Highly contiguous genome assemblies of Photobacterium strains isolatedfrom fish light organs using nanopore sequencing technology

Abstract

Several species of luminous bacteria in the genus Photobacterium are the light organ symbionts of teleost fishes. Photobacterium leiognathi and its subspecies, P. mandapamensis, in particular, commonly form bioluminescent symbioses with fish hosts in the Leiognathidae and Acropomatidae families as well as with cardinalfish in the genus Siphamia (Apogonidae). These two closely related lineages of Photobacterium are right at the cutoff average nucleotide identity used to delimit bacterial species (95-96%) and show overlapping ecological niches, including their host fish range. However, there are only a few whole genome assemblies available for these bacterial species, particularly for symbiotic strains isolated from fish light organs, that can be used to explore genome evolution of these two lineages. Here we used Oxford Nanopore Technologies sequencing to produce long reads for assembling highly contiguous genomes of Photobacterium strains isolated from fish light organs, including several P. kishitanii strains isolated from deep water fishes. We were able to assemble 31 high-quality genomes with near complete BUSCO scores, many at the chromosome-level, and compare their gene contents, including plasmid genes. In doing so, we discovered a new candidate species of Photobacterium, Candidatus Photobacterium acropomis, which originated from the light organ of the acropomid fish, Acropoma japonicum. We also describe a lack of congruency between the presence of the luxF gene, which is involved in light production, and the phylogenetic relationships between closely related P. leiognathi and P. mandapamensis strains. In contrast, there was strong congruency between luxF and the host fish family of origin, suggesting this gene might be essential to initiate bioluminescent symbioses with certain hosts, including Siphamia and Acropoma species. Our study shows the benefit of using long reads in the assembly of bacterial genomes and outlines an assembly pipeline that results in highly contiguous genomes, even from low-coverage ONT reads.