Comparative genomics and phylogenomics of Xylella fastidiosa

• Ano de defesa: 2019
• Autor(a) principal: Campos, Guillermo Uceda
• Tipo de documento: Dissertação
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Biblioteca Digitais de Teses e Dissertações da USP
• Palavras-chave em Português: Anotação genômica; Elementos genéticos móveis; Gene de virulência; Genome annotation; GTACG; Mobile genetic elements; Prófago; Prophage; Virulence gene; Xylella fastidiosa
• Link de acesso: https://www.teses.usp.br/teses/disponiveis/95/95131/tde-23112020-184504/

The gamma-proteobacterium Xylella fastidiosa is an insect-transmitted, xylem-inhabiting pathogen and the causal agent of several plant diseases, most notably Pierce\'s disease of grapes (PD), citrus variegated chlorosis (CVC) and olive quick decline syndrome (OQDS). The first two complete genomes of X. fastidiosa sequenced in the early 2000s were from CVC (9a5c) and PD (Temecula1) strains. Since then, genomes of various isolates of X. fastidiosa have been sequenced, which are very similar to each other regardless of the host and/or geographical region from which such strains were isolated. Despite the available genomes in public databases, potential determinants of host adaptation and the heterogenicity among the prophage regions are still unknown in a wide genomic level. In this study, the CDSs of 46 X. fastidiosa genomes were compared using the new computational tool GTACG that deals with phylogenetically close organisms. Also, in order to explore the content of Mobile Genetic Elements (MGE) we have analyzed predicted prophages, genomic islands and insertion sequences harbored in X. fastidiosa chromosome. A total of 4942 and 1518 orthologs were found in the pan- and core-genome of X. fastidiosa, respectively. The phylogenomic trees showed three main clades related with the subspecies pauca, fastidiosa and multiplex, and subclades most related with the predicted sequence type and geographic region of isolation while the plant host information had less relationship. Most of the virulence and pathogenicrelated orthologs were found in the core-genome of X. fastidiosa. In one case, the afimbrial adhesin orthologs XadA1 and XadA3 sequence diversities showed a relative congruence with the plant host. The MGE content per genome ranged from 12% to 28% in the 46 strains of X. fastidiosa analyzed. The mean of prophages and genomic island regions per genome were 8.6 and 8.9, respectively. Around half (56%) of predicted insertion sequences were located into prophage regions. In summary, the X. fastidiosa comparative genomics and phylogenomics analyses showed that the geographic region of isolation is strongly supported at the strains genomic level differently from strain-plant host adaptation. Moreover, a relevant and heterogeneous amount of MGE are harbored in the chromosome of all 46 X. fastidiosa strains analyzed.