Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences

Area of Science:

• Microbial genomics
• Bacterial evolution
• Symbiosis research

Background:

• Luminous bacteria in fish light organs are crucial symbionts.
• Understanding Photobacterium genome evolution aids in studying bacterial speciation.
• Comparative genomics reveals adaptations in symbiotic bacteria.

Purpose of the Study:

• To assemble and comparatively analyze genomes of luminous Photobacterium strains.
• To investigate genome structure and gene content differences between P. leiognathi and P. 'mandapamensis'.
• To identify potential new Photobacterium species and their evolutionary relationships.

Main Methods:

• Oxford Nanopore Technologies (ONT) sequencing for high-continuity genome assembly.
• Comparative genomic analysis of assembled chromosomes and plasmids.
• Average Nucleotide Identity (ANI) calculation for species delineation.

Main Results:

• Achieved chromosome-level assemblies for most Photobacterium strains, with distinct large and small chromosome structures.
• Expanded genomic data for P. leiognathi and P. 'mandapamensis', revealing subtle gene content differences but variations in genome size and horizontal gene transfer potential.
• Proposed a new species, Photobacterium acropomis sp. nov., based on ANI values.
• Identified conserved luxF gene presence correlating with host family, not lineage differentiation.
• Observed metabolic differences, including respiratory complex I presence and T2S gene variations.

Conclusions:

• The study provides a comprehensive genomic resource for luminous Photobacterium, advancing understanding of their evolution.
• Findings support secondary chromosome evolution from megaplasmids in Vibrionaceae.
• Subtle genomic distinctions between P. leiognathi and P. 'mandapamensis' offer insights into early bacterial speciation.
• Long-read sequencing is beneficial for bacterial genome and pangenome analysis.