Evolution of a plant-like gene anciently acquired as part of a genomic island in Xanthomonas

Abstract

In this thesis, I determine that XAC3314, a plant-like gene, was anciently transferred to Xanthomonas axonopodis pv. citri strain 306 (Xac_306). An XAC3314 homolog has also been reported in the sequenced strain Xanthomonas axonopodis pv. vesicatoria strain 85-10, but is absent from three sequenced strains of X. campestris and three sequenced strains of X. oryzae. XAC3314 may have been lost in these species. The genetic diversity of XAC3314 and the evolution of this gene in Xanthomonas were characterized. Furthermore, I show that XAC3314 was acquired by an ancestral genome and transferred to Xanthomonas as part of a genomic island. Anciently acquired genes are expected to have ameliorated to the native genome; therefore, these genes cannot be identified using characteristics common to a horizontal transfer event. I compared Xac_306 to other sequenced genomes to identify potential gene clusters in the vicinity of XAC3314. Analysis of these genomes revealed that XAC3314 was likely acquired as a small gene cluster, which inserted in Xanthomonas after the split of X. albilineans. Xanthomonas albilineans and Stenotrophomonas have unique gene clusters inserted at the same region as those in X. axonopodis. XAC3314 homologs were also identified in the sequenced strains of X. vasicola and X. gardneri. The diversity of XAC3314 was analyzed in Xanthomonas strains from the Pacific Bacterial Collection. A total of 307 Xanthomonas strains were classified with the RIF marker. Trees constructed from Xanthomonas RIF sequences are similar in structure to a completed multi-locus analysis of the genus [Young et al., 2008]. XAC3314 homologs are present in 98 of the 307 strains in the Pacific Bacterial Collection. The XAC3314 sequences revealed that HGT may have occurred among some strains of X. axonoodis. This work expands our understanding of bacterial genome evolution and anciently acquired gene clusters.