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Generation and Analysis of Draft Sequences of 'Stolbur' Phytoplasma from Multiple Displacement Amplification Templates

Title:
Generation and Analysis of Draft Sequences of 'Stolbur' Phytoplasma from Multiple Displacement Amplification Templates
Abstract:
Phytoplasma-associated diseases are reported for more than 1,000 plant species worldwide. Only a few genome sequences are available in contrast to the economical importance of these bacterial pathogens. A new strategy was used to retrieve phytoplasma strain-specific genome data. Multiple displacement amplification was performed on DNA obtained from <3 g of plant tissue from tobacco and parsley samples infected with 'stolbur' strains. Random hexamers and Phi29 polymerase were evaluated with and without supplementation by group-assigned oligonucleotides providing templates for Illumina's sequencing approach. Metagenomic drafts derived from individual and pooled strain-specific de novo assemblies were analyzed. Supplementation of the Phi29 reaction with the group-assigned oligonucleotides resulted in an about 2-fold enrichment of the percentage of phytoplasma-assigned reads and thereby improved assembly results. The obtained genomic drafts represent the largest datasets available from 'stolbur' phytoplasmas. Sequences of the two strains (558 kb, 448 proteins and 516 kb, 346 proteins, respectively) were annotated allowing the identification of prominent membrane proteins and reconstruction of core pathways. Analysis of a putative truncated sucrose phosphorylase provides hints on sugar degradation. Furthermore, it is shown that drafts obtained from repetitive-rich genomes allow only limited analysis on multicopy regions and genome completeness. (C) 2013 S. Karger AG, Basel
Year:
2014
Publication type:
Journal article
Journal:
Journal of Molecular Microbiology and Biotechnology
ISSN:
1464-1801
Number:
1
Volume:
24
Pages:
1-11
Language:
English
Document status:
Open access
PubListerURL:
https://publister.bib.th-wildau.de/publister/public/publication/285
Mitrovic, J., Siewert, C., Duduk, B., Hecht, J., Molling, K., Bröcker, F., et al. (2014). Generation and Analysis of Draft Sequences of 'Stolbur' Phytoplasma from Multiple Displacement Amplification Templates Journal of Molecular Microbiology and Biotechnology. 24 (1), 1-11.
@article{285,
    author           = {Mitrovic, Jelena and Siewert, Christin and Duduk, Bojan and Hecht, J. and Molling, Karin and Bröcker, Felix and Beyerlein, Peter and Büttner, Carmen and Bertaccini, Assunta and Kube, Michael},
    title            = {Generation and Analysis of Draft Sequences of 'Stolbur' Phytoplasma from Multiple Displacement Amplification Templates},
    journal          = {Journal of Molecular Microbiology and Biotechnology},
    year             = {2014},
    volume           = {24},
    number           = {1},
    pages            = {1-11},
    doi              = {10.1159/000353904},
}


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