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Complete genome sequence of the biocontrol agent Serratia marcescens strain N4–5 uncovers an assembly artefact

  • Bacterial Fungal and Virus Molecular Biology - Short Communication
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Abstract

Serratia marcescens are gram-negative bacteria found in several environmental niches, including the plant rhizosphere and patients in hospitals. Here, we present the genome of Serratia marcescens strain N4–5 (=NRRL B-65519), which has a size of 5,074,473 bp (664-fold coverage) and contains 4840 protein coding genes, 21 RNA genes, and an average G + C content of 59.7%. N4–5 harbours a plasmid of 11,089 bp and 43.5% G + C content that encodes six unique CDS repeated 2.5× times totalling 13 CDS. Our genome assembly and manual curation uncovered the insertion of two extra copies of the 5S rRNA gene in the assembled sequence, which was confirmed by PCR and Sanger sequencing to be a misassembly. This artefact was subsequently removed from the final assembly. The occurrence of extra copies of the 5S rRNA gene was also observed in most complete genomes of Serratia spp. deposited in public databases in our comparative analysis. These elements, which also occur naturally, can easily be confused with true genetic variation. Efforts to discover and correct assembly artefacts should be made in order to generate genome sequences that represent the biological truth underlying the studied organism. We present the genome of N4–5 and discuss genes potentially involved in biological control activity against plant pathogens and also the possible mechanisms responsible for the artefact we observed in our initial assembly. This report raises awareness about the extra copies of the 5S rRNA gene in sequenced bacterial genomes as they may represent misassemblies and therefore should be verified experimentally.

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Acknowledgements

LCF and JTS acknowledge the financial support from CNPq, Brazil.

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Authors and Affiliations

  1. Plant Pathology Department, Federal University of Lavras, Lavras, MG, 37200-000, Brazil

    Larissa Carvalho Ferreira

  2. Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK

    Larissa Carvalho Ferreira & Jorge Teodoro de Souza

  3. Sustainable Agricultural Systems Laboratory, USDA-Agricultural Research Service, Beltsville, MD, 20705, USA

    Jude E. Maul & Daniel P. Roberts

  4. Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil

    Marcus Vinicius Canário Viana, Thiago Jesus de Sousa & Vasco Ariston de Carvalho Azevedo

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  1. Larissa Carvalho Ferreira
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Correspondence to Jorge Teodoro de Souza.

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Responsible Editor: Rodrigo Galhardo.

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Data deposition: Trimmed sequence data and assembly are deposited in GenBank (accession numbers: NZ_CP031316.1 and NZ_CP031315.1).

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Ferreira, L.C., Maul, J.E., Viana, M.V.C. et al. Complete genome sequence of the biocontrol agent Serratia marcescens strain N4–5 uncovers an assembly artefact. Braz J Microbiol 52, 245–250 (2021). https://doi.org/10.1007/s42770-020-00382-2

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