title: Prediction of the in planta Phakopsora pachyrhizi secretome and potential effector families.
abstract: Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, can cause losses greater than 80%. Despite its economic importance, there is no soybean cultivar with durable ASR resistance. In addition, the P. pachyrhizi genome is not yet available. However, the availability of other rust genomes, as well as the development of sample enrichment strategies and bioinformatics tools, has improved our knowledge of the ASR secretome and its potential effectors. In this context, we used a combination of laser capture microdissection (LCM), RNAseq and a bioinformatics pipeline to identify a total of 36 350 P. pachyrhizi contigs expressed in planta and a predicted secretome of 851 proteins. Some of the predicted secreted proteins had characteristics of candidate effectors: small size, cysteine rich, do not contain PFAM domains (except those associated with pathogenicity) and strongly expressed in planta. A comparative analysis of the predicted secreted proteins present in Pucciniales species identified new members of soybean rust and new Pucciniales- or P. pachyrhizi-specific families (tribes). Members of some families were strongly up-regulated during early infection, starting with initial infection through haustorium formation. Effector candidates selected from two of these families were able to suppress immunity in transient assays, and were localized in the plant cytoplasm and nuclei. These experiments support our bioinformatics predictions and show that these families contain members that have functions consistent with P. pachyrhizi effectors.
authors.affiliation: Universidade Estadual do Norte do Paraná, Bandeirantes, Paraná, CEP 86360-000, Brazil.
authors.forename: Mayra C da C G
authors.initials: MC
authors.lastname: de Carvalho
authors.affiliation: Laboratório de Genômica e Expressão (LGE) - Instituto de Biologia - Universidade Estadual de Campinas, Campinas, São Paulo, CEP 13083-862, Brazil.
authors.forename: Leandro
authors.initials: L
authors.lastname: Costa Nascimento
authors.affiliation: Embrapa soja, Plant Biotechnology, Londrina, Paraná, CEP 70770-901, Brazil.
authors.forename: Luana M
authors.initials: LM
authors.lastname: Darben
authors.affiliation: Embrapa soja, Plant Biotechnology, Londrina, Paraná, CEP 70770-901, Brazil.
authors.forename: Adriana M
authors.initials: AM
authors.lastname: Polizel-Podanosqui
authors.affiliation: Embrapa soja, Plant Biotechnology, Londrina, Paraná, CEP 70770-901, Brazil.|Universidade Estadual de Londrina, Londrina, Paraná, CEP 86057-970, Brazil.
authors.forename: Valéria S
authors.initials: VS
authors.lastname: Lopes-Caitar
authors.affiliation: Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.
authors.forename: Mingsheng
authors.initials: M
authors.lastname: Qi
authors.affiliation: Embrapa soja, Plant Biotechnology, Londrina, Paraná, CEP 70770-901, Brazil.
authors.forename: Carolina S
authors.initials: CS
authors.lastname: Rocha
authors.affiliation: Laboratório de Genômica e Expressão (LGE) - Instituto de Biologia - Universidade Estadual de Campinas, Campinas, São Paulo, CEP 13083-862, Brazil.
authors.forename: Marcelo Falsarella
authors.initials: MF
authors.lastname: Carazzolle
authors.affiliation: Embrapa soja, Plant Biotechnology, Londrina, Paraná, CEP 70770-901, Brazil.
authors.forename: Márcia K
authors.initials: MK
authors.lastname: Kuwahara
authors.affiliation: Laboratório de Genômica e Expressão (LGE) - Instituto de Biologia - Universidade Estadual de Campinas, Campinas, São Paulo, CEP 13083-862, Brazil.
authors.forename: Goncalo A G
authors.initials: GA
authors.lastname: Pereira
authors.affiliation: Embrapa soja, Plant Biotechnology, Londrina, Paraná, CEP 70770-901, Brazil.
authors.forename: Ricardo V
authors.initials: RV
authors.lastname: Abdelnoor
authors.affiliation: Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Whitham
authors.affiliation: Embrapa soja, Plant Biotechnology, Londrina, Paraná, CEP 70770-901, Brazil.
authors.forename: Francismar C
authors.identifier: 0000-0002-5828-7249
authors.initials: FC
authors.lastname: Marcelino-Guimarães
mesh_terms: D000595:Amino Acid Sequence; D002467:Cell Nucleus / Q000378:metabolism; D016000:Cluster Analysis; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D063990:Gene Ontology; D055442:Metabolome / Q000235:genetics; D005810:Multigene Family; D000067563:Phakopsora pachyrhizi / Q000235:genetics / Q000378:metabolism*; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology; D057865:Plant Immunity; D018515:Plant Leaves / Q000382:microbiology; D013025:Glycine max / Q000382:microbiology; D014026:Nicotiana / Q000276:immunology / Q000382:microbiology*; D059467:Transcriptome / Q000235:genetics
chemical_list: D005656:Fungal Proteins
keywords: ETI suppression; LCM; P. pachyrhizi; effectors; secretome; soybean rust; transcriptome