De novo transcriptome assembly, functional annotation and expression profiling of sweet passion fruit (Passiflora alata) in response to Xanthomonas axonopodis pv. passiflorae infection

• Ano de defesa: 2022
• Autor(a) principal: Cardoso, Jéssica Luana Souza
• 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: Passiflora alata; Xanthomonas; Análise de transcriptoma; Maracujá doce; Plant susceptibility; RNA-Seq; Suscetibilidade de plantas; Sweet passion fruit; Transcriptome analysis
• Link de acesso: https://www.teses.usp.br/teses/disponiveis/11/11137/tde-14102022-113459/

Xanthomonas is one of the most important phytopathogens; it severely attacks over 500 different hosts around the world. Plants have evolved various defense mechanisms aimed at preventing pathogen proliferation and controlling disease. To improve our understanding of the defense mechanisms deployed by different hosts in response to Xanthomonas attack, a broad review of the literature was conducted and forms the first chapter of this thesis. We outline our current knowledge of the molecular basis of immunity systems in different crops susceptible to Xanthomonas. Among its tropical hosts, cultivated passion fruits are very vulnerable to this pathogen, leading to severe losses in commercial orchards. The disease, known as bacterial spot, is caused by Xanthomonas axonopodis pv. passiflorae (Xap). There is no molecular information on the interaction between Passiflora alata (sweet passion fruit) and Xap, and studies are therefore required to improve our understanding of this pathosystem. Thus, our aim was to analyze the transcriptome profile of P. alata in response to Xap infection. The results of this analysis are given in Chapter 2. Total RNA of healthy and Xap-infected leaves was isolated 5 days post inoculation and sequenced on the Illumina NextSeq platform, resulting in some 50 million paired-end reads per sample. Since there is no P. alata genome available for use as a reference, de novo assembly was performed, followed by functional annotation of sequence reads. Differential expression analysis revealed 638 upregulated and 604 downregulated transcripts, based on an FDR-adjusted p-value ≤ 0.05 and a fold change ≥ 1.5 and ≤ -1.5. Pattern recognition receptors (PRRs) and resistance genes were detected. On perceiving the pathogen, these receptors trigger defense response signaling entailing a rapid increase in calcium influx and the production of reactive oxygen species (ROS). Next, calcium-dependent kinases activate pathogenesis-related genes and result in the production of volatile compounds (germacrene D and nerolidol) to signal hormone production. Importantly, two susceptibility genes, LOB1 and SWEET10, were identified as upregulated in sweet passion fruit in the presence of pathogen infection. LOB1 is a member of the Lateral Organ Boundaries family of transcription factors, and SWEET10 is a sugar transporter. We suggest that knocking out these genes might result in increased tolerance or even resistance to Xap, since two resistance genes containing the CC/TIR-NBS-LRR domain were also identified. A quantitative RT-PCR of selected genes was performed to validate differential gene expression analysis. Our findings not only provide the first complete transcriptome analysis of the molecular mechanisms in the sweet passion fruit\'s response to Xap infection, but also supply valuable information on potential target genes for plant gene editing.