Comparative genomics reveals a genomic and functional continuum among secondary replicons in Halobacteriota

Recent research has unveiled a continuous genomic and functional spectrum among secondary replicons in the Halobacteriota group of archaea. The study examined 211 complete genomes, encompassing 766 replicons, including 211 primary chromosomes and 555 secondary replicons. By analyzing various genomic features such as replicon size, GC content, and codon usage, scientists discovered a gradual shift from plasmid-like to chromosome-like characteristics in secondary replicons.

Larger secondary replicons exhibited more chromosome-like genomic and functional attributes, such as a greater overlap of protein families with the primary chromosome (chr1) and a higher percentage of conserved gene families. At the phylum level, functional profiles displayed significant overlap among replicon types, further suggesting a continuum of functional classes rather than distinct categories.

Moreover, larger replicons displayed an increased occurrence of protein-family duplication. Pangenome analysis also revealed a higher proportion of conserved gene families, with accessory families being most abundant at intermediate sizes and rare and singleton families declining as replicon size increased. Collectively, these findings propose a model wherein secondary replicons within Halobacteriota exist across a genomic and functional continuum, ranging from plasmid-like to chromosome-like states.

The study suggests that increasing replicon size is associated with greater conservation, gene duplication, and a progressively more chromosome-like gene content and functional profile.