Whole genome sequencing and comparative genomic analysis of Photobacterium ganghwense CF1.2, the bacterial host of the lytic marine bacteriophage PhCF1.2: Insights into its mobilome and metabolic potential

Keerthi R Babu; K. S. Sobhana; Aleena Alex; K. P. Neethu; Md Umar; V. S. Jayasree; Grinson George

doi:10.21077/

Authors

Keerthi R Babu ICAR-Central Marine Fisheries Research Institute, Ernakulam North P. O., Kochi-682 018, Kerala, India,Cochin University of Science and Technology, Cochin University P. O., Kochi-682 022, Kerala, India
Dr. K. S. Sobhana
Aleena Alex ICAR-Central Marine Fisheries Research Institute, Ernakulam North P. O., Kochi-682 018, Kerala, India,3Mangalore University, Mangalagangotri, Mangaluru - 574 199, Karnataka, India
Dr.K P Neethu
Dr.Md Umar
Dr.V. S. Jayasree
Dr.Grinson George

Keywords:

Average nucleotide identity, Biosynthetic gene clusters, CAZymes, Clusters of orthologous groups, Genome annotation, Taxonomic placement

Abstract

Photobacterium species are abundant in marine ecosystems, where they help break down organic matter and serve as hosts of lytic bacteriophages that influence the dynamics of bacterial populations. Here, we report the draft genome sequence and comparative genome analysis of Photobacterium ganghwense strain CF1.2, isolated from Cochin Fisheries Harbour, Kochi, on the south-west coast of India, and identified as the host bacterium of the marine lytic phage PhCF1.2. The isolate was identified based on phenotypic and biochemical traits as well as 16S rRNA gene sequence (GenBank accession MZ489219) and further characterised by Illumina 2×150 bp paired-end whole genome sequencing. The draft scaffolded genome had a total length of 5.42 Mb with a GC content of 50.59%. The assembly showed high contiguity (N50 = 3,527,779 bp; L50 = 1), with the two largest scaffolds mapped to Chromosome 1 (3.53 Mb) and Chromosome 2 (1.89 Mb). Genome annotation predicted 4,807 protein coding genes. The genome contained 101 CAZyme encoding genes corresponding to 115 CAZyme family assignments. Annotation based on the clusters of orthologous groups (COG) assigned 3,963 genes (82.44% of the predicted proteome) to 26 functional categories. AntiSMASH analysis identified 10 biosynthetic gene clusters (BGCs) distributed in both chromosomes. Pairwise comparison with the reference genome of P. ganghwense strain C2.2 gave FastANI value of 98.77%, which was well above the species delimitation threshold of 95–96% and confirmed the taxonomic classification of CF1.2. The genome revealed a range of metabolic pathways, mobile genetic elements and biosynthetic capabilities, suggesting the adaptive capacity of this marine bacterium. The genome of CF1.2, the bacterial host of a newly identified lytic phage, is a useful resource for studying phage–host interactions, bacterial adaptation, and the ecological roles of Photobacterium species in marine ecosystems. The raw sequencing reads and genome assembly have been deposited in GenBank under BioProject accession PRJNA1490486, BioSample accession SAMN61429489 and Whole Genome Shotgun (WGS) accession JCAQNK000000000.

Keywords: Average nucleotide identity, Biosynthetic gene clusters, CAZymes, Clusters of orthologous groups, Genome annotation, Taxonomic placement

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