Comparative genomics and transcriptomics analyses reveal genetic complexity of soybean anthracnose caused by Colletotrichum species

• Ano de defesa: 2021
• Autor(a) principal: Boufleur, Thaís Regina
• Tipo de documento: Tese
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Biblioteca Digitais de Teses e Dissertações da USP
• Palavras-chave em Português: Colletotrichum orchidearum; Colletotrichum truncatum; Glycine max; Defesa da planta; Efetor; Effector; Plant defense; RNA sequencing; Sequenciamento de RNA
• Link de acesso: https://www.teses.usp.br/teses/disponiveis/11/11135/tde-28052021-115408/

Soybean (Glycine max) cultivation occupies around 6% of the world\'s arable land. Currently, there are more than 90 diseases that threaten soybean production, due to its global importance and multiple uses, as a source of human and animal feeds, may imply in food security. Among these diseases is soybean anthracnose, a disease of complex etiology which can be caused by several species of the genus Colletotrichum. The advent of next-generation sequencing technologies (NGS) allowed the high throughput sequencing of entire genomes and transcriptomes. Comparative genomic analyses are useful to reveal repertoires of effector candidates of important plant pathogens, potentially involved in plant infection; while the deep sequencing of transcriptomes of plant and pathogens during their interaction can allow the identification of important genes and pathways involved in plant defense. To gain insights into soybean anthracnose and its causal agents, we used a combined approach of biological experiments with NGS technologies. A revision of all public-available Colletotrichum ITS sequences associated with soybean revealed that more than 37% of those are assigned to the wrong species complex (s.c) level. We found at least 9 s.c. and one singleton species of Colletotrichum associated with soybean anthracnose worldwide, being the C. orchidearum s.c. and C. truncatum the most common and distributed. We reported for the first time that C. musicola, a member of the C. orchidearum s.c. was associated with soybean. Draft genomes of C. sojae, C. plurivorum and C. musicola were produced and compared with C. truncatum and eight additional Colletotrichum species not pathogenic to soybean. Comparative genomic analyses suggested that species belonging to the C. orchidearum s.c. and C. truncatum acquired the capability to infect soybean separately, due to the absence of secreted effector candidates (SECs) shared only among these four species. The transcriptomic sequencing of four different combinations of soybean/C. truncatum revealed that soybean defense against C. truncatum relies on the activation of several defense genes upon the recognition of the pathogen by the plant. Results revealed a higher modulation of the soybean transcriptome in more resistant interactions, when compared with more susceptible ones, independently of soybean cultivar and C. truncatum strain.