Filogenômica de novas espécies do complexo Burkholderia cepacia e genômica comparativa de isolados de B. cenocepacia linhagens IIIA e IIIB, causadoras de podridão das escamas da cebola

Abstract

In Brazil, the onion (Allium cepa L.) has high socioeconomic importance, standing out as the most produced vegetable within the Allium genus. Several diseases can affect onion growing, both during production and in the post-harvest process. Among those with high economic importance, the onion sour skin has great importance. This disease is associated with several bacterial species, among which species of the Burkholderia cepacia complex (BCC), such as B. cepacia and B. cenocepacia, in addition to B. gladioli pv. alliicola, Pseudomonas aeruginosa and Serratia marcescens. BCC strains are the most frequently associated with disease symptoms, and B. cenocepacia strains are predominant in the São Francisco Valley region. After a polyphasic approach including rep-PCR analyses, biochemical and pathological profiles, and multilocus sequence analysis (MLSA) with the strains, a predominance of B. cenocepacia lineages IIIA and IIIB and five strains belonging to two new lineages of this bacterium was observed, which act exclusively as phytopathogens. Thus, the aim of this thesis was to sequence, assemble and annotate five genomes of strains of two new strains of B. cenocepacia associated with onion sour skin in Northeastern Brazil and analyze the taxonomic position of these strains through a phylogenomic approach, and sequence, assemble and annotate the genomes of phytopathogenic strains of B. cenocepacia belonging to IIIA and IIIB lineages, aiming to characterize the virulence and pathogenicity factors involved in the plant-pathogen interaction and comparison with strains obtained from different ecological niches. The analysis of the core genome sequences revealed that they belong to the CBC, but they are not related to any previously described species of this complex. Comparative analysis of the total genome of the five strains against the CBC member-like strain revealed average nucleotide identity (ANI) values of 86.73 to 94.82%. Combined data from ANI, digital DNA-DNA hybridization (dDDH), and analysis of the core genome indicated that the strains IBSBF 3371T and IBSBF 3372T represent two new species of the genus Burkholderia, belonging to the Burkholderia cepacia complex. Additionally, 12 strains of B. cenocepacia, five from lineage IIIA and seven from lineage IIIB isolated from onion, were compared with 21 complete genomes isolated from human pathogens and environmental groups. Through the ANI, dDDH, and core genome, we verify that the phytopathogenic strains from lineage IIIA and IIIB showed little variation in relation to the other studied groups. However, according to them to the results obtained, they behave as two distinct species. Phytopathogenic strains of B. cenocepacia lineage IIIA and IIIB showed a more significant amount of pathogenicity and virulence factors to humans. Our data will therefore be a valuable resource for future studies. In addition, our data contribute to the extensive genomic resources available for Burkholderiaceae species.