Genomic studies in Phakopsora pachyrhizi and in its hyperparasite Simplicillium lanosoniveum

• Ano de defesa: 2023
• Autor(a) principal: Melo, Bernardo do Vale Araújo
• Tipo de documento: Tese
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Universidade Federal de Viçosa; Fitopatologia
• Palavras-chave em Português: Fungos fitopatogênicos - Controle - Aspectos genéticos; Fungos fitopatogênicos - Controle biológico; Virulência (Microbiologia); Genômica; Fitopatologia
• Link de acesso: https://locus.ufv.br//handle/123456789/31189; https://doi.org/10.47328/ufvbbt.2023.385

Phakopsora pachyrhizi and P. meibomiae are the etiological agents of Asian soybean rust (ASR) and American soybean rust, respectively. Asian soybean rust is the most important fungal disease of soybean in Brazil and the use of genetic resistance is one of the methods of control recommended for the ASR management. Currently, seven loci containing dominant genes that confer resistance to Phakopsora pachyrhizi (Rpp) were identified, but the complementary avirulence genes of the pathogen have not yet been cloned and characterized. The P. pachyrhizi genome complexity, the absence of sexual reproduction, the obligate biotrophy, and the absence of transformation protocols limit the gene mapping and functional studies with this fungus. Recent advances in the DNA sequencing technologies and tools for genome assembly opened new possibilities to study genome structure, organization, and function for complex genomes such as the P. pachyrhizi one, avoiding difficulties posed by the fungus’ biology. In addition, the assembly of complete genomes and comparative analysis allow the identification and characterization of complex loci and evolutionary processes related to pathogenicity, virulence, and hyperparasitism. Although the hyperparasitism of P. pachyrhizi by Simplicillium lanosoniveum has already been very well documented from a microscopic point of view, associated genes, and molecular mechanisms are still unknown. Therefore, in this study, genomic analyses were used to: a) Identification of P. pachyrhizi candidate avirulence genes corresponding to resistance genes Rpp1b (Avr1) and Rpp5 (Avr5); b) Characterization of the genetic and genomic structure of the Mating-type system in Phakopsora sp., P. meibomiae, and P. pachyrhizi; and c) Assembly and annotation of S. lanosoniveum genome and identification of molecular mechanisms possibly associated with hyperparasitism of P. pachyrhizi. Two candidate genes for Avr1 and four Avr5 of P. pachyrhizi predicted to encode secreted proteins were identified. The mating-type system in the Phakopsora species that were analyzed is heterothallic, possibly tetrapolar, and one hormone receptor protein with an atypical structure was identified in P. pachyrhizi. The genome of the mycoparasite S. lanosoniveum was sequenced and chromosome-level assembly was obtained. The annotation of the S. lanosoniveum genome revealed enzymes and secondary metabolites unique to this species that may be related to its parasitism on P. pachyrhizi. The genetic and genomic resources developed create new perspectives for cloning and characterization of avirulence genes of P. pachyrhizi, genes of S. lanosoniveum that encode specific enzymes and secondary metabolites, and also expand the understanding of the importance of sexual reproduction in the reproductive biology of P. pachyrhizi. Keywords: Avirulence genes. Mating-type. Comparative genomics. Genetic control. Biological control. Rpp1b. Rpp5.