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

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.

Inhibition of Foodborne Pathogenic Bacteria by Excreted Metabolites of Serratia marcescens Strains Isolated from a Dairy-Producing Environment

“…S. marcescens biocontrol strains were isolated and characterized earlier, but the reported bacteria can be used for field application in order to minimize the use of chemical fungicides and insecticides for disease control [ 8 , 44 , 45 , 46 , 47 ]. The isolated and investigated S. marcescens strains investigated in this study have potential as effective and persistent biological control agents for food industrial application.…”

Whole-genome sequencing analysis of multidrug-resistant Serratia marcescens isolates in an intensive care unit in Brazil

“…Genomic libraries were prepared using an Illumina HiSeq 2500 system (Illumina Inc., California, USA) with coverage greater than 1000×. We based the 1000x coverage parameter on genomic analysis of whole genome sequence (WGS) of other strains with a coverage of 662x [19]. The raw data obtained were reassembled using the SPAdes v.3.10.0 algorithm in Pathosystems Resource Integration Centre assembly (PATRIC) server (https://www.patricbrc.org/) [36], and annotations were made using Rapid Annotation using Subsystem Server Technology (RAST) [37].…”

Complete Genome Sequences of One Prodigiosin-Producing Serratia marcescens Strain ZPG19

“…As the typical species of the genus Serratia, Serratia marcescens is a rod-shaped, facultatively anaerobic, Gram-negative bacterium of the family Enterobacteriaceae (Hejazi and Falkiner, 1997 ; Matsushita et al, 2009 ; Gaultier et al, 2018 ). It has been reported as an opportunistic human pathogen that may cause the hospital-acquired infections (Ferreira et al, 2020 ). Remarkably, S. marcescens has the ability to produce a series of valuable products, including prodigiosin, chitinase, protease, lipase, nuclease, bacteriocin, surfactant, and wetting agent.…”