Refining Salinivibrio pangenome dynamics and biotechnological potential through comparative analysis

Area of Science:

• Genomics
• Microbial Ecology
• Biotechnology

Background:

• Understanding genomic diversity in the halophilic genus Salinivibrio is limited by reliance on draft genomes.
• Previous analyses suggested a closed pangenome and a lack of polyhydroxyalkanoate (PHA) degradation capacity in Salinivibrio.

Purpose of the Study:

• To present complete Salinivibrio genomes and re-analyze public genomes to clarify genomic diversity.
• To investigate the polyhydroxyalkanoate (PHA) biosynthesis and degradation capacities within the genus Salinivibrio.

Main Methods:

• Generated eight complete Salinivibrio genomes using Oxford Nanopore long-read sequencing.
• Re-analyzed 38 high-quality public genomes and performed pangenome and Panstripe analyses.
• Utilized Hidden Markov Model-based homology searches to identify putative PHA depolymerases.

Main Results:

• Pangenome analysis revealed a more open genomic structure for Salinivibrio than previously reported.
• Identified seven putative PHA depolymerases in 15% of strains, previously overlooked by standard annotation.
• PHA biosynthesis operons are conserved across all analyzed genomes, indicating a maintained pathway.

Conclusions:

• Salinivibrio exhibits significant genomic dynamism, with substantial core and accessory genomes.
• The identified putative depolymerases suggest Salinivibrio possesses PHA degradation capabilities, contrary to prior conclusions.
• Standardized homology-based re-analysis is crucial for uncovering genomic diversity and novel enzyme families in non-model organisms, highlighting potential for halophilic bioplastic production.