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Volume 9, Issue 12

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

Abstract

This study presents the assembly and comparative genomic analysis of luminous strains isolated from the light organs of 12 fish species using Oxford Nanopore Technologies (ONT) sequencing. The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near complete BUSCO scores along with varying plasmid sequences. Leveraging this dataset, this study significantly expanded the available genomes for and its subspecies , enabling a comparative genomic analysis between the two lineages. An analysis of the large and small chromosomes unveiled distinct patterns of core and accessory genes, with a larger fraction of the core genes residing on the large chromosome, supporting the hypothesis of secondary chromosome evolution from megaplasmids in Vibrionaceae. In addition, we discovered a proposed new species, sp. nov., isolated from an acropomatid host, with an average nucleotide identify (ANI) of 93 % compared to the and strains. A comparison of the and lineages revealed minimal differences in gene content, yet highlighted the former’s larger genome size and potential for horizontal gene transfer. An investigation of the operon, responsible for light production, indicated congruence between the presence of and host family, challenging its role in differentiating from . Further insights were derived from the identification of metabolic differences, such as the presence of the NADH:quinone oxidoreductase respiratory complex I in as well as variations in the type II secretion system (T2S) genes between the lineages, potentially impacting protein secretion and symbiosis. In summary, this study advances our understanding of genome evolution, highlighting subtle differences between closely related lineages, specifically and . These findings highlight the benefit of long read sequencing for bacterial genome assembly and pangenome analysis and provide a foundation for exploring early bacterial speciation processes of these facultative light organ symbionts.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bioluminescence , Oxford Nanopore Technology , symbiosis and Vibrionaceae
Funding
This study was supported by the:
  • Foundation for the National Institutes of Health (Award DP5OD026405)
    • Principle Award Recipient: AlisonL Gould
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2023-12-19
2024-05-20
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Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences
M Gen 9, 001161 (2023); https://doi.org/10.1099/mgen.0.001161
/content/journal/mgen/10.1099/mgen.0.001161
/content/journal/mgen/10.1099/mgen.0.001161
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