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

Larissa Carvalho Ferreira, Jude E. Maul, Marcus Vinicius Canário Viana, Thiago Jesus de Sousa, Vasco Ariston de Carvalho Azevedo, Daniel P. Roberts, Jorge Teodoro de Souza*

*Awdur cyfatebol y gwaith hwn

Allbwn ymchwil: Cyfraniad at gyfnodolynErthygladolygiad gan gymheiriaid

3 Dyfyniadau(SciVal)
267 Wedi eu Llwytho i Lawr (Pure)

Crynodeb

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.

Iaith wreiddiolSaesneg
Tudalennau (o-i)245-250
Nifer y tudalennau6
CyfnodolynBrazilian Journal of Microbiology
Cyfrol52
Rhif cyhoeddi1
Dyddiad ar-lein cynnar23 Medi 2020
Dynodwyr Gwrthrych Digidol (DOIs)
StatwsCyhoeddwyd - 01 Maw 2021

Ôl bys

Gweld gwybodaeth am bynciau ymchwil 'Complete genome sequence of the biocontrol agent Serratia marcescens strain N4–5 uncovers an assembly artefact'. Gyda’i gilydd, maen nhw’n ffurfio ôl bys unigryw.

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