Pacific Biosciences of California Inc (PACB)

[Paulieme]

Posted July 19, 2016.-- SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis-- Abstract

The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of its virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing. Our assembly reveals that the number of H37Ra-specific variants is less than half of what the Sanger-based H37Ra reference sequence indicates, undermining and, in some cases, invalidating the conclusions of several studies. PE_PPE family genes, which are intractable to commonly-used sequencing platforms because of their repetitive and GC-rich nature, are overrepresented in the set of genes in which all reported H37Ra-specific variants are contradicted. We discuss how our results change the picture of virulence attenuation and the power of SMRT sequencing for producing high-quality reference genomes.-- Tweets referencing this article:
Logan Fink
@logan_d_fink
RT @ZaminIqbal: PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6…
05:47PM
Afif Elghraoui
@afif_elghraoui
We @Valafarlab used @PacBio to correct attenuated Mtb strain reference genome. Much clearer genetics of virulence! https://t.co/ffMey7wv6p
05:40PM
Pacific Biosciences
@PacBio
RT @ZaminIqbal: PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6…
04:24PM
Dan
@danielkein
RT @ZaminIqbal: PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6…
04:00PM
Literature Bot
@litscraper
SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium… https://t.co/18vichfXdE
02:33PM
Keith Robison
@OmicsOmicsBlog
RT @ZaminIqbal: PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6…
12:42PM
Lei ZHANG
@jameslz
RT @ZaminIqbal: PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6…
11:59AM
Zamin Iqbal
@ZaminIqbal
PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6i67T
11:48AM
Carlos Magalhães
@CarlosARMagal
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
11:07AM
madhu
@madhubioinfo
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
10:44AM
Jan-Jaap Wesselink
@janjwesselink
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
10:26AM
Afonso Henriques
@AfonsoHenriques
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
10:25AM
Nick Loman
@pathogenomenick
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
10:23AM
Nouri Ben Zakour
@genomiss
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
10:18AM
Brian Forde
@fordebm
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
10:04AM
Paul R Johnston
@Paul_R_Johnston
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
09:58AM
Philipp Bayer
@PhilippBayer
SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t.co/DBGJqqdSVP
09:51AM
Tim Stinear
@tstinear
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
09:01AM
Anders G da Silva
@drandersgs
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
06:47AM
Matteo Floris
@babamatteo
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
06:05AM
Russell Orr
@RJSOrr77
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
06:04AM
Biswapriya Misra
@BiswapriyaMisra
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
04:51AM
Pooled Sequencing
@pooledseq
bioArXiv_ SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium… https://t.co/WpeikUJLC6
04:46AM
bxv_genomics
@bxv_genomics
SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium… https://t.co/zspgZEvd0S #genomics
04:17AM
bioRxiv
@biorxivpreprint
SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
04:00AM
bioRxiv Genomics
@biorxiv_genomic
SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic ... https://t.co/zYF3YdMK8g #biorxiv_genomic
04:00AM
http://biorxiv.org/content/early/2016/07/19/064840