124 lines
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124 lines
13 KiB
XML
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<mods:title id="2ABD82447155953E4E9DDA6E7EA4615F">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="3E155B014D389C4FAC0D548EEAF3F7A1">Deshmukh, Aaditi B.</mods:namePart>
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<mods:affiliation id="5DE6CE3A6128DC7D1BE3B772B6126610">∗ & 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="902C4E7274F279DD2C6EAAA0072937C9">Datir, Sagar S.</mods:namePart>
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<mods:namePart id="8A8BC43BAA7333463ACFA2A135C7C3BB">Bhonde, Yogesh</mods:namePart>
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<mods:namePart id="E50F4F7CBD8CEEBE213936A7A52EFD55">Kelkar, Natasha</mods:namePart>
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<mods:namePart id="84F42C5C74EA1531AD601D6212721DF3">Samdani, Pawan</mods:namePart>
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<mods:namePart id="1CCF0121D7435821B93F3700A34ED3B2">Tamhane, Vaijayanti A.</mods:namePart>
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<mods:title id="09BAC512858D385970E8C02E69FF413D">Phytochemistry</mods:title>
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<mods:date id="A685E24D9804B75D19C19B39F14DC24F">2018</mods:date>
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<mods:number id="0D7DC05CBA3ACDA045472E1CDE1E4EA3">2018-12-31</mods:number>
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<subSubSection id="C33BF9EB835D7F05FCCDE87485C9FBB6" box="[818,1442,1029,1048]" pageId="1" pageNumber="202" type="nomenclature">
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<paragraph id="8B9EAA60835D7F05FCCDE87485C9FBB6" blockId="1.[818,1442,1029,1048]" box="[818,1442,1029,1048]" pageId="1" pageNumber="202">
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<heading id="D0D61D0C835D7F05FCCDE87485C9FBB6" bold="true" box="[818,1442,1029,1048]" fontSize="36" level="1" pageId="1" pageNumber="202" reason="1">
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<emphasis id="B9557672835D7F05FCCDE87485C9FBB6" bold="true" box="[818,1442,1029,1048]" italics="true" pageId="1" pageNumber="202">
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2.1. Sequencing and De novo assembly of
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<taxonomicName id="4C21D1E3835D7F05FB4EE874857FFBB6" authority="(L.) Kurz" box="[1201,1300,1029,1048]" class="Magnoliopsida" family="Bignoniaceae" genus="Oroxylum" kingdom="Plantae" order="Lamiales" pageId="1" pageNumber="202" phylum="Tracheophyta" rank="subSpecies" species="indicum" subSpecies="root">O. indicum</taxonomicName>
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root transcripts
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<emphasis id="B9557672835D7F05FCACE84C83F6FBFE" bold="true" box="[851,925,1085,1104]" italics="true" pageId="1" pageNumber="202">De novo</emphasis>
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transcriptome analysis is an excellent platform for generation of comprehensive information to deduce the basic biological, molecular and cellular processes for non-model organisms lacking whole genome sequences. To generate a transcriptome database for
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<taxonomicName id="4C21D1E3835D7F05FA45E8E18312FB11" authority="(L.) Kurz" class="Magnoliopsida" family="Bignoniaceae" genus="Oroxylum" kingdom="Plantae" order="Lamiales" pageId="1" pageNumber="202" phylum="Tracheophyta" rank="species" species="indicum">
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<emphasis id="B9557672835D7F05FA45E8E18312FB11" bold="true" italics="true" pageId="1" pageNumber="202">O. indicum</emphasis>
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</taxonomicName>
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, cDNA libraries of root tissue were sequenced using Illumina NextSeq 500. A total of 24,625,398 raw reads were generated comprising 3,718,435,098 nucleotides with an average size of 151 bp and 44% GC content (
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<tableCitation id="C6A39FDB835D7F05FC21E971844EFABD" box="[990,1061,1280,1299]" captionStart="Table 1" captionStartId="1.[886,936,1728,1745]" captionTargetPageId="1" captionText="Table 1 Throughput and quality of Illumina sequencing of O. indicum root transcriptome." pageId="1" pageNumber="202">Table 1</tableCitation>
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). Reads with Q <
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<materialsCitation id="3B49A03D835D7F05FB1CE9718332FA14" collectionCode="N" pageId="1" pageNumber="202" specimenCode="N50" specimenCount="1">
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20 were removed. Reads were mapped to human reference transcriptome which showed absence of contamination of human transcripts. These high quality reads were used for
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<emphasis id="B9557672835D7F05FC7AE92583A0FAC9" bold="true" box="[901,971,1364,1383]" italics="true" pageId="1" pageNumber="202">de novo</emphasis>
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assembly using Trinity (
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<bibRefCitation id="EFB0D791835D7F05FB4AE9258538FAC9" author="Hass, B. J. & Papanicolaou, A. & Yassour, M. & Grabherr, M. & Blood, P. D. & Bowden, J. & Couger, M. B. & Eccles, D. & Li, B. & Lieber, M. & MacManes, M. D. & Ott, M. & Orvis, J. & Pochet, N. & Strozzi, F. & Weeks, N. & Westerman, R. & William, T. & Dewey, C. N. & Henschel, R. & LeDuc, R. D. & Friedman, N. & Regev, A." box="[1205,1363,1364,1383]" pageId="1" pageNumber="202" pagination="1494 - 1512" refId="ref11622" refString="Hass, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., MacManes, M. D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C. N., Henschel, R., LeDuc, R. D., Friedman, N., Regev, A., 2013. De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494 - 1512." type="journal article" year="2013">Hass et al., 2013</bibRefCitation>
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). It has been reported that the quality of a
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<emphasis id="B9557672835D7F05FBAEE90184F3FA2D" bold="true" box="[1105,1176,1392,1411]" italics="true" pageId="1" pageNumber="202">de novo</emphasis>
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assembly is dependent on many factors, such as the
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of assembler used, followed by parameters like
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value and coverage (
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<bibRefCitation id="EFB0D791835D7F05FBD5E9D684B0FA14" author="Reddy, N. & Mehta, R. H. & Soni, P. H. & Makasana, J. & Gajbhiye, N. A. & Ponnuchamy, M. & Kumar, J." box="[1066,1243,1447,1466]" pageId="1" pageNumber="202" pagination="0129422" refId="ref13148" refString="Reddy, N., Mehta, R. H., Soni, P. H., Makasana, J., Gajbhiye, N. A., Ponnuchamy, M., Kumar, J., 2015. Next generation sequencing and transcriptome analysis predicts biosynthetic pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a non-model plant with potent laxative properties. PloS One 10 (6), e 0129422. https: // doi. org / 10.1371 / journal. pone. 0129422." type="journal article" year="2015">Reddy et al., 2015</bibRefCitation>
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). The data has been submitted to NCBI,
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<materialsCitation id="3B49A03D835D7F05FC01E9B283C4FA5C" collectionCode="SRA" pageId="1" pageNumber="202" specimenCode="SUB2988844" specimenCount="1">
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Sequence Read Archive (
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<collectionCode id="ED3032A5835D7F05FAE6E9B2852FFA78" box="[1305,1348,1475,1494]" pageId="1" pageNumber="202">SRA</collectionCode>
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) submission:
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<specimenCode id="DB87021B835D7F05FCCDE9AE83C4FA5C" box="[818,943,1503,1522]" collectionCode="SUB" country="Germany" httpUri="http://grbio.org/cool/iz3p-2r7s" name="Universitat Bonn" pageId="1" pageNumber="202">SUB2988844</specimenCode>
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</materialsCitation>
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.
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</paragraph>
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<paragraph id="8B9EAA60835D7F05FCACE98A84A2F934" blockId="1.[818,1488,1085,1690]" pageId="1" pageNumber="202">
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The assembly resulted in a total of 121,286 transcripts with N50 value of 1783 bp with an average contig length of 1080 bp (
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<tableCitation id="C6A39FDB835D7F05FA85EA6685AAF984" box="[1402,1473,1559,1578]" captionStart="Table 2" captionStartId="2.[100,150,161,178]" captionTargetPageId="2" captionText="Table 2 Assembly and CDS statistics of Illumina sequencing of O. indicum in root transcriptome." pageId="1" pageNumber="202">Table 2</tableCitation>
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). Furthermore, transcript clustering (CD-HIT-EST) resulted into 81,002 transcripts with an average contig length of 1071 bp and 1788 N50 value (
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<tableCitation id="C6A39FDB835D7F05FC88EA1A83A9F9D0" box="[887,962,1643,1662]" captionStart="Table 2" captionStartId="2.[100,150,161,178]" captionTargetPageId="2" captionText="Table 2 Assembly and CDS statistics of Illumina sequencing of O. indicum in root transcriptome." pageId="1" pageNumber="202">Table 2</tableCitation>
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). These 81,002 transcripts were further targeted for BLASTx analysis for functional annotation.
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</paragraph>
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</subSubSection>
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</treatment>
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