporisorium scitamineum were expressed only in planta. RNAseq data was also used to reassure gene predictions. (AU)

FAPESP's process: 10/05591-9 - Genetic studies of the Sporosorium scitamineum, the causal agent of sugarcane smut
Grantee:Claudia Barros Monteiro Vitorello
Support Opportunities: Regular Research Grants
FAPESP's process: 08/52074-0 - Sugarcane genome sequence: plant transposable elements are active contributors to gene structure variation, regulation and function
Grantee:Marie-Anne Van Sluys
Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
FAPESP's process: 12/09524-0 - Molecular studies on the interaction sugarcane x Sporisorium scitamineum, the smut causal agent
Grantee:Alessandra Carolina Palhares
Support Opportunities: Scholarships in Brazil - Doctorate
FAPESP's process: 13/15014-7 - Genetic and biochemical analysis of signaling of reactive oxygen species in the interaction sugarcane and Sporisorium scitamineum
Grantee:Leila Priscila Peters
Support Opportunities: Scholarships in Brazil - Doctorate
FAPESP's process: 14/21802-0 - Comparative genomics perspective of host specialization by smut fungi and genetic diversity of Sporisorium scitamineum isolates (sugarcane smut agent)
Grantee:Juliana Benevenuto
Support Opportunities: Scholarships in Brazil - Doctorate
FAPESP's process: 13/25599-2 - Study of sugarcane metabolism modulation by the plant pathogenic fungus Sporisorium scitamineum
Grantee:Patricia Dayane Carvalho Schaker
Support Opportunities: Scholarships in Brazil - Doctorate