Study Info
INDA Accessions: INRP000767
INSDC Accessions: ERP206918, PRJEB127406
- Title: Isolation and characterization of Agrobacterium pusense (MKUTJ01) strain
- Data Type : Whole Genome Sequencing
- Descriptive Title: Comparative genome analysis of Agrobacterium pusense MKUTJ01 reveals evolutionary diversification and plant-associated functions.
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Organism:
Scientific Name(Taxon Id): Agrobacterium pusense (648995) Common Name:
Other Info
- Abstract: Agrobacterium species are Gram-negative, soil-associated bacteria that are widely distributed in diverse environmental habitats and are recognized for their interactions with plants. While several Agrobacterium species are well characterized for their plant-associated traits and genetic diversity, genomic information on Agrobacterium pusense remains comparatively limited. In the present study, the genomic characteristics of Agrobacterium pusense strain MKUTJ01, an environmental isolate, were investigated using whole-genome sequencing and comparative genomic analyses. The MKUTJ01 strain was isolated and characterized using morphological and biochemical approaches. The isolate exhibited characteristics consistent with Gram-negative, motile, rod-shaped bacteria. Genomic DNA was extracted from the isolate and subjected to whole-genome sequencing using an Illumina paired-end sequencing platform. The generated sequencing reads were quality assessed and processed prior to de novo genome assembly. Genome assembly was performed using Unicycler, followed by quality assessment. Genome annotation was performed using Prokka, followed by functional characterization using Cluster of Orthologous Groups (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and other comparative genomic approaches. The genome was further investigated for antimicrobial resistance determinants, virulence-associated genes, genomic islands, and CRISPR-associated defense systems. Antimicrobial resistance analysis using the Comprehensive Antibiotic Resistance Database (CARD) identified genetic determinants associated with tetracycline and benzalkonium chloride resistance, including genes related to antimicrobial efflux and resistance mechanisms. Phenotypic antimicrobial susceptibility testing was also performed to compare the genomic predictions with the observed resistance phenotype. Comparative genomic analyses were performed using Average Nucleotide Identity (ANI), digital DNA-DNA hybridization (dDDH), multilocus sequence-based approaches, and phylogenomic analyses to establish the genomic relationship of MKUTJ01 with closely related Agrobacterium taxa. The genome was also examined for plasmid-associated sequences and genes potentially involved in plant-associated functions. A genomic region showing high similarity to symbiotic plasmid sequences was detected; however, typical nodulation, nitrogen fixation, and related symbiosis-associated genes and virulence genes were not identified in the corresponding region, suggesting that the plasmid-associated sequence may represent a distinct or incomplete symbiotic element. Plant-bacteria interaction assays using a hairy-root induction system further indicated that the isolate can influence root development, with treated plants showing increased lateral root formation and fine root clusters compared with controls. Overall, the genome sequence of Agrobacterium pusense MKUTJ01 provides a valuable resource for understanding the genomic organization, antimicrobial resistance potential, phage-associated elements, defense systems, and plant-associated characteristics of this species. The study contributes to the genomic characterization of an environmental Agrobacterium isolate and provides a foundation for further investigation of the evolutionary relationship, mobile genetic elements, bacterial defense mechanisms, and potential plant–microbe interactions of A. pusense.
- Linked publications:
- Center Name: Jebasingh Tennyson, Department of Plant Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai-21.
- Number of Base(Total) Mbp: 0
- Size in bytes(Total):
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- Number of Sequences:
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- Number of Variant files:
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