Here, we report the complete genome sequence of Mesorhizobium mediterraneum R31, a rhizobial strain recommended and used as a commercial inoculant for chickpea in Argentina. The genome consists of 7.25 Mb, distributed into four circular replicons: a chromosome of 6.72 Mbp and three plasmids of 0.29, 0.17, and 0.07 Mbp.This work was supported by grants from the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), PID2020-113207GBI00, funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe,” P20_0047, funded by the Junta de Andalucía PAIDI/FEDER/EU; and the Biotechnology and Biosciences Research Council (BBSRC). We thank OGC at the Wellcome Center for Human Genetics for the sequencing data and BMRC for processing (supported by Wellcome Trust Core Award grant 203141/Z/16/Z and the NIHR Oxford BRC).M INCyT | Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) PICT-2018-01727 Pablo Bogin

Alzari, P.

Ben-Assaya, M.

Bogino, P.

Carezzano, M.E.

Foresto, E.

Giordano, W.

Martinez, M.

Martínez-Abarca, Francisco

Mornico, D.

Nievas, F.

Puente, M.

Revale, S.

Santoro, M.

English

Digital.CSIC

 | Bacteriology | AnnouncementGenome sequence of Mesorhizobium mediterraneum strain R31, a nitrogen-fixing rhizobium used as an inoculant for chickpea in ArgentinaEmiliano Foresto,1 Santiago Revale,2 Fiorela Nievas,1 María Evangelina Carezzano,1 Mariana Puente,3 Pedro Alzari,4 Mariano Martinez,4 Mathilde Ben-Assaya,4 Damien Mornico,5 Maricel Santoro,6 Francisco Martinez-Abarca,7 Walter Giordano,1 Pablo Bogino1AUTHOR AFFILIATIONS See affiliation list on p. 2.ABSTRACT Here, we report the complete genome sequence of Mesorhizobium mediterraneum R31, a rhizobial strain recommended and used as a commercial inoculant for chickpea in Argentina. The genome consists of 7.25 Mb, distributed into four circular replicons: a chromosome of 6.72 Mbp and three plasmids of 0.29, 0.17, and 0.07 Mbp.KEYWORDS Mesorhizobium mediterraneumI noculating legumes with rhizobia is a sustainable agricultural strategy. Rhizobia fertilize the crop biologically through nitrogen-fixing symbiosis and thus prevent nitrogen deficiency (1, 2). The Instituto Nacional de Tecnología Agropecuaria (INTA) in Argentina provides two strains of different species to inoculate chickpea, Mesorhizobium ciceri R30 and Mesorhizobium mediterraneum R31 (3). We recently reported the com­plete annotated genome of the former, M. ciceri strain R30 (4); here, we announce the complete annotated genome of the latter, M. mediterraneum R31. To date, only two incomplete genomes for M. mediterraneum strains (CCBAU 01399 and USDA 3392) are available in NCBI.A pure culture of M. mediterraneum R31, grown in yeast extract-mannitol medium at 30°C with 150 rpm rotation for four4 days (optical density at 600 nm [OD600], 1.0) (5), was the source for the total DNA. It was obtained with a DNeasy Blood && Tissue Kit (Qiagen) for Illumina sequencing and a Promega Wizard HMW DNA Extraction Kit (Promega) for Oxford Nanopore Technologies sequencing. The genome was assembled through a hybrid approach, including short Illumina reads and long Oxford Nanopore reads. Illumina’s library was prepared with a Nextera XT DNA Library Preparation Kit and sequenced on Illumina NextSeq 500 with a paired-end 150-bp read configura-tion. Nanopore’s library was prepared with an Oxford Nanopore Technologies Rapid Barcoding sequencing kit (SQK-RBK004) and sequenced in two Flongle flowcells. Data were base-called on Guppy v4.2.2, using the high-accuracy model and the --trim_barco­des option. We obtained 6,441,624 Illumina PE reads predicting a 132-fold coverage, and 119,523 Nanopore long reads which averaged 5,027 bp and predicted an 83-fold coverage. The raw reads were quality controlled by manually inspecting the reports obtained on FastQC (6) (Illumina) and PycoQC (7) (Nanopore). Hybrid genome assembly was performed with the raw reads in the nf-core/bacass pipeline (commit ceebac0) set at default parameters (8). This resulted in four contigs that were closed by man­ually analyzing the overlapped ends on Geneious software version 2019 2.1 (9). DNA content analysis revealed a genome made up of one large chromosome (6,720,795 bp, G+C content 62.2%) and three minor replicons from the repABC plasmid family (10) October 2023  Volume 12  Issue 10 10.1128/MRA.00581-23 1Editor Julie C. Dunning HotoppAddress correspondence to Pablo Bogino, pbogino@exa.unrc.edu.ar, or Walter Giordano, wgiordano@exa.unrc.edu.ar.Emiliano Foresto and Santiago Revale contributed equally to this article. Author order was determined by seniority in working with chickpea nodulating strains.The authors declare no conflict of interest.See the funding table on p. 3.Received 1 July 2023Accepted 24 August 2023Published 29 September 2023Copyright © 2023 Foresto et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Downloaded from https://journals.asm.org/journal/mra on 26 February 2024 by 161.111.252.200.(293,882 bp, G+C content 60.1%; 175,478 bp, G+C content 60.2%; and 66,723 bp, G+C 58.6%).The complete genome, which was annotated in the NCBI Prokaryotic Genomes Annotation Pipeline (PGAP) (11–13), consists of 6,695 protein-coding sequences, two complete ribosomal operons, and 53 tRNAs. The genes for nodulation (nod) and nitrogen fixation (nif and fix) appear to be located on a chromosomal 480 kb symbiosis island (1,850,730 to 2,330,771 bp), flanked by direct repeat sequences (22 nt) identical to those in the ICE region in other mesorhizobia, and adjacent to one of four serine tRNA genes (4, 14). This region also harbors mobile genes (transposases, integrases, and recombinases) probably associated with the island’s excision and transfer (15, 16).This complete genome sequence of an M. mediterraneum strain could be crucial for more in-depth research into its symbiotic performance and other biological features of this species.ACKNOWLEDGMENTSThis work was supported by grants from the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), PID2020-113207GBI00, funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe,” P20_0047, funded by the Junta de Andalucía PAIDI/FEDER/EU; and the Biotechnology and Biosciences Research Council (BBSRC). We thank OGC at the Wellcome Center for Human Genetics for the sequencing data and BMRC for processing (supported by Wellcome Trust Core Award grant 203141/Z/16/Z and the NIHR Oxford BRC).We are also grateful to Vincent Enouf from Unité de Génétique Moléculaire des Virus à ARN-UMR3569 CNRS, Université de Paris, Center 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.AUTHOR AFFILIATIONS1Departamento de Biología Molecular, Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina2Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom3Instituto de Microbiología y Zoología Agrícola, Instituto Nacional de Tecnología Agropecuaria (IMYZA-INTA), Castelar, Argentina4Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France5Département Biologie Computationnelle, Hub de Bioinformatique et Biostatistique, CNRS USR 3756, Institut Pasteur, Paris, France6Department of Biochemistry, Max Planck for Chemical Ecology, Jena, Germany7Grupo de Ecología Genética de la Rizósfera, Estación Experimental del Zaidín (CSIC), Granada, SpainAUTHOR ORCIDsPedro Alzari  http://orcid.org/0000-0002-4233-1903Walter Giordano  http://orcid.org/0000-0002-2436-922XPablo Bogino  http://orcid.org/0000-0001-7841-6119Announcement Microbiology Resource AnnouncementsOctober 2023  Volume 12  Issue 10 10.1128/MRA.00581-23 2Downloaded from https://journals.asm.org/journal/mra on 26 February 2024 by 161.111.252.200.FUNDINGFunder Grant(s) Author(s)MINCyT | Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT)PICT-2018-01727 Pablo BoginoDATA AVAILABILITYThe complete genome sequence of Mesorhizobium mediterraneum R31 is available at NCBI GenBank under accession numbers CP088151 for the chromosome, CP088152, CP088153, and CP088154 for the plasmids with BioProject ID PRJNA782313. and BioSample accession SAMN23372083. Raw data reads are available at NCBI’s Sequence Read Archive under accession numbers SRR16993324 to SRR16993326.REFERENCES1. Foresto E, Nievas F, Revale S, Giordano W, Bogino P. 2021. Deciphering the phylogenetic affiliation of rhizobial strains recommended as chickpea inoculants in Argentina. App Soil Ecol166:104069. https://doi.org/10.1016/j.apsoil.2021.1040692. Yang J, Lan L, Jin Y, Yu N, Wang D, Wang E. 2022. Mechanisms underlying legume-rhizobium symbioses. J Integr Plant Biol 64:244–267. https://doi.org/10.1111/jipb.132073. Santos MS, Nogueira MA, Hungria M. 2019. Microbial inoculants: reviewing the past, discussing the present and previewing an outstanding future for the use of beneficial bacteria in agriculture. AMB Express 9:205. https://doi.org/10.1186/s13568-019-0932-04. Foresto E, Revale S, Primo E, Nievas F, Carezzano E, Puente M, Alzari P, Martínez M, Ben-Assaya M, Mornico D, Santoro M, Martínez-Abarca F, Giordano W, Bogino P. 2022. Complete genome sequence of Mesorhi­zobium ciceri strain R30, a rhizobium used as a commercial Inoculant for chickpea in Argentina. Microbiol Resour Announc 11:e0077922. https://doi.org/10.1128/mra.00779-225. Somasegaran PH, Hoben H. 1994. Appendix 3: Media and staining solutions, p 383–384. In In Handbook for rhizobia: methods in legume-rhizobium technology. xvi. Springer, New York, NY. https://doi.org/10.1007/978-1-4613-8375-86. Andrews S. 2010. Fastqc: a quality control tool for high throughput sequence data. Available online at. Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/7. Leger A, Leonardi T. 2019. pycoQC, interactive quality control for oxford nanopore sequencing. JOSS 4:1236. https://doi.org/10.21105/joss.012368. Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. 2020. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol 38:276–278. https://doi.org/10.1038/s41587-020-0439-x9. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. https://doi.org/10.1093/bioinfor­matics/bts19910. MacLellan SR, Zaheer R, Sartor AL, MacLean AM, Finan TM. 2006. Identification of a megaplasmid centromere reveals genetic structural diversity within the repABC family of basic replicons. Mol Microbiol 59:1559–1575. https://doi.org/10.1111/j.1365-2958.2006.05040.x11. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw56912. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V, O’Neill K, Li W, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu F, Marchler GH, Song JS, Thanki N, Yamashita RA, Zheng C, Thibaud-Nissen F, Geer LY, Marchler-Bauer A, Pruitt KD. 2018. Refseq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 46:851–860. https://doi.org/10.1093/nar/gkx106813. Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, Coulouris G, Chitsaz F, Derbyshire MK, Durkin AS, Gonzales NR, Gwadz M, Lanczycki CJ, Song JS, Thanki N, Wang J, Yamashita RA, Yang M, Zheng C, Marchler-Bauer A, Thibaud-Nissen F. 2021. Refseq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res 49:D1020–D1028. https://doi.org/10.1093/nar/gkaa110514. Hill Y, Colombi E, Bonello E, Haskett T, Ramsay J, O’Hara G, Terpolilli J. 2021. Evolution of diverse effective N2-Fixing Microsymbionts of Cicer arietinum following horizontal transfer of the Mesorhizobium ciceri CC1192 Symbiosis integrative and conjugative element. Appl Environ Microbiol 87:e02558-20. https://doi.org/10.1128/AEM.02558-2015. Ramsay JP, Sullivan JT, Stuart GS, Lamont IL, Ronson CW. 2006. Excision and transfer of the Mesorhizobium loti R7A Symbiosis Island requires an Integrase IntS, a novel recombination directionality factor RdfS, and a putative relaxase RlxS. Mol Microbiol 62:723–734. https://doi.org/10.1111/j.1365-2958.2006.05396.x16. Haskett TL, Terpolilli JJ, Bekuma A, O’Hara GW, Sullivan JT, Wang P, Ronson CW, Ramsay JP. 2016. Assembly and transfer of tripartite integrative and conjugative genetic elements. Proc Natl Acad Sci U S A 113:12268–12273. https://doi.org/10.1073/pnas.1613358113Announcement Microbiology Resource AnnouncementsOctober 2023  Volume 12  Issue 10 10.1128/MRA.00581-23 3Downloaded from https://journals.asm.org/journal/mra on 26 February 2024 by 161.111.252.200.

Genome sequence of Mesorhizobium mediterraneum strain R31, a nitrogen-fixing rhizobium used as an inoculant for chickpea in Argentina

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Genome sequence of Mesorhizobium mediterraneum strain R31, a nitrogen-fixing rhizobium used as an inoculant for chickpea in Argentina

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