130 lines
13 KiB
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130 lines
13 KiB
XML
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<mods:title id="F79BF505408B3ACC6B863C2863ABB101">De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway</mods:title>
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<mods:namePart id="52B847A837CED7420BEE4F880F0EBB54">Deshmukh, Aaditi B.</mods:namePart>
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<mods:affiliation id="A8D72ED503CF34AB775ADF831FA65BF3">∗ & Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India</mods:affiliation>
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<mods:namePart id="616D93D88F0F0357A6EE028EDB590F1C">Datir, Sagar S.</mods:namePart>
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<mods:namePart id="F211A90F05F09F68BCF394AE132C76BC">Bhonde, Yogesh</mods:namePart>
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<mods:namePart id="450465F2AB36B094922239268F04DC29">Kelkar, Natasha</mods:namePart>
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<mods:namePart id="FC9A1FB89660495F06EBEB46CC4CAC1E">Samdani, Pawan</mods:namePart>
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<mods:namePart id="49E9ABB76362D54C5ABAA4EEAF5BD60E">Tamhane, Vaijayanti A.</mods:namePart>
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<mods:title id="606D5AC9475E0811F0446E10E9C13C75">Phytochemistry</mods:title>
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<mods:part id="572D91632BA6E8EAEEA811DC25D2DE92">
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<mods:date id="B3D5BF251A691C9139E38FD4A42870DB">2018</mods:date>
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<mods:number id="06B74DAF0A5D4DC7FED2553095AEB62D">2018-12-31</mods:number>
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<mods:number id="DC80180DEDDA1F36CC49749DDA3EBB16">156</mods:number>
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<mods:classification id="2B3EFAB74973848C2DB00A6CCCE603AD">journal article</mods:classification>
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<mods:identifier id="2A1197D9D18DD1FF896513757AF16E29" type="DOI">10.1016/j.phytochem.2018.09.013</mods:identifier>
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<mods:identifier id="056F1F2C20FA349DADF30544D392BB95" type="ISSN">1873-3700</mods:identifier>
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<mods:identifier id="0E1CE087BD70AEDC750DD50F0BB93FC6" type="Zenodo-Dep">10484692</mods:identifier>
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<treatment id="03881B7683567F0FFF9BE956816CFE90" LSID="urn:lsid:plazi:treatment:03881B7683567F0FFF9BE956816CFE90" httpUri="http://treatment.plazi.org/id/03881B7683567F0FFF9BE956816CFE90" lastPageId="11" lastPageNumber="211" pageId="10" pageNumber="211">
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<subSubSection id="C33BF9EB83567F0EFF9BE95682EAFA94" box="[100,641,1319,1338]" pageId="10" pageNumber="211" type="nomenclature">
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<paragraph id="8B9EAA6083567F0EFF9BE95682EAFA94" blockId="10.[100,641,1319,1338]" box="[100,641,1319,1338]" pageId="10" pageNumber="211">
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<heading id="D0D61D0C83567F0EFF9BE95682EAFA94" bold="true" box="[100,641,1319,1338]" fontSize="36" level="1" pageId="10" pageNumber="211" reason="1">
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<emphasis id="B955767283567F0EFF9BE95682EAFA94" bold="true" box="[100,641,1319,1338]" italics="true" pageId="10" pageNumber="211">
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4.11. Phylogenetic analysis of
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<taxonomicName id="4C21D1E383567F0EFE84E9568234FA94" ID-CoL="4WYTB" authority="cytochrome P" authorityName="Cytochrome P" box="[379,607,1319,1338]" class="Magnoliopsida" family="Pedaliaceae" genus="Sesamum" kingdom="Plantae" order="Lamiales" pageId="10" pageNumber="211" phylum="Tracheophyta" rank="species" species="indicum">O. indicum cytochrome P</taxonomicName>
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450
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</emphasis>
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</paragraph>
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<paragraph id="8B9EAA6083567F0EFF7AE92E8147F998" blockId="10.[100,770,1375,1590]" pageId="10" pageNumber="211">
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<materialsCitation id="3B49A03D83567F0EFF7AE92E8143F998" collectionCode="P, FPKM, BLAST" pageId="10" pageNumber="211" specimenCode="P450, MEGA7" specimenCount="1">
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Genes annotated as Cytochrome
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<collectionCode id="ED3032A583567F0EFE36E92E81BDFADC" box="[457,470,1375,1394]" country="France" lsid="urn:lsid:biocol.org:col:15763" name="Museum National d' Histoire Naturelle, Paris (MNHN) - Vascular Plants" pageId="10" pageNumber="211" type="Herbarium">P</collectionCode>
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<quantity id="4CD9078583567F0EFE29E92E827EFADC" box="[470,533,1375,1394]" metricMagnitude="1" metricUnit="m" metricValue="1.143" pageId="10" pageNumber="211" unit="in" value="450.0">450 in</quantity>
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the transcriptome were shortlisted (Supplementary
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<tableCitation id="C6A39FDB83567F0EFE97E90A81C6FA20" box="[360,429,1403,1422]" captionStart="Table 4" captionStartId="2.[818,868,161,178]" captionTargetBox="[834,1472,226,490]" captionText="Table 4 Protein domain analysis of the O. indicum transcriptome." pageId="10" pageNumber="211">Table 4</tableCitation>
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). They were used to identify the full length ORFs of OinCyp450s with high
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<collectionCode id="ED3032A583567F0EFE35E9E68269FA04" box="[458,514,1431,1450]" pageId="10" pageNumber="211">FPKM</collectionCode>
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values (above 5.5). Protein
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<collectionCode id="ED3032A583567F0EFF9BE9C280C9FA68" box="[100,162,1459,1478]" pageId="10" pageNumber="211">BLAST</collectionCode>
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of the genes annotated as cytochrome
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<specimenCode id="DB87021B83567F0EFDE5E9C28220FA68" box="[538,587,1459,1478]" collectionCode="P" country="France" lsid="urn:lsid:biocol.org:col:15763" name="Museum National d' Histoire Naturelle, Paris (MNHN) - Vascular Plants" pageId="10" pageNumber="211" type="Herbarium">P450</specimenCode>
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s was performed to identify the
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<typeStatus id="549A14C283567F0EFF23E9BE816EFA4C" box="[220,261,1487,1506]" pageId="10" pageNumber="211">type</typeStatus>
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/function of the specific Cytochrome
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<specimenCode id="DB87021B83567F0EFD8EE9BE82CFFA4C" box="[625,676,1487,1506]" collectionCode="P" country="France" lsid="urn:lsid:biocol.org:col:15763" name="Museum National d' Histoire Naturelle, Paris (MNHN) - Vascular Plants" pageId="10" pageNumber="211" type="Herbarium">P450</specimenCode>
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. Phylogenetic tree of the newly identified, full length protein OinCyps was performed using
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<specimenCode id="DB87021B83567F0EFEF6EA76813BF9B4" box="[265,336,1543,1562]" collectionCode="MEGA" pageId="10" pageNumber="211">MEGA7</specimenCode>
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by the maximum likelihood method (
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<bibRefCitation id="EFB0D79183567F0EFD3CEA7680BAF998" author="Kumar, S. & Stecher, G. & Tamura, K." pageId="10" pageNumber="211" pagination="1870 - 1874" refId="ref12175" refString="Kumar, S., Stecher, G., Tamura, K., 2016. MEGA 7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870 - 1874. https: // doi. org / 10.1093 / molbev / msw 054." type="journal article" year="2016">Kumar et al., 2016</bibRefCitation>
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) (
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<figureCitation id="131AB6E583567F0EFF17EA528175F998" box="[232,286,1571,1590]" captionStart="Fig" captionStartId="10.[100,130,1231,1248]" captionTargetBox="[264,1322,154,1207]" captionTargetId="figure-160@10.[263,1325,152,1208]" captionTargetPageId="10" captionText="Fig. 5. Phylogenetic analysis of full length O. indicum Cytochrome P450 using maximum likelihood method. Phylogenetic tree of the newly identified, full length OinCyps (Tables 7 and 8) was performed using MEGA7 by maximum likelihood method." figureDoi="http://doi.org/10.5281/zenodo.10484702" httpUri="https://zenodo.org/record/10484702/files/figure.png" pageId="10" pageNumber="211">Fig. 5</figureCitation>
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)
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</materialsCitation>
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.
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</paragraph>
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<paragraph id="8B9EAA6083567F0EFCCDE9568392FA94" blockId="10.[818,1017,1319,1338]" box="[818,1017,1319,1338]" pageId="10" pageNumber="211">
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<emphasis id="B955767283567F0EFCCDE9568392FA94" bold="true" box="[818,1017,1319,1338]" pageId="10" pageNumber="211">Conflicts of interest</emphasis>
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</paragraph>
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<paragraph id="8B9EAA6083567F0EFCACE92E8481FADC" blockId="10.[851,1258,1375,1394]" box="[851,1258,1375,1394]" pageId="10" pageNumber="211">The authors declare no conflict of interest.</paragraph>
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<paragraph id="8B9EAA6083567F0EFCCDE9DE8386FA6C" blockId="10.[818,1005,1455,1474]" box="[818,1005,1455,1474]" pageId="10" pageNumber="211">
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<emphasis id="B955767283567F0EFCCDE9DE8386FA6C" bold="true" box="[818,1005,1455,1474]" pageId="10" pageNumber="211">Acknowledgement</emphasis>
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</paragraph>
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<paragraph id="8B9EAA6083567F0FFCACE996816CFE90" blockId="10.[818,1487,1511,1669]" lastBlockId="11.[100,771,159,318]" lastPageId="11" lastPageNumber="212" pageId="10" pageNumber="211">
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The authors would like to acknowledge the Department of Biotechnology (DBT), Government of
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<collectingCountry id="F336EAF083567F0EFB63EA7284A7F9B8" box="[1180,1228,1539,1558]" name="India" pageId="10" pageNumber="211">India</collectingCountry>
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for the DBT-BioCARE project to Dr. Vaijayanti Tamhane (BT/Bio-CARe/07/320/2012) and Departmental Research and Developmental Program (DRDP), Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University (SPPU), Pune,
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<collectingRegion id="49E5648283567F0EFBDEEA0384F1F92B" box="[1057,1178,1650,1669]" country="India" name="Maharashtra" pageId="10" pageNumber="211">Maharashtra</collectingRegion>
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,
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<collectingCountry id="F336EAF083567F0EFB5CEA0384B8F92B" box="[1187,1235,1650,1669]" name="India" pageId="10" pageNumber="211">India</collectingCountry>
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for funding this work. The authors are thankful to Ms. Meenakshi Kapse, Project Assistant, IBB, SPPU for helping with command line BLAST analysis of the transcriptome. The authors are grateful to Dr. Sneha Bansode, Department of Biotechnology, SPPU for her critical comments and suggestions. The transcriptome sequencing service was provided by Genotypic, Bangalore,
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<collectingCountry id="F336EAF083577F0FFF2FED5A8168FE90" box="[208,259,299,318]" name="India" pageId="11" pageNumber="212">India</collectingCountry>
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.
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</paragraph>
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</subSubSection>
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</treatment>
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