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. 2025 Nov 4;14(12):e01048-25. doi: 10.1128/mra.01048-25

Genome sequence of a native nitrogen-fixing Bradyrhizobium sp. strain RCAM1614 isolated from lupine nodules

Eugenia Yu Denisova 1,2, Evgenii A Kirichek 2, Viktor E Tsyganov 2,✉
Editor: André O Hudson3
PMCID: PMC12697108  PMID: 41186223

ABSTRACT

This report describes the genome sequence of Bradyrhizobium sp. strain RCAM1614, which was isolated from the root nodules of Lupinus angustifolius L. in the Leningrad district of Russia. The genome has a size of 9.77 Mbp and shows 96.1% completeness, which enables precise taxonomic classification.

KEYWORDS: legume-rhizobial symbiosis, symbiotic nodules, Bradyrhizobium barranii

ANNOUNCEMENT

Species of the genus Bradyrhizobium are recognized as important nitrogen-fixing symbionts of various legumes, including lupine, groundnut, and soybean (1–3). Strain RCAM1614 was isolated according to Vincent (4) approximately 20 years ago from effective nodules of Lupinus angustifolius L. in the Leningrad district, Russia and deposited into the network collection of bioresources in the field of genetic technologies for agriculture (RCAM) as Bradyrhizobium sp.

Strain was preserved in yeast extract mannitol (YEM) (5) medium with 40% glycerol at −80°C. For DNA isolation, strain was cultivated on YEM at 28°C for 5 days. Genomic DNA was extracted using the Monarch Genomic DNA Purification Kit T3010L (New England Biolabs, USA) according to the manufacturer’s recommendations without size selection.

Oxford Nanopore Technologies (ONT) sequencing was carried out in the All-Russia Research Institute for Agricultural Microbiology (ARRIAM). Sequencing libraries were prepared using the Native Barcoding Kit 24 V14 (SQK-NBD114.24) (Oxford Nanopore, United Kingdom) according to the manufacturer’s instructions, skipping the DNA-shearing step, and sequenced on a MinION (Oxford Nanopore) device with FLO-MIN114 flow cell. Basecalling was performed with Dorado v1.0.1 (https://github.com/nanoporetech/dorado/) using the dna_r10.4.1_e8.2_400bps_sup@v5.2.0 model. Raw read quality control was performed with NanoPlot (6) v1.44.1. In total, 285,977 reads with N50 = 6,796 bp were obtained.

The genome was assembled de novo using Flye (7) v2.9.6 with the (--nano-raw) option, followed by polishing with Medaka v1.7.2 (https://github.com/nanoporetech/medaka). Assembly quality was assessed with QUAST (8) v5.3.0 and completeness was evaluated with BUSCO (9, 10) v5.8.0 using the rhizobiales_odb10 data set. The genome assembly was deposited at GenBank and annotated using the NCBI Prokaryotic Genome Annotation Pipeline (11) v6.10. Default parameters were used for all listed software unless otherwise noted.

The draft genome consists of 5 contigs, with a total length of 9,773,268 bp, a GC content of 63.48%, an assembly N50 value of 9,330,649 bp, an estimated coverage of 112×, and a completeness of 96.1%. It contains 9,089 protein-coding genes, 55 tRNAs, and 6 rRNAs.

Primary taxonomic identification was performed using the Type (Strain) Genome Server (TYGS) (12, 13) v401 platform. Phylogenomic analysis based on whole-genome sequences using the Genome BLAST Distance Phylogeny (GBDP) method placed strain RCAM1614 within a well-supported clade alongside Bradyrhizobium barranii strains. The most closely related type strain was B. barranii subsp. apii 38S5ᵀ with a digital DNA-DNA hybridization value of 75.1% (Fig. 1). The final taxonomy check was provided by GenBank with B. barranii 97.36% average nucleotide identity match.

Fig 1.

A phylogenetic tree illustrates evolutionary relationships among Bradyrhizobium species, with bootstrap support values marking branch confidence and close genetic association between Bradyrhizobium sp. RCAM1614 and related strains.

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Bradyrhizobium sp. RCAM1614 whole-genome based phylogenetic analysis. The numbers above the branches are the GBDP pseudo-bootstrap support values greater than 60%. Strain RCAM1614 (bold), B. barranii subsp. apii 38S5ᵀ (green dot), B. japonicum USDA 6ᵀ (red dot).

ACKNOWLEDGMENTS

This work was supported by the Ministry of Science and Higher Education of the Russian Federation within the framework of the Agreement of May 29, 2025 No. 075-15-2025-472 on the provision of a grant in the form of a subsidy from the federal budget for the implementation of the project: "Expansion of the fund and development of genomic research in the collection of microorganisms the Network Collection of Bioresources in the field of genetic technologies for agriculture (RCAM)".

The research was performed using equipment of the Core Centrum "Genomic Technologies, Proteomics and Cell Biology" in ARRIAM.

Data analysis was performed using the Galaxy server (https://usegalaxy.org/).

Contributor Information

Viktor E. Tsyganov, Email: vetsyganov@arriam.ru.

André O. Hudson, Rochester Institute of Technology, Rochester, New York, USA

DATA AVAILABILITY

Assembly and sequence data have been deposited in the GenBank under the BioProject accession number PRJNA1311437. Assembly has been deposited under the accession number GCA_052402455.1. The demultiplexed FASTQ file, with barcodes removed, from the MinION run has been deposited in the Sequence Read Archive (SRA) under number SRX30289055. This announcement describes the first version of the genome assembly.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

Assembly and sequence data have been deposited in the GenBank under the BioProject accession number PRJNA1311437. Assembly has been deposited under the accession number GCA_052402455.1. The demultiplexed FASTQ file, with barcodes removed, from the MinION run has been deposited in the Sequence Read Archive (SRA) under number SRX30289055. This announcement describes the first version of the genome assembly.

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