Hybrid assembly using long reads resolves repeats and completes the genome sequence of a laboratory strain of Staphylococcus aureus subsp. aureus RN4220

Suresh Panthee, Hiroshi Hamamoto, Atmika Paudel, Chikara Kaito, Yutaka Suzuki, Kazuhisa Sekimizu

Research output: Contribution to journalArticlepeer-review

Abstract

Staphylococcus aureus RN4220 has been extensively used by staphylococcal researchers as an intermediate strain for genetic manipulation due to its ability to accept foreign DNA. Despite its wide use in laboratories, its complete genome is not available. In this study, we used a hybrid genome assembly approach using minION long reads and Illumina short reads to sequence the complete genome of S. aureus RN4220. The comparative analysis of the annotated complete genome showed the presence of 39 genes fragmented in the previous assembly, many of which were located near the repeat regions. Using RNA-Seq reads, we showed that a higher number of reads could be mapped to the complete genome than the draft genome and the gene expression profile obtained using the complete genome also differs from that obtained from the draft genome. Furthermore, by comparative transcriptomic analysis, we showed the correlation between expression levels of staphyloxanthin biosynthetic genes and the production of yellow pigment. This study highlighted the importance of long reads in completing microbial genomes, especially those possessing repetitive elements.

Original languageEnglish
Article numbere11376
JournalHeliyon
Volume8
Issue number11
DOIs
Publication statusPublished - Nov 2022

Keywords

  • Complete genome
  • Hybrid assembly
  • Repeat regions
  • RN4220
  • RNA-Seq
  • Staphylococcus aureus
  • Staphyloxanthin

ASJC Scopus subject areas

  • General

Fingerprint

Dive into the research topics of 'Hybrid assembly using long reads resolves repeats and completes the genome sequence of a laboratory strain of Staphylococcus aureus subsp. aureus RN4220'. Together they form a unique fingerprint.

Cite this