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

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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]

Afiliação do(s) autor(es)

^[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

• Tipo de documento: Artigo Científico
• Fonte: PLoS One; v. 10, n. 6 JUN 12 2015.
• Citações Web of Science: 38

Resumo

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)

• Processo FAPESP: 10/05591-9 - Estudos genéticos do fungo Sporosorium scitamineum, agente causador de carvão em cana-de-açúcar
• Beneficiário: Claudia Barros Monteiro Vitorello
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 08/52074-0 - Sugarcane genome sequence: plant transposable elements are active contributors to gene structure variation, regulation and function
• Beneficiário: Marie-Anne Van Sluys
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOEN - Temático
• Processo FAPESP: 12/09524-0 - Estudos moleculares sobre a interação cana-de-açúcar x Sporisorium scitamineum, o agente causal do carvão
• Beneficiário: Alessandra Carolina Palhares
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 13/15014-7 - Análise genética e bioquímica da sinalização de espécies reativas de oxigênio na interação cana-de-açúcar e Sporisorium scitamineum
• Beneficiário: Leila Priscila Peters
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 14/17034-8 - Tratamento Bioinformático em Larga Escala de Sequências de Cana de Açúcar
• Beneficiário: Lucas Mitsuo Taniguti
• Modalidade de apoio: Bolsas no Brasil - Programa Capacitação - Treinamento Técnico
• Processo FAPESP: 14/21802-0 - Especialização ao hospedeiro por fungos causadores do carvão pela perspectiva da genômica comparativa e diversidade genética de isolados de Sporisorium scitamineum (agente causal do carvão na cana-de-açúcar)
• Beneficiário: Juliana Benevenuto
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 13/25599-2 - Estudo da modulação do metabolismo da cana-de-açúcar pelo fungo fitopatogênico Sporisorium scitamineum
• Beneficiário: Patricia Dayane Carvalho Schaker
• Modalidade de apoio: Bolsas no Brasil - Doutorado