Complete genome sequences of Streptococcus pyogenes type strain reveal 100%-match between PacBio-solo and Illumina-Oxford Nanopore hybrid assemblies.

Scientific Reports
Francisco Salvà-SerraEdward R B Moore

Abstract

We present the first complete, closed genome sequences of Streptococcus pyogenes strains NCTC 8198T and CCUG 4207T, the type strain of the type species of the genus Streptococcus and an important human pathogen that causes a wide range of infectious diseases. S. pyogenes NCTC 8198T and CCUG 4207T are derived from deposit of the same strain at two different culture collections. NCTC 8198T was sequenced, using a PacBio platform; the genome sequence was assembled de novo, using HGAP. CCUG 4207T was sequenced and a de novo hybrid assembly was generated, using SPAdes, combining Illumina and Oxford Nanopore sequence reads. Both strategies yielded closed genome sequences of 1,914,862 bp, identical in length and sequence identity. Combining short-read Illumina and long-read Oxford Nanopore sequence data circumvented the expected error rate of the nanopore sequencing technology, producing a genome sequence indistinguishable to the one determined with PacBio. Sequence analyses revealed five prophage regions, a CRISPR-Cas system, numerous virulence factors and no relevant antibiotic resistance genes. These two complete genome sequences of the type strain of S. pyogenes will effectively serve as valuable taxonomic and genomic references fo...Continue Reading

References

Dec 1, 1992·Infection and Immunity·P P ClearyJ Handley
Oct 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·M R WesselsT J DiCesare
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Apr 11, 2001·Proceedings of the National Academy of Sciences of the United States of America·J J FerrettiR McLaughlin
Mar 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·James C SmootJames M Musser
Apr 3, 2002·The EMBO Journal·Ulrich von Pawel-RammingenLars Björck
Jul 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Stephen B BeresJames M Musser
Sep 9, 2004·Frontiers in Bioscience : a Journal and Virtual Library·Wayne Hynes
Jan 26, 2005·Proceedings of the National Academy of Sciences of the United States of America·Paul SumbyJames M Musser
Mar 18, 2005·Annual Review of Immunology·Ren-Feng Guo, Peter A Ward
Sep 15, 2005·Journal of Bacteriology·Konstantinos T Konstantinidis, James M Tiedje
Oct 29, 2005·The Lancet Infectious Diseases·Jonathan R CarapetisMartin Weber
Nov 30, 2005·Proceedings of the National Academy of Sciences of the United States of America·Nicola L SmithGary W Black
Dec 22, 2005·Infection and Immunity·Clarise Rivera Starr, N Cary Engleberg
Jan 16, 2007·International Journal of Systematic and Evolutionary Microbiology·Johan GorisJames M Tiedje
May 16, 2007·Molecular Microbiology·Andrea G O ManettiImmaculada Margarit
Jun 1, 2007·Nucleic Acids Research·Ibtissem GrissaChristine Pourcel
Aug 16, 2008·Science·Stan J J BrounsJohn van der Oost
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jul 21, 2009·Journal of Bacteriology·Christian LinkeEdward N Baker
Oct 27, 2009·Proceedings of the National Academy of Sciences of the United States of America·Michael Richter, Ramon Rosselló-Móra
Mar 31, 1933·The Journal of Experimental Medicine·R C Lancefield
Apr 23, 2010·Systematic and Applied Microbiology·H-P Klenk, M Göker
Oct 20, 2010·Bioinformatics·Aaron PetkauGary Van Domselaar
Nov 11, 2010·Nucleic Acids Research·Rasko LeinonenUNKNOWN International Nucleotide Sequence Database Collaboration
May 17, 2011·PloS One·Takashi NozawaIchiro Nakagawa
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Dec 18, 2012·Current Topics in Microbiology and Immunology·Anna P Ralph, Jonathan R Carapetis
Feb 21, 2013·Bioinformatics·Alexey GurevichGlenn Tesler
Feb 26, 2013·BMC Bioinformatics·Jan P Meier-KolthoffMarkus Göker
May 7, 2013·Nature Methods·Chen-Shan ChinJonas Korlach
Sep 17, 2013·Genome Biology·Sergey KorenAdam M Phillippy
Mar 20, 2014·Bioinformatics·Torsten Seemann

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Datasets Mentioned

BETA
ERR550482
ERR550487
SRR8631872
SRR10092043
LN831034
CP028841

Software Mentioned

Sickle
Canu
Pilon
PGAP
QUAST
BLASTN
SPAdes
Albacore
JSpecies - Genome Distance Calculator ( GGDC )
CRISPRFinder

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