# Complete Genome Sequence of Bradyrhizobium sp. Strain C-145, a Nitrogen-Fixing Rhizobacterium Used as a Peanut Inoculant in Argentina

Fiorela Nievas, Santiago Revale, Emiliano Foresto, Sacha Cossovich, Mariana Puente, Pedro Alzari, Mariano Martínez, Mathilde Ben-Assaya, Damien Mornico, Maricel Santoro, et al.

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Fiorela Nievas, Santiago Revale, Emiliano Foresto, Sacha Cossovich, Mariana Puente, et al. Complete Genome Sequence of Bradyrhizobium sp. Strain C-145, a Nitrogen-Fixing Rhizobacterium Used as a Peanut Inoculant in Argentina. Microbiology Resource Announcements, 2022, 11 (8), pp.e0050522. 10.1128/mra.00505-22. pasteur-03790333

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# Complete Genome Sequence of *Bradyrhizobium* sp. Strain C-145, a Nitrogen-Fixing Rhizobacterium Used as a Peanut Inoculant in Argentina

Fiorela Nievas,ª Santiago Revale,ᵇ Emiliano Foresto,ª Sacha Cossovich,ª Mariana Puente,ᶜ Pedro Alzari,ᵈ Mariano Martínez,ᵈ Mathilde Ben-Assaya,ᵈ Damien Mornico,ᵉ Maricel Santoro,ᵉ Francisco Martínez-Abarca,ᵉ Walter Giordano,ª Pablo Boginoª

**ABSTRACT** We present the complete genome sequence of *Bradyrhizobium* sp. strain C-145, one of the most widely used nitrogen-fixing rhizobacteria for inoculating peanut crops in Argentina. The genome consists of 9.53 Mbp in a single circular chromosome and was determined using a hybrid long- and short-read assembly approach.

The symbiosis between legumes and bacteria from the *Bradyrhizobium* genus is one of the most efficient and economically important worldwide (1). Inoculation of soybean and peanut crops with effective bradyrhizobia is an environmentally friendly alternative to chemical fertilization (2–4). The peanut-nodulating strain *Bradyrhizobium* sp. strain TAL 1371 (NifTAL code) was acquired by the Instituto Nacional de Tecnología Agropecuaria (INTA; Argentina) from the University of Texas (5). After being evaluated and reisolated from peanut cultivars, it was renamed *Bradyrhizobium* sp. strain C-145 and became the recommended choice for peanut inoculation. In symbiosis with this legume, it outperforms other *Bradyrhizobium* sp. strains in terms of nitrogen-fixing ability, productivity, and environmental competitiveness (4, 6–8). This is particularly relevant given the prominence of peanut cultivation in central Argentina (9). Knowledge of the strain’s genome is crucial for maintaining and developing further the current agricultural model.

To date, although 581 genome assemblies are registered in NCBI for *Bradyrhizobium* strains, most are draft sequences. No genome data were available until now for strains used in commercial peanut inoculants.

Here, we introduce the complete genome sequence of *Bradyrhizobium* sp. C-145. A pure culture of the strain, provided by INTA, was grown in liquid yeast extract-mannitol medium (5). This was the source for the total DNA, obtained using a DNeasy blood and tissue kit (Qiagen) for Illumina sequencing and using a Promega Wizard high-molecular-weight (HMW) DNA extraction kit (Promega) for Oxford Nanopore Technologies sequencing. Illumina sequencing was performed on the P2M (Plateforme de Microbiologie Mutualisée) platform at Institut Pasteur. The library was prepared using a Nextera XT DNA library preparation kit and then sequenced on an Illumina NextSeq 500 instrument in paired-end (PE) 150-bp read configuration. Nanopore sequencing was carried out at the Oxford Genomics Centre. The sample was processed using both an Oxford Nanopore Technologies rapid barcoding

Editor David A. Baltrus, University of Arizona

Copyright © 2022 Nievas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

Address correspondence to Pablo Bogino, pbogino@exa.unrc.edu.ar, or Walter Giordano, wgiordano@exa.unrc.edu.ar.

The authors declare no conflict of interest.

Received 24 May 2022

Accepted 5 July 2022

Published 19 July 2022

<footnote>ªInstituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina</footnote>

<footnote>ᵇWellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom</footnote>

<footnote>ᶜInstituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola, Castelar, Argentina</footnote>

<footnote>ᵈUnité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France</footnote>

<footnote>ᵉHub de Bioinformatique et Biostatistique—Département Biologie Computationnelle, CNRS USR 3756, Institut Pasteur, Paris, France</footnote>

<footnote><fDepartment of Biochemistry, Max Planck for Chemical Ecology, Jena, Germany</footnote>

<footnote n="9">⁹Structure, Dynamics, and Function of Rhizobacterial Genomes, Department of Plant and Soil Microbiology, Estación Experimental del Zaidín—CSIC, Granada, Spain</footnote>

<footnote>Fiorela Nievas and Santiago Revale contributed equally to this work. Author order was determined by seniority in working with peanut nodulating strains.</footnote>
sequencing kit (SQK-RBK004) and a native barcoding genomic DNA sequencing kit (SQK-LSK109 with EXP-NBD104). The products of each were sequenced in two Flongle flow cells. Data were base called using Guppy v4.2.2 using high-accuracy mode and the -trim_barcodes option. We obtained 6,542,626 Illumina PE reads and 41,545 Nanopore long reads (average, 5,030 bp), predicting 102-fold and 22-fold coverage, respectively. Hybrid genome assembly was performed on the raw reads using the nf-core/bacass pipeline (commit ceebac0) with default parameters (10). The assembly resulted in one contig that was closed by manually analyzing the overlapping ends using Geneious Basic (11). Accordingly, the assembly revealed a single chromosome of 9,529,571 bp with 62.9% G+C content, in line with what is known about the genus *Bradyrhizobium* (12). The genome, annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (13–15), consists of 8,500 protein-coding sequences, a single ribosomal operon, and 49 tRNAs. Like other *Bradyrhizobium* strains (16), C-145 features symbiotic islands in two zones (coordinates 1250 to 1535 kb and 6370 to 6750 kb), with a low GC content (59.8 and 58.5%, respectively), including most of the *nod*, *nif*, and *fix* genes. There are also several genes associated with the rhizospheric lifestyle (motility, exopolysaccharide production) and type I, II, III, and IV secretion systems.

This complete genome of a strain extensively used for peanut inoculation will enable
more in-depth, comparative genomic analyses to elucidate the specific mechanisms behind
*Bradyrhizobium*-peanut interactions.

**Data availability.** The complete genome sequence of *Bradyrhizobium* sp. C145 is available at NCBI GenBank under accession CP088150, BioProject accession number PRJNA782308, and BioSample accession number SAMN23371896. The raw data reads are available at NCBI's Sequence Read Archive under accession numbers SRR17030678 to SRR17030682.

ACKNOWLEDGMENTS

This work was supported by grants from the Consejo Nacional de Investigaciones
Científicas y Técnicas (CONICET), Agencia Nacional de Promoción Científica y Tecnológica
(ANPCyT), the Spanish Ministerio de Ciencia e Innovación (research grant PID2020-113207GB-
100), ERDF (European Regional Development Funds), and the Biotechnology and Biosciences
Research Council (BBSRC). It was also supported by Wellcome Trust Core Award grant number
203141/Z/16/Z and the NIHR Oxford BRC. We 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.

We 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 the Pasteur
International Bioresources network (PIBnet); to Institut Pasteur Paris for providing the resources
for Illumina sequencing; and finally, to F. Sgarlatta for proofreading the manuscript.

The views expressed are those of the author(s) and not necessarily those of the NHS,
the NIHR or the Department of Health.

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