Complete genome sequence of the biocontrol agent Serratia marcescens strain N4–5 uncovers an assembly artefact
| Autor: | Daniel P. Roberts, Larissa Carvalho Ferreira, Jorge Teodoro de Souza, Marcus Vinicius Canário Viana, Vasco Azevedo, Thiago Jesus de Sousa, Jude E. Maul |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Sequence assembly
Bacterial genome size Microbiology Genome Serratia Bacterial Fungal and Virus Molecular Biology - Short Communication 03 medical and health sciences symbols.namesake RNA Ribosomal 16S Media Technology Gene Phylogeny Serratia marcescens 030304 developmental biology Whole genome sequencing Sanger sequencing Genetics Base Composition 0303 health sciences Whole Genome Sequencing biology 030306 microbiology Sequence Analysis DNA biology.organism_classification Biological Control Agents symbols Genome Bacterial |
| Zdroj: | Braz J Microbiol |
| ISSN: | 1678-4405 1517-8382 |
| Popis: | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s42770-020-00382-2) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full text from SpringerLink