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

Taniguti, Lucas M., Schaker, Patricia D. C., Benevenuto, Juliana, Peters, Leila P., Carvalho, Giselle, Palhares, Alessandra, Quecine, Maria C., Nunes, Filipe R. S., Kmit, Maria C. P., Wai, Alvan, Hausner, Georg, Aitken, Karen S., Berkman, Paul J., Fraser, James A., Moolhuijzen, Paula M., Coutinho, Luiz L., Creste, Silvana, Vieira, Maria L. C., Kitajima, João P. and Monteiro-Vitorello, Claudia B. (2015) Complete genome sequence of Sporisorium scitamineum and biotrophic interaction transcriptome with sugarcane. PLoS One, 10 6: . doi:10.1371/journal.pone.0129318


Author Taniguti, Lucas M.
Schaker, Patricia D. C.
Benevenuto, Juliana
Peters, Leila P.
Carvalho, Giselle
Palhares, Alessandra
Quecine, Maria C.
Nunes, Filipe R. S.
Kmit, Maria C. P.
Wai, Alvan
Hausner, Georg
Aitken, Karen S.
Berkman, Paul J.
Fraser, James A.
Moolhuijzen, Paula M.
Coutinho, Luiz L.
Creste, Silvana
Vieira, Maria L. C.
Kitajima, João P.
Monteiro-Vitorello, Claudia B.
Title Complete genome sequence of Sporisorium scitamineum and biotrophic interaction transcriptome with sugarcane
Formatted title
Complete genome sequence of Sporisorium scitamineum and biotrophic interaction transcriptome with sugarcane
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2015-06-01
Sub-type Article (original research)
DOI 10.1371/journal.pone.0129318
Open Access Status DOI
Volume 10
Issue 6
Total pages 31
Place of publication San Francisco, CA, United States
Publisher Public Library of Science
Language eng
Subject 1300 Biochemistry, Genetics and Molecular Biology
1100 Agricultural and Biological Sciences
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.
Formatted 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.
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID 2008/52074-0
2010/05591-9
2012/09524-0
2013/15014-7
2013/25599-2
2014/17034-8
2014/21802-0
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2016 Collection
School of Chemistry and Molecular Biosciences
 
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Created: Fri, 19 Jun 2015, 19:42:33 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences