EurekaMag.com logo
+ Site Statistics
References:
52,725,316
Abstracts:
28,411,598
+ Search Articles
+ Subscribe to Site Feeds
EurekaMag Most Shared ContentMost Shared
EurekaMag PDF Full Text ContentPDF Full Text
+ PDF Full Text
Request PDF Full TextRequest PDF Full Text
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter
Follow on Google+Follow on Google+
Follow on LinkedInFollow on LinkedIn

+ Translate

Inter- and intra-strain variability of tandem repeats in Mycoplasma pneumoniae based on next-generation sequencing data


Future Microbiology (): -
Inter- and intra-strain variability of tandem repeats in Mycoplasma pneumoniae based on next-generation sequencing data
To characterize inter- and intra-strain variability of variable-number tandem repeats (VNTRs) in Mycoplasma pneumoniae to determine the optimal multilocus VNTR analysis scheme for improved strain typing. Whole genome assemblies and next-generation sequencing data from diverse M. pneumoniae isolates were used to characterize VNTRs and their variability, and to compare the strain discriminability of new VNTR and existing markers. We identified 13 VNTRs including five reported previously. These VNTRs displayed different levels of inter- and intra-strain copy number variations. All new markers showed similar or higher discriminability compared with existing VNTR markers and the P1 typing system. Our study provides novel insights into VNTR variations and potential new multilocus VNTR analysis schemes for improved genotyping of M. pneumoniae.


Accession: 058133583

PMID: 27728978

DOI: 10.2217/fmb-2016-0111



Related references

The accuracy, feasibility and challenges of sequencing short tandem repeats using next-generation sequencing platforms. Plos One 9(12): E113862-E113862, 2015

Variability of trinucleotide tandem repeats in the MgPa operon and its repetitive chromosomal elements in Mycoplasma genitalium. Journal of Medical Microbiology 61(Pt 2): 191-197, 2012

Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching. Genomics Data 7: 307-317, 2016

A comparison of inter-site, intra-site, intra-sample and instrument variability in environmental magnetic data: An example based on the Gwendraeth estuary, south Wales, U.K. Journal of Coastal Research 20(3): 808-813, 2004

Whole-Genome Sequencing of Macrolide-Resistant Mycoplasma pneumoniae Strain S355, Isolated in China. Genome Announcements 4(2): -, 2016

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. Genome Research 25(5): 736-749, 2016

Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe's oldest Camellia japonica. Chromosome Research 23(4): 791-806, 2016

Determination of inter- and intra-species genetic relationships among six Eucalyptus species based on inter-simple sequence repeats (ISSR). Tree Physiology 25(10): 1295-1302, 2005

Direct repeats in the non-coding region of rabbit mitochondrial DNA. Involvement in the generation of intra- and inter-individual heterogeneity. European Journal of Biochemistry 194(2): 561-571, 1990

Molecular typing of of Mycobacterium tuberculosis using variable number tandem repeats based on mycobacterial interspersed repetitive units alone and in association with exact tandem repeats. Abstracts of the General Meeting of the American Society for Microbiology 103: C-238, 2003