Aug 2026· Marine Genomics· Vol 87, pp.
101269
· 0 citations· 25 references
Medicine
TL;DR
Findings suggest that strain D18 possesses adaptive strategies for survival in deep-sea environments and highlight its potential as a source of novel secondary metabolites.
Abstract
Idiomarina sp. D18 is a deep-sea marine bacterium isolated from seawater at a depth of 5069 m in the western Pacific Ocean. The complete genome of strain D18 consists of a circular chromosome of 2,765,208 bp and three plasmids, with a G + C content of 47.28%. Genome annotation identified 2587 predicted protein-coding genes, 57 tRNA genes, and 14 rRNA genes. Functional analysis revealed genes involved in diverse metabolic processes, including amino acid metabolism, signal transduction, and energy production. In addition, multiple carbohydrate-active enzymes were identified, suggesting the ability to utilize complex substrates in marine environments. Genome mining identified two biosynthetic gene clusters, including a RiPP-like cluster and a β-lactone cluster. These clusters are predicted to encode bioactive compounds, which may contribute to microbial competition and interaction through antimicrobial activity and enzyme inhibition. These findings suggest that strain D18 possesses adaptive strategies for survival in deep-sea environments and highlight its potential as a source of novel secondary metabolites.
OBJECTIVE
This Data Note reports the complete genome sequence and associated functional-genomic data of Methylomonas sp. strain 2F7, a methane-oxidizing bacterium isolated from rice paddy soil in South Korea. These data were generated to support comparative genomic analyses of methanotrophic bacteria and to document the genome-based taxonomic position and C1 metabolism gene repertoire of strain 2F7.
DATA DESCRIPTION
The dataset includes Oxford Nanopore Technologies MinION raw reads, a two-replicon genome assembly, annotation summaries, functional classifications, a phylogenetic analysis, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons, and a curated C1 metabolism gene table. The genome consists of a 4,979,984-bp chromosome and a 23,603-bp plasmid, with an overall G+C content of 51.4%. Annotation identified 4,520 genes, including 4,429 coding sequences (CDSs), nine rRNA genes, 46 tRNA genes, and four ncRNAs. The 16S rRNA gene sequence showed the highest similarity to Methylomonas fluvii EbBᵀ, whereas ANI/dDDH analysis identified Methylomonas rosea WSC-7ᵀ as the closest related type strain by genome-distance criteria, with ANI/dDDH values of 89.6% and 38.0%, respectively. Additional ANI/dDDH comparisons with M. fluvii EbBᵀ and M. defluvii OY6ᵀ yielded values of 89.3%/37.4% and 89.4%/36.9%, respectively. These genome-based values fall below accepted species-boundary thresholds and support placement of strain 2F7 as a putative novel species within the genus Methylomonas. The curated gene table documents pMMO-like and sMMO gene clusters and genes involved in methanol oxidation, formaldehyde oxidation, and ribulose monophosphate (RuMP)-linked C1 assimilation.
Y. Gwak, Sang Eun Jeong, Si Chul Kim et al.· BMC Genomic Data· 0 citations
This article presents the draft genome sequence of strain MF0224, an anaerobic bacterium representing an unclassified Fusobacterium-related lineage isolated from a coastal sediment sample collected in Puducherry, India. Whole-genome sequencing was performed using the Illumina paired-end sequencing platform and assembled into a draft genome of 2.02 Mb comprising 26 contigs with a genomic DNA G+C content of 28.19%. Genome annotation predicted 1889 coding sequences, 47 tRNA genes, and multiple genes associated with anaerobic carbon metabolism, acetate production, sulfur metabolism, volatile fatty acid metabolism, and carbohydrate-active enzymes. Genome quality assessment indicated high completeness with low contamination. Comparative genomic analysis using TYGS identified the strain as a potential novel species within the genus Fusobacterium, supported by low digital DNA–DNA hybridization (dDDH) values (∼20%) relative to currently described species. Average amino acid identity (AAI; 68.9%) supported its placement within the genus Fusobacterium while indicating substantial genomic divergence. Comparative genomic analysis also determined a percentage of conserved proteins (POCP) value of 65.9%, providing additional genomic characterization of strain MF0224. Phylogenetic analyses based on 16S rRNA gene sequences and whole-genome phylogeny consistently positioned strain MF0224 within the Fusobacterium-associated clade. The genome provides a valuable resource for investigating anaerobic carbon metabolism, acetate biosynthesis, sulfur-associated pathways, and the ecological adaptation of Fusobacterium-related bacteria in coastal sediment ecosystems.
M. Prathaban, R. Prathiviraj, M. Sobanaa et al.· Data in Brief· 0 citations
A genomic framework for understanding the high glycosphingolipid-producing capacity of NKG400013 is established and insights into the evolutionary diversification of sphingolipid metabolism in green algae are provided.
Rein Yasui, Aoi Hosaka, N. Ogata et al.· DNA Research· 0 citations
The findings reveal S. rubidaea MJ24 as a metabolically versatile bacterium with a rich secondary metabolite repertoire and significant agricultural and biotechnological promise.
Yaseera N. Bhombal, Surabhi Yeole, V. Barvkar et al.· Functional & Integrative Gen...· 0 citations
