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 displacemen...
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| Veröffentlicht in: | Journal of molecular microbiology and biotechnology 2014-01, Vol.24 (1), p.1-11 |
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| container_title | Journal of molecular microbiology and biotechnology |
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| creator | Mitrović, Jelena Siewert, Christin Duduk, Bojan Hecht, Jochen Mölling, Karin Broecker, Felix Beyerlein, Peter Büttner, Carmen Bertaccini, Assunta Kube, Michael |
| description | 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 |
| doi_str_mv | 10.1159/000353904 |
| format | Article |
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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.</description><identifier>ISSN: 2673-1665</identifier><identifier>ISSN: 1464-1801</identifier><identifier>EISSN: 2673-1673</identifier><identifier>EISSN: 1660-2412</identifier><identifier>DOI: 10.1159/000353904</identifier><identifier>PMID: 24158016</identifier><language>eng</language><publisher>Basel, Switzerland: S. 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Karger AG, Basel</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c468t-d6b6846f3c335d462ca90250654c559d77468234bbb538e15c6584991b344973</citedby><cites>FETCH-LOGICAL-c468t-d6b6846f3c335d462ca90250654c559d77468234bbb538e15c6584991b344973</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,2429,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24158016$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mitrović, Jelena</creatorcontrib><creatorcontrib>Siewert, Christin</creatorcontrib><creatorcontrib>Duduk, Bojan</creatorcontrib><creatorcontrib>Hecht, Jochen</creatorcontrib><creatorcontrib>Mölling, Karin</creatorcontrib><creatorcontrib>Broecker, Felix</creatorcontrib><creatorcontrib>Beyerlein, Peter</creatorcontrib><creatorcontrib>Büttner, Carmen</creatorcontrib><creatorcontrib>Bertaccini, Assunta</creatorcontrib><creatorcontrib>Kube, Michael</creatorcontrib><title>Generation and Analysis of Draft Sequences of ‘Stolbur' Phytoplasma from Multiple Displacement Amplification Templates</title><title>Journal of molecular microbiology and biotechnology</title><addtitle>Microb Physiol</addtitle><description>Phytoplasma-associated diseases are reported for more than 1,000 plant species worldwide. 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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.</description><subject>DNA, Bacterial - chemistry</subject><subject>DNA, Bacterial - genetics</subject><subject>DNA, Bacterial - isolation & purification</subject><subject>Genome, Bacterial</subject><subject>Molecular Sequence Data</subject><subject>Nicotiana - microbiology</subject><subject>Nucleic Acid Amplification Techniques - methods</subject><subject>Petroselinum - microbiology</subject><subject>Phytoplasma - genetics</subject><subject>Phytoplasma - isolation & purification</subject><subject>Plant species</subject><subject>Plant tissues</subject><subject>Research Article</subject><subject>Sequence Analysis, DNA</subject><issn>2673-1665</issn><issn>1464-1801</issn><issn>2673-1673</issn><issn>1660-2412</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqF0cFO3DAQAFCrKiqIcui9QpY4tD0stWOPEx9XQGklUCux98hxJm3AiYPtSN1bP4Pv40sw3e0euPRij0fPY3mGkHecnXIO-jNjTIDQTL4iB4UqxYLn5fUuVrBPjmK8zayQvKhKeEP2cwQV4-qA_L7EEYNJvR-pGVu6HI1bxz5S39HzYLpEb_B-xtHi39Tjn4eb5F0zhw_0x6918pMzcTC0C36g17NL_eSQnvcx5y0OOCa6HCbXd73dvLHCfDQJ41uy1xkX8Wi7H5LVl4vV2dfF1ffLb2fLq4WVqkqLVjWqkqoTVghopSqs0awApkBaAN2WZWaFkE3TgKiQg1VQSa15I6TUpTgkHzdlp-DzP2Kqhz5adM6M6OdY81JVuRUVqP9TqUWpQRUs05MX9NbPIbcuK-CFYhzUc8FPG2WDjzFgV0-hH0xY15zVz7Ord7PL9nhbcW4GbHfy36QyeL8Bdyb8xLAD2_tP2uabrA</recordid><startdate>20140101</startdate><enddate>20140101</enddate><creator>Mitrović, Jelena</creator><creator>Siewert, Christin</creator><creator>Duduk, Bojan</creator><creator>Hecht, Jochen</creator><creator>Mölling, Karin</creator><creator>Broecker, Felix</creator><creator>Beyerlein, Peter</creator><creator>Büttner, Carmen</creator><creator>Bertaccini, Assunta</creator><creator>Kube, Michael</creator><general>S. 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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.</abstract><cop>Basel, Switzerland</cop><pub>S. Karger AG</pub><pmid>24158016</pmid><doi>10.1159/000353904</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 2673-1665 |
| ispartof | Journal of molecular microbiology and biotechnology, 2014-01, Vol.24 (1), p.1-11 |
| issn | 2673-1665 1464-1801 2673-1673 1660-2412 |
| language | eng |
| recordid | cdi_pubmed_primary_24158016 |
| source | MEDLINE; Karger Journals; Alma/SFX Local Collection |
| subjects | DNA, Bacterial - chemistry DNA, Bacterial - genetics DNA, Bacterial - isolation & purification Genome, Bacterial Molecular Sequence Data Nicotiana - microbiology Nucleic Acid Amplification Techniques - methods Petroselinum - microbiology Phytoplasma - genetics Phytoplasma - isolation & purification Plant species Plant tissues Research Article Sequence Analysis, DNA |
| title | Generation and Analysis of Draft Sequences of ‘Stolbur' Phytoplasma from Multiple Displacement Amplification Templates |
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