ABSTRACT
We present the complete genome sequence of Bradyrhizobium sp. 62B, a strain isolated from the root nodules of peanut plants that grow in central Argentina. The genome consists of 8.15 Mbp, distributed into a chromosome of 7.29 Mbp and a plasmid of 0.86 Mbp.
KEYWORDS: Bradyrhizobium
ANNOUNCEMENT
The genus Bradyrhizobium (1) comprises genetically diverse rhizobia, which can establish symbiosis with different legumes (2), including peanut (Arachis hypogaea L.) (3–5). The isolation and characterization of native nitrogen-fixing strains may be key for the development of sustainable agriculture models (6–10).
Here, we announce the complete annotated genome of Bradyrhizobium sp. 62B, a native strain isolated from peanut grown in central Argentina (33°06′27″S, 64°17′60″W). The strain was isolated from a single root nodule, which was sterilized, stabbed, and aerobically cultivated on YEM agar plates (11) for 7 days at 28°C (7). After restreaking to obtain a single colony, a pure culture grown on YEM liquid for 7 days at 28°C was used to confirm the symbiotic ability on peanut plants (7), and was the source of total gDNA for sequencing. DNA was obtained either with a DNeasy Blood & Tissue kit (Qiagen, MD, USA) for Illumina sequencing (P2M platform, Institut Pasteur, France), or a Wizard HMW DNA extraction kit (Promega, WI, USA) for Oxford Nanopore Tech (Oxford Genomic Centre Services, UK). The Illumina library was prepared using a Nextera XT DNA Library Preparation kit and then sequenced on an Illumina NextSeq 500 instrument with a paired-end 150 bp read configuration. Two libraries were prepared for Nanopore sequencing: one with an Oxford Nanopore Technologies Rapid Barcoding sequencing kit (SQK-RBK004, transposase fragmentation) and the other with a Native Barcoding Genomic DNA sequencing kit (SQK-LSK109 with EXP-NBD104, mechanical fragmentation). Each library was individually sequenced in two Flongle flow cells. Data were basecalled with Guppy v4.2.2, using the high-accuracy model and the --trim_barcodes option. We obtained a combination of Illumina PE reads and Nanopore long reads (Table 1). All bioinformatic analyses were performed using default parameters unless otherwise specified. Hybrid genome assembly was performed using all the libraries together with the nf-core/bacass pipeline (commit date 2021-03-23) (12). QC filtering and trimming were performed on both read sets as part of the nf-core/bacass pipeline. The assembly resulted in two contigs that were closed by manually analyzing the overlapping ends on Geneious version 2019 2.1 (13). Replicons were rotated based on the fixstart method, with dnaA and repA as the start positions for chromosome and plasmid, respectively (14), and annotated with Prokaryotic Genome Annotation Pipeline v6.6 (15–17). The whole genome consists of one chromosome (7,289,796 bp, G + C content 64.5%) containing a single ribosomal operon and 48 tRNAs, and a repABC plasmid (859,431 bp, G + C content 60%) (18), encoding a total of 7,518 proteins across both replicons. Average nucleotide identity analysis (ANI calculator on line version) (19) revealed taxonomic identification of 62B at the genus level, being the closest genome (97.63%) Bradyrhizobium sp. CCBAU 53351 (NZ_CP030059.1).
TABLE 1.
Main metric data associated with the sequenced Bradyrhizobium sp. 62B strain
| Accession | Technology | Number of reads | Total sequencing data (Mbp) | GC content (%) | Coverage | Average length (bp) | Longest sequence (bp) | N50 (bp) |
|---|---|---|---|---|---|---|---|---|
| SRR17042237 | Nanopore | 39,581 | 164.5 | 63.61 | 20 | 4,156 | 48,037 | 7,771 |
| SRR17042238 | Nanopore | 5,560 | 24.8 | 63.27 | 3 | 4,453 | 67,593 | 12,925 |
| SRR17042239 | Nanopore | 10,135 | 53.3 | 63.31 | 7 | 5,257 | 70,559 | 12,787 |
| SRR17042240 | Nanopore | 6,531 | 34.6 | 63.73 | 4 | 5,296 | 66,708 | 12,464 |
| Total Nanopore | 61,807 | 277.2 | 63.54 | 34 | 4,484 | 70,559 | 8,926 | |
| SRR17042241 | Illumina | 6,537,438 | 965.1 | 63.7 | 119 | 151 |
In contrast to other Bradyrhizobium, which generally harbor genes involved in symbiosis on chromosomic islands, the Bradyrhizobium sp. 62B genome contains them in the plasmid (20, 21). It also carries genes predicted to be related to conjugative transfer proteins and the type three secretion system (22), features related to broader host specificity and putative plasmid transfer toward other strains (23).
ACKNOWLEDGMENTS
The authors thank the Oxford Genomics Centre at the Wellcome Centre for Human Genetics (funded by Wellcome Trust grant reference 203141/Z/16/Z) for the sequencing data. The authors are also grateful to Vincent Enouf from Unité de Génétique Moléculaire des Virus à ARN - UMR3569 CNRS, Université de Paris, Centre National de Référence Virus des Infections Respiratoires (dont la grippe); to Plateforme de Microbiologie Mutualisée (P2M) and Pasteur International Bioresources network (PIBnet); to Institut Pasteur Paris for providing the resources for Illumina sequencing; and finally to Ms. F. Sgarlatta for proofreading the manuscript.
This work was supported by grants from the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT); and the Spanish Ministerio de Ciencia e Innovación research grant PID2020-113207GB-I00, including the ERDF (European Regional Development Funds) and the Biotechnology and Biosciences Research Council (BBSRC). It was also supported by the Wellcome Trust Core Award Grant Number 203141/Z/16/Z and the NIHR Oxford BRC. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health.
Contributor Information
Walter Giordano, Email: wgiordano@exa.unrc.edu.ar.
Pablo Bogino, Email: pbogino@exa.unrc.edu.ar.
Leighton Pritchard, University of Strathclyde, United Kingdom.
DATA AVAILABILITY
The complete genome sequence of Bradyrhizobium sp. 62B is available at NCBI GenBank under accession CP092841 for the chromosome and CP092842 for the plasmid with BioProject ID PRJNA782308 and BioSample accession SAMN23371906. Raw data reads are available at NCBI’s Sequence Read Archive under accessions SRR17042237, SRR17042238, SRR17042239, SRR17042240, and SRR17042241.
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Associated Data
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Data Availability Statement
The complete genome sequence of Bradyrhizobium sp. 62B is available at NCBI GenBank under accession CP092841 for the chromosome and CP092842 for the plasmid with BioProject ID PRJNA782308 and BioSample accession SAMN23371906. Raw data reads are available at NCBI’s Sequence Read Archive under accessions SRR17042237, SRR17042238, SRR17042239, SRR17042240, and SRR17042241.