xenoGI

xenoGI reconstructs the evolutionary history of genomic island insertions within clades of closely related bacteria by identifying genomic islands and mapping their insertion points in a species-tree-aware manner.

Key Features:

• Phylogeny-aware identification: Uses a species tree to assign insertion points of genomic islands within a clade rather than relying on single-strain or pairwise comparisons.
• Synteny-based gene family construction: Builds gene families using synteny information to respect local gene order and evolutionary history.
• Island delineation by MRCA adjacency: Combines adjacent gene family members that share a most recent common ancestor into coherent genomic islands.
• Mapping of insertion events: Places genomic island insertions onto specific branches of the provided phylogenetic tree.
• Output and export: Provides text-based analysis outputs and supports exporting identified genomic islands into formats compatible with genome browsers.

Scientific Applications:

• Adaptive evolution studies: Determines the branches on which genomic islands inserted to inform analyses of adaptive change and niche acquisition in bacteria.
• Case studies in enteric bacteria: Enables reconstruction of genomic island evolution in taxa such as Escherichia, including tracing islands like the acid fitness island.

Methodology:

Requires sequenced genomes and a phylogenetic tree as input; constructs gene families using synteny while incorporating species-tree information, identifies genomic islands by grouping adjacent families with shared MRCA, and maps island insertion points onto the phylogenetic tree.