Annotation-free delineation of prokaryotic homology groups

• DOI: 10.1371/journal.pcbi.1010216
• Publication Date: 2022-06-08T17:45:02Z
• Authors: Yongze Yin; Huw A. Ogilvie; Luay Nakhleh
• Keywords: Homology; Bacterial genome size

Phylogenomic studies of prokaryotic taxa often assume conserved marker genes are homologous across their length. However, processes such as horizontal gene transfer or duplication and loss may disrupt this homology by recombining only parts genes, causing fission fusion. We show using simulation that it is necessary to delineate groups in a set bacterial genomes without relying on annotations define the boundaries regions. To solve problem, we have developed graph-based algorithm partition into Maximal Homologous Groups sequences ( MHGs ) where each MHG maximal maximum-length which entire sequence alignment. applied our dataset 19 Enterobacteriaceae species found cover much greater proportions than markers and, relatedly, less biased terms functions they cover. zoomed correlation between individual overlapping MHGs, few phylogenetic splits supported while many marker-supported contradicted MHGs. A comparison tree inferred from with suggests increased bias lack genome coverage causes incorrect inferences overall relationship taxa.