Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.

ABSTRACT:

Background

A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multicopy gene families, which are recognizable by synteny conservation, and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes.

Results

Clustering criteria affect pangenome functional characterizat

SUBMITTER: Manzano-Morales S 

PROVIDER: S-EPMC10614367 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature