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

  • 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.

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Metadaten
Author:Jelena Mitrović, Christin Siewert, Bojan Duduk, Jochen Hecht, Karin Mölling, Felix Broecker, Peter Beyerlein, Carmen Büttner, Assunta Bertaccini, Michael Kube
URN:urn:nbn:de:kobv:526-opus4-10959
DOI:https://doi.org/10.1159/000353904
ISSN:1660-2412
Parent Title (English):Journal of Molecular Microbiology and Biotechnology
Document Type:Article
Language:English
Year of Publication:2014
Publishing Institution:Technische Hochschule Wildau
Release Date:2019/02/14
Volume:24
Issue:1
First Page:1
Last Page:11
Source:Mitrović J, Siewert C, Duduk B, Hecht J, Mölling K, Broecker F, Beyerlein P, Büttner C, Bertaccini A, Kube M: Generation and Analysis of Draft Sequences of ‘Stolbur' Phytoplasma from Multiple Displacement Amplification Templates. J Mol Microbiol Biotechnol 2014;24:1-11. doi: 10.1159/000353904
Faculties an central facilities:Fachbereich Ingenieurwesen / Wirtschaftsingenieurwesen (bis 8/2014)
Dewey Decimal Classification:6 Technik, Medizin, angewandte Wissenschaften / 66 Chemische Verfahrenstechnik / 660 Chemische Verfahrenstechnik
Licence (German):DFG-geförderte Allianz- bzw. Nationallizenz
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