Long-Read Sequencing Reveals Divergent ITS Identities among Multiple rRNA Operons on Halococcus dombrowskii Chromosome and Plasmids

De novo long read sequencing of the euryachaeon Halococcus dombrowskii reveals a
genome with multiple copies of rRNA operons interspersed across both chromosome and
plasmids, making it the first known member among genus Halococcus to display this
organization.

Analysis of the multiple rRNA operon ITS (Internal Transcribed Spacer) sites show drastic
sequence divergence between chromosomal rRNA operon ITS and those on plasmids,
hinting at different evolutionary pressures at play on vital operons sharing identical genes
with presumed identical functional roles. The sequence-based inferred phylogeny of the H.
dombrowskii chromosomal ITS closely tracks the phylogenetic placement of H. dombrowskii
against closely-related species. However, the plasmid ITS sequences show more unusual
differences that are more divergent from the chromosomal ITS sequence.

Few if any other Halococcus spp. have long-read genome resources available. Our results
suggest that resequencing other members of the Halococcus genus using long-read methods
might give us additional vital insight into genomic organization of these species, and help us
explore a model for Archaeal chromosome-plasmid evolution in action.