is usually a Gram negative herb pathogen causing many economically important diseases, and analyses of completely sequenced genome strains allowed the identification of many prophage-like elements and possibly phage remnants, accounting for up to 15% of the genome composition. from the gapped-genomes of strains Dixon (Xf-ALS) and Ann1 (Xf-OLS) [2] and the complete genome of the Pierce Disease associated Temecula-1 strain (Xf-PD) [3]. Genomic analyses in different strains reveal interesting biological and evolutionary aspects regarding genome structure and gene content. Previous studies exhibited that 98% of the Xf-PD genes are shared with Xf-CVC, with an average amino acid identity (considering only the coding regions) of 95.7%, and the main differences are from bacteriophage-derived regions. These bacteriophage-derived regions are responsible for chromosomal rearrangements and deletions in strains, thus playing a decisive role around the genome evolution of this herb pathogen [1], [3]. Recently published work demonstrate that virus particles, including bacteriophages, DLEU7 appear to be strikingly abundant, with a typical estimated concentration of 107 particles/ml in coastal sea water and even higher in some other habitats, such as freshwater ponds [4]. Costunolide Based on these data, it is proposed that these particles represent the most abundant biological form on Earth [5] and potentially an efficient vehicle for lateral gene transfer (LGT). A large body of sequence data is generated by projects of bacteriophage genome sequencing, and almost 500 phage genomes have been decided and deposited in Genbank, and together with metagenomics studies (mainly from environmental samples), indicate a broad genetic diversity, representing the largest reservoir of sequence information in the biosphere [6], [7]. Moreover completely sequenced phage genomes have a high degree of mosaicism probably derived from extensive horizontal genetic exchange occurring over perhaps as many as 3 billion years [8]C[10]. Furthermore, bacteriophages have a central role in the evolution of their bacterial hosts and the emergence of new pathogens, by moving genes from host to host as a mechanism that generate gene and genome diversity, thus constituting, in many bacterial species, a substantial part of acquired DNA [5], [11]. In some instances, lysogenic conversion of Costunolide phages are of selective advantage to the bacterial host, as they can dramatically affect host phenotype [12]. To accomplish integration, temperate bacteriophages encode a phage integrase enzyme that mediates recombination between short sequences of phage DNA, the phage attachment site sequences and are grouped into two major families, based on their mode of catalysis: the tyrosine and the serine recombinases [14]. At least 75% of the phage tyrosine recombinases use tRNA Costunolide sequences as attachment sites in bacteria, indicating that tRNAs are directly involved in the phage acquisition process [15]. In this work, the genomes of four strains, Xf-CVC, Xf-PD, Xf-OLS, and Xf-ALS, were compared with regard to their prophage content and respective predicted integrase genes. A total of 56 predicted Costunolide integrases were identified, and network analysis and phylogenetic reconstructions support the presence of five major lineages related to known bacteriophages that infect gamma and beta-proteobacteria. By Bidirectional Best Hit (BBH) analysis (against 402 bacteriophage genomes), the integrases were all found to be associated mainly to phages made up of structural genes of Caudovirales viruses. gene expression analysis of Xf-CVC prophage-like regions reveals these prophages are probably actively transcribed, and this finding is supported by the presence of putative phage-like particles in cells both (almond petiole and hibiscus leaves) and [16]. Comparative studies conducted around the structure of the prophage regions and their relative genomic positions strengthen their impact in the genome organization and differentiation of these closely related strains. Results 1. Prophage-like elements: organization, diversity and comparative analysis a) Identification of prophage-like regions Identification and definition of prophage-like elements is not trivial task, but an empirical approach that needs a lot of insight [17]. In the previously reported Xf-ALS and Xf-OLS assemblies [2], prophage-like elements were not identified, and candidate molecules were not determined for each strain. A specific strategy to resolve the assembly of phage-related regions was developed which generated candidate molecules for each strain, thus making possible the identification of prophage-like components and phage remnants (data not really shown) Just as, recognition of most predicted integrase genes and prophage-like areas were carried in Xf-CVC Xf-PD and 9a5c Temecula stress genomes. All genomes had been scanned for the current presence of predicted integrases connected to clusters of genes linked to phages. Areas encompassing a lot more than 10,000.