Comparative genomic analysis of coffee-infecting Xylella fastidiosa strains isolated from Brazil

Abstract

Strains of Xylella fastidiosa constitute a complex group of bacteria that develop within the xylem of many plant hosts, causing diseases of significant economic importance, such as Pierce's disease in North American grapevines and citrus variegated chlorosis in Brazil. X. fastidiosa has also been obtained from other host plants, in direct correlation with the development of diseases, as in the case of coffee leaf scorch (CLS) -a disease with potential to cause severe economic losses to the Brazilian coffee industry. This paper describes a thorough genomic characterization of coffeeinfecting X. fastidiosa strains, initially performed through a microarray-based approach, which demonstrated that CLS strains could be subdivided in two phylogenetically distinct subgroups. Whole-genomic sequencing of two of these bacteria (one from each subgroup) allowed identification of ORFs and horizontally transferred elements (HTEs) that were specific to CLSrelated X. fastidiosa strains. Such analyses confirmed the size and importance of HTEs as major mediators of chromosomal evolution amongst these bacteria, and allowed identification of differences in gene content, after comparisons were made with previously sequenced X. fastidiosa strains, isolated from alternative hosts. Although direct experimentation still needs to be performed to elucidate the biological consequences associated with such differences, it was interesting to verify that CLS-related bacteria display variations in genes that produce toxins, as well as surface-related factors (such as fimbrial adhesins and LPS) that have been shown to be involved with recognition of specific host factors in different pathogenic bacteria.

New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination

“…As the MLSA and MLST analyses revealed that the two coffee-infecting strains were phylogenetically distant and distinct from previously described CLSrelated strains (16,55) Phylogenetic analysis of CFBP 8072 and CFBP 8073 based on genomic data. Based on these data, an entire genome-based phylogenetic tree was built using CV-Tree (44) by comparing protein sequences predicted from annotation analysis performed on CFBP 8072 and CFBP 8073 to 17 publicly available predicted proteomes (Fig.…”

“…The genome sequences of the following four X. fastidiosa strains that were isolated from coffee plants are available: CFBP 8072 isolated from C. arabica originating from Ecuador, CFBP 8073 isolated from C. canephora originating from Mexico, and strains 6c and 32 (isolated from Coffea spp. from Brazil) (55,58). To identify potential determinants of coffee plant adaptation, we compared these genome sequences to the 13 other available X. fastidiosa genome sequences representing X. fastidiosa strains which are not known to infect coffee plants (Table 3, excluding the PLS 229 strain that does not belong to X. fastidiosa).…”

“…multiplex), and Ann-1 (X. fastidiosa subsp. sandyi) (15,46,55,57,65), none of these were identified in CFBP 8072 or CFBP 8073 by PHAST but were identified, at least partially and/or fragmented, in the genome sequences of CFBP 8072 or CFBP 8073, based on a blast search. The prophage Xfp6 shared by the 9a5c and 6c strains (55) was also found in strains CFBP 8072 and CFBP 8073 with a very high level of conservation.…”

“…Recombination is an important driving force of genome evolution in X. fastidiosa, including homologous recombination but also gene acquisition through HGT (15,55). X. fastidiosa has the largest ratio of phage genes to genome size (7 to 9%) in a set of 37 phytopathogenic bacterial genomes (65).…”

Xylella fastidiosa: Host Range and Advance in Molecular Identification Techniques

“…By whole genome approach, the complete set of unique genes present in each strain can be characterized, together with those that are common to all strains (Bhattacharyya et al, 2002; Barbosa et al, 2015). Sets of genes involved in important functions can be compared and studied (da Silva et al, 2007; Barbosa et al, 2015), SNPs can be identified and PCR primers can be designed for the identification of specific strains (Doddapaneni et al, 2006; Marcelletti and Scortichini, 2016b) and detailed phylogenetic analysis can be performed. As an example, by genome-wide comparison of 21 X. fastidiosa strains, Marcelletti and Scortichini (2016a) constructed a phylogenetic tree analyzing 820,088 nucleotides, ~30% of the entire X. fastidiosa genome.…”