xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria

Abstract

BackgroundGenomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based and comparative, have been developed to identify them. Some of these methods are explicitly designed to work in single strains, while others make use of multiple strains. In general, existing methods do not identify islands in the context of the phylogeny in which they evolved. Even multiple strain approaches are best suited to identifying genomic islands that are present in one strain but absent in others. They do not automatically recognize islands which are shared between some strains in the clade or determine the branch on which these islands inserted within the phylogenetic tree.ResultsWe have developed a software package, xenoGI, that identifies genomic islands and maps their origin within a clade of closely related bacteria, determining which branch they inserted on. It takes as input a set of sequenced genomes and a tree specifying their phylogenetic relationships. Making heavy use of synteny information, the package builds gene families in a species-tree-aware way, and then attempts to combine into islands those families whose members are adjacent and whose most recent common ancestor is shared. The package provides a variety of text-based analysis functions, as well as the ability to export genomic islands into formats suitable for viewing in a genome browser. We demonstrate the capabilities of the package with several examples from enteric bacteria, including an examination of the evolution of the acid fitness island in the genus Escherichia. In addition we use output from simulations and a set of known genomic islands from the literature to show that xenoGI can accurately identify genomic islands and place them on a phylogenetic tree.ConclusionsxenoGI is an effective tool for studying the history of genomic island insertions in a clade of microbes. It identifies genomic islands, and determines which branch they inserted on within the phylogenetic tree for the clade. Such information is valuable because it helps us understand the adaptive path that has produced living species.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2038-0) contains supplementary material, which is available to authorized users.

Salmonella Pathogenicity Island 1 (SPI-1): The Evolution and Stabilization of a Core Genomic Type Three Secretion System

“…Analysis was run using default parameters in xenoGI v2.2.0 [45] with the following exceptions: rootFocalClade was set to i26 ( Figure S1) and evalueThresh was set to 1e-8. Computing time took approximately 3 h with 29 strains.…”

“…Many genomic island-finding programs exist [reviewed in [62,63]], but unlike other methodologies, xenoGI requires a phylogenetic tree for input. The phylogeny is used to determine which islands are shared by a clade and to identify at which branch they were acquired [45].…”

“…Another gene island containing mobile elements, a toxin-antitoxin system, and a restriction endonuclease has inserted between the pig genes and mutS (Figure 4). [45]: fhlA (dark brown), ygbA (blue), sitABCD (orange), avrA -invH (green), pig genes and pphB (light blue/purple) and mutS (grey). Genomic island in S. Senftenberg N17-509 with no homology to SPI-1 is coloured beige.…”

“…The most robust approach to find genomic islands and their boundaries is through comparative genomics. xenoGI is a recently released comparative genomics program that identifies genomic islands that are shared by a clade of bacteria as well as islands that are unique to certain strains by grouping genes by origin on a phylogenetic tree [45]. Using this locus-based approach, the objectives of our study were to: (1) identify the genomic islands of SPI-1, (2) examine the evolutionary history of the SPI-1 locus, and (3) evaluate the evolutionary history of SPI-1-encoded transcriptional regulators hilA, hilC, and hilD.…”

“…Whole-genome phylogeny was constructed with PATRIC. Gene colouring corresponds to different gene clusters identified by xenoGI [45]: fhlA (dark brown), ygbA (blue), sitABCD (orange), avrA -invH (green), pig genes and pphB (light blue/purple) and mutS (grey). S. enterica Senftenberg strain ATCC 43845 is included in this figure.…”