Phytoseiid mite species composition in Japanese peach orchards estimated using quantitative sequencing
We attempted a population survey of spider mites and phytoseiid mites in Japanese peach orchards with different pesticide practices; however, we had difficulty discriminating phytoseiid mites. To estimate phytoseiid mite species composition, ribosomal gene fragments were amplified from genomic DNA o...
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| Veröffentlicht in: | Experimental & applied acarology 2012-01, Vol.56 (1), p.9-22 |
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| creator | Sonoda, Shoji Kohara, Yoko Siqingerile Toyoshima, Shingo Kishimoto, Hidenari Hinomoto, Norihide |
| description | We attempted a population survey of spider mites and phytoseiid mites in Japanese peach orchards with different pesticide practices; however, we had difficulty discriminating phytoseiid mites. To estimate phytoseiid mite species composition, ribosomal gene fragments were amplified from genomic DNA of five phytoseiid mite species using PCR. Cloning and nucleotide sequencing of amplified fragments identified species-specific polymorphic sites. Newly amplified fragments from recombinant plasmids were mixed in various ratios to produce standard DNA template mixtures. After direct sequencing, the signal ratios between two nucleotides at each species-specific polymorphic site were calculated and shown against the corresponding expected ratios. Quadratic regression equations were used to estimate the phytoseiid mite species composition. Results showed that the phytoseiid mite species composition changed during the survey period and varied among study sites. |
| doi_str_mv | 10.1007/s10493-011-9485-x |
| format | Article |
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To estimate phytoseiid mite species composition, ribosomal gene fragments were amplified from genomic DNA of five phytoseiid mite species using PCR. Cloning and nucleotide sequencing of amplified fragments identified species-specific polymorphic sites. Newly amplified fragments from recombinant plasmids were mixed in various ratios to produce standard DNA template mixtures. After direct sequencing, the signal ratios between two nucleotides at each species-specific polymorphic site were calculated and shown against the corresponding expected ratios. Quadratic regression equations were used to estimate the phytoseiid mite species composition. Results showed that the phytoseiid mite species composition changed during the survey period and varied among study sites.</description><identifier>ISSN: 0168-8162</identifier><identifier>EISSN: 1572-9702</identifier><identifier>DOI: 10.1007/s10493-011-9485-x</identifier><identifier>PMID: 21909824</identifier><identifier>CODEN: EAACEM</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Agriculture ; Animal Ecology ; Animal Genetics and Genomics ; Animal Systematics/Taxonomy/Biogeography ; Animals ; Araneae ; Base Sequence ; Biodiversity ; Biomedical and Life Sciences ; Cloning ; Deoxyribonucleic acid ; DNA ; Entomology ; genomics ; Japan ; Life Sciences ; Mathematical models ; Mites ; Molecular Sequence Data ; Nucleotide sequence ; Nucleotides ; Orchards ; Pesticides ; Plasmids ; Polymerase chain reaction ; Prunus ; RNA, Ribosomal, 28S - genetics ; Sequence Analysis, DNA ; Species composition ; Tetranychidae - classification ; Tetranychidae - genetics</subject><ispartof>Experimental & applied acarology, 2012-01, Vol.56 (1), p.9-22</ispartof><rights>Springer Science+Business Media B.V. 2011</rights><rights>Springer Science+Business Media B.V. 2012</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c468t-c7378e2b7f6c7b85d432bcb3ed7344302e970c9ac7f0b186297f01653f8a70c33</citedby><cites>FETCH-LOGICAL-c468t-c7378e2b7f6c7b85d432bcb3ed7344302e970c9ac7f0b186297f01653f8a70c33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10493-011-9485-x$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10493-011-9485-x$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21909824$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sonoda, Shoji</creatorcontrib><creatorcontrib>Kohara, Yoko</creatorcontrib><creatorcontrib>Siqingerile</creatorcontrib><creatorcontrib>Toyoshima, Shingo</creatorcontrib><creatorcontrib>Kishimoto, Hidenari</creatorcontrib><creatorcontrib>Hinomoto, Norihide</creatorcontrib><title>Phytoseiid mite species composition in Japanese peach orchards estimated using quantitative sequencing</title><title>Experimental & applied acarology</title><addtitle>Exp Appl Acarol</addtitle><addtitle>Exp Appl Acarol</addtitle><description>We attempted a population survey of spider mites and phytoseiid mites in Japanese peach orchards with different pesticide practices; however, we had difficulty discriminating phytoseiid mites. To estimate phytoseiid mite species composition, ribosomal gene fragments were amplified from genomic DNA of five phytoseiid mite species using PCR. Cloning and nucleotide sequencing of amplified fragments identified species-specific polymorphic sites. Newly amplified fragments from recombinant plasmids were mixed in various ratios to produce standard DNA template mixtures. After direct sequencing, the signal ratios between two nucleotides at each species-specific polymorphic site were calculated and shown against the corresponding expected ratios. Quadratic regression equations were used to estimate the phytoseiid mite species composition. Results showed that the phytoseiid mite species composition changed during the survey period and varied among study sites.</description><subject>Agriculture</subject><subject>Animal Ecology</subject><subject>Animal Genetics and Genomics</subject><subject>Animal Systematics/Taxonomy/Biogeography</subject><subject>Animals</subject><subject>Araneae</subject><subject>Base Sequence</subject><subject>Biodiversity</subject><subject>Biomedical and Life Sciences</subject><subject>Cloning</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Entomology</subject><subject>genomics</subject><subject>Japan</subject><subject>Life Sciences</subject><subject>Mathematical models</subject><subject>Mites</subject><subject>Molecular Sequence Data</subject><subject>Nucleotide sequence</subject><subject>Nucleotides</subject><subject>Orchards</subject><subject>Pesticides</subject><subject>Plasmids</subject><subject>Polymerase chain reaction</subject><subject>Prunus</subject><subject>RNA, Ribosomal, 28S - 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Academic</collection><jtitle>Experimental & applied acarology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sonoda, Shoji</au><au>Kohara, Yoko</au><au>Siqingerile</au><au>Toyoshima, Shingo</au><au>Kishimoto, Hidenari</au><au>Hinomoto, Norihide</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Phytoseiid mite species composition in Japanese peach orchards estimated using quantitative sequencing</atitle><jtitle>Experimental & applied acarology</jtitle><stitle>Exp Appl Acarol</stitle><addtitle>Exp Appl Acarol</addtitle><date>2012-01-01</date><risdate>2012</risdate><volume>56</volume><issue>1</issue><spage>9</spage><epage>22</epage><pages>9-22</pages><issn>0168-8162</issn><eissn>1572-9702</eissn><coden>EAACEM</coden><abstract>We attempted a population survey of spider mites and phytoseiid mites in Japanese peach orchards with different pesticide practices; however, we had difficulty discriminating phytoseiid mites. To estimate phytoseiid mite species composition, ribosomal gene fragments were amplified from genomic DNA of five phytoseiid mite species using PCR. Cloning and nucleotide sequencing of amplified fragments identified species-specific polymorphic sites. Newly amplified fragments from recombinant plasmids were mixed in various ratios to produce standard DNA template mixtures. After direct sequencing, the signal ratios between two nucleotides at each species-specific polymorphic site were calculated and shown against the corresponding expected ratios. Quadratic regression equations were used to estimate the phytoseiid mite species composition. Results showed that the phytoseiid mite species composition changed during the survey period and varied among study sites.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>21909824</pmid><doi>10.1007/s10493-011-9485-x</doi><tpages>14</tpages></addata></record> |
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| subjects | Agriculture Animal Ecology Animal Genetics and Genomics Animal Systematics/Taxonomy/Biogeography Animals Araneae Base Sequence Biodiversity Biomedical and Life Sciences Cloning Deoxyribonucleic acid DNA Entomology genomics Japan Life Sciences Mathematical models Mites Molecular Sequence Data Nucleotide sequence Nucleotides Orchards Pesticides Plasmids Polymerase chain reaction Prunus RNA, Ribosomal, 28S - genetics Sequence Analysis, DNA Species composition Tetranychidae - classification Tetranychidae - genetics |
| title | Phytoseiid mite species composition in Japanese peach orchards estimated using quantitative sequencing |
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