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This bacterium has a high efficiency against <jats:italic>Meloidogyne incognita<\/jats:italic> (<jats:italic>M. incognita<\/jats:italic>) <jats:italic>in vitro<\/jats:italic> and under greenhouse conditions. The complete genome of <jats:italic>P. putida<\/jats:italic> 1A00316 was sequenced using PacBio single molecule real-time (SMRT) technology. A comparative genomic analysis of 16 <jats:italic>Pseudomonas<\/jats:italic> strains revealed that although <jats:italic>P. putida<\/jats:italic> 1A00316 belonged to <jats:italic>P. putida<\/jats:italic>, it was phenotypically more similar to nematicidal <jats:italic>Pseudomonas fluorescens<\/jats:italic> (<jats:italic>P. fluorescens<\/jats:italic>) strains. We characterized the diversity and specificity of nematicidal factors in <jats:italic>P. putida<\/jats:italic> 1A00316 with comparative genomics and functional analysis and found that <jats:italic>P. putida<\/jats:italic> 1A00316 has diverse nematicidal factors including protein alkaline metalloproteinase AprA and two secondary metabolites, hydrogen cyanide and cyclo-(<jats:sc>l<\/jats:sc>-isoleucyl-<jats:sc>l<\/jats:sc>-proline). We show for the first time that cyclo-(<jats:sc>l<\/jats:sc>-isoleucyl-<jats:sc>l<\/jats:sc>-proline) exhibit nematicidal activity in <jats:italic>P. putida<\/jats:italic>. Interestingly, our study had not detected common nematicidal factors such as 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin in <jats:italic>P. putida<\/jats:italic> 1A00316. The results of the present study reveal the diversity and specificity of nematicidal factors in <jats:italic>P. putida<\/jats:italic> strain 1A00316.<\/jats:p>","DOI":"10.1038\/srep29211","type":"journal-article","created":{"date-parts":[[2016,7,7]],"date-time":"2016-07-07T09:21:16Z","timestamp":1467883276000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316"],"prefix":"10.1038","volume":"6","author":[{"given":"Jing","family":"Guo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xueping","family":"Jing","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen-Lei","family":"Peng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiyu","family":"Nie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yile","family":"Zhai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zongze","family":"Shao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Longyu","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minmin","family":"Cai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guangyu","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huaiyu","family":"Zuo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhitao","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui-Ru","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dian","family":"Huang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wanli","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ziniu","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ling-Ling","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jibin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,7,7]]},"reference":[{"key":"BFsrep29211_CR1","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1046\/j.1462-2920.2002.00310.x","volume":"4","author":"T Nakazawa","year":"2002","unstructured":"Nakazawa, T. 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