223 lines
31 KiB
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223 lines
31 KiB
XML
<document id="9D147369E7E78FBBA46D4F5090E25E77" ID-CLB-Dataset="264478" ID-DOI="10.1016/j.phytochem.2019.112164" ID-GBIF-Dataset="43cf731e-852b-434a-a837-ab8cfefc7491" ID-ISSN="1873-3700" ID-Zenodo-Dep="8293818" IM.bibliography_approvedBy="felipe" IM.illustrations_approvedBy="carolina" IM.materialsCitations_approvedBy="felipe" IM.metadata_approvedBy="felipe" IM.tables_approvedBy="carolina" IM.taxonomicNames_approvedBy="carolina" IM.treatments_approvedBy="carolina" checkinTime="1693253953757" checkinUser="felipe" docAuthor="Uda, Kouji, Edashige, Yumika, Nishimura, Rie, Shikano, Yuuna, Matsui, Tohru, Radkov, Atanas D. & Moe, Luke A." docDate="2020" docId="039087E6FF93FF97FCFCF8F8FDF49542" docLanguage="en" docName="Phytochemistry.169.112164.pdf" docOrigin="Phytochemistry (112164) 169" docSource="http://dx.doi.org/10.1016/j.phytochem.2019.112164" docStyle="DocumentStyle:F36D69FC8B198FBE91029DF9C24697D3.5:Phytochemistry.2020-.journal_article" docStyleId="F36D69FC8B198FBE91029DF9C24697D3" docStyleName="Phytochemistry.2020-.journal_article" docStyleVersion="5" docTitle="Solanum lycopersicum" docType="treatment" docVersion="4" lastPageNumber="5" masterDocId="FFA9FF9EFF90FF92FFCEFFBDFFDD9635" masterDocTitle="Distribution and evolution of the serine / aspartate racemase family in plants" masterLastPageNumber="8" masterPageNumber="1" pageNumber="4" updateTime="1693404348888" updateUser="ExternalLinkService">
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<mods:titleInfo id="3D721624026459767B826943AF778C5F">
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<mods:title id="EFCECC39B39B781AD5316F73EBB94828">Distribution and evolution of the serine / aspartate racemase family in plants</mods:title>
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<mods:namePart id="487FE7DD24CA574064087D40AB0A917C">Uda, Kouji</mods:namePart>
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<mods:affiliation id="7CF803BB4CBECE4DB2B8EFCD1B0118EE">Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780 - 8520, Japan</mods:affiliation>
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<mods:namePart id="CDAE71A205FD899BFFDEFD7B7FCF242A">Edashige, Yumika</mods:namePart>
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<mods:namePart id="A55C9754E4EFB3F16E733E4786656709">Nishimura, Rie</mods:namePart>
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<mods:namePart id="1C3B16D4E753F00B7D35B33A82AD1CAC">Shikano, Yuuna</mods:namePart>
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<mods:namePart id="A3A02EA11C084BB378FA3795C47BCC02">Matsui, Tohru</mods:namePart>
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<mods:namePart id="F1DD34EB36C00E8604B235B3745EF932">Radkov, Atanas D.</mods:namePart>
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<mods:namePart id="872137CFE4B2B5C2CA68D0D84170D406">Moe, Luke A.</mods:namePart>
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<mods:title id="4B5A4293624B9D0DD5490415602E6356">Phytochemistry</mods:title>
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<mods:date id="FC3ACF7A4ED26B8E42CB615D1A9720CF">2020</mods:date>
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<mods:title id="C51AC7DED1E2D442149F361A5A42AD6F">112164</mods:title>
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<mods:number id="40505DDC5F3554E2552C9F8511B8232E">2020-01-31</mods:number>
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<mods:number id="6977B0F2D367A23987D9C2162F5C5D7F">169</mods:number>
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<mods:identifier id="3D3E82E0D535FC79FF630337B3542020" type="DOI">10.1016/j.phytochem.2019.112164</mods:identifier>
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<treatment id="039087E6FF93FF97FCFCF8F8FDF49542" ID-DOI="http://doi.org/10.5281/zenodo.8301790" ID-Zenodo-Dep="8301790" LSID="urn:lsid:plazi:treatment:039087E6FF93FF97FCFCF8F8FDF49542" httpUri="http://treatment.plazi.org/id/039087E6FF93FF97FCFCF8F8FDF49542" lastPageId="5" lastPageNumber="5" pageId="3" pageNumber="4">
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<subSubSection id="C323657BFF93FF91FCFCF8F8FCB59141" pageId="3" pageNumber="4" type="nomenclature">
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<paragraph id="8B8636F0FF93FF91FCFCF8F8FCB59141" blockId="3.[818,1452,1860,1880]" lastBlockId="3.[818,872,1889,1908]" pageId="3" pageNumber="4">
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<heading id="D0CE819CFF93FF91FCFCF8F8FA719162" bold="true" box="[818,1452,1860,1880]" fontSize="36" level="1" pageId="3" pageNumber="4" reason="1">
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<emphasis id="B94DEAE2FF93FF91FCFCF8F8FA719162" bold="true" box="[818,1452,1860,1880]" italics="true" pageId="3" pageNumber="4">
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2.4. Gene expression level analysis of
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<taxonomicName id="4C394D73FF93FF91FB45F8F9FA8F9162" ID-CoL="4Y369" ID-ENA="4081" authority="L." box="[1163,1362,1860,1879]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="lycopersicum">Solanum lycopersicum</taxonomicName>
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SerR and
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</emphasis>
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</heading>
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<heading id="D0CE819CFF93FF91FCFCF8DCFCB59141" box="[818,872,1889,1908]" fontSize="8" level="3" pageId="3" pageNumber="4" reason="8">
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<emphasis id="B94DEAE2FF93FF91FCFCF8DCFCB59141" bold="true" box="[818,872,1889,1908]" italics="true" pageId="3" pageNumber="4">AspRs</emphasis>
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</heading>
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</paragraph>
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</subSubSection>
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<subSubSection id="C323657BFF93FF96FC9DF824FD1E92F1" lastPageId="4" lastPageNumber="5" pageId="3" pageNumber="4" type="description">
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<paragraph id="8B8636F0FF93FF91FC9DF824FA1291F2" blockId="3.[818,1487,1944,1991]" pageId="3" pageNumber="4">
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To compare the gene expression levels, we analyzed publicly available RNA-Seq data of
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<taxonomicName id="4C394D73FF93FF91FB95F809FAF191F2" box="[1115,1324,1972,1991]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="lycopersicum">
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<emphasis id="B94DEAE2FF93FF91FB95F809FAF191F2" bold="true" box="[1115,1324,1972,1991]" italics="true" pageId="3" pageNumber="4">Solanum lycopersicum</emphasis>
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</taxonomicName>
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obtained from
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</paragraph>
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<caption id="DF466678FF94FF96FBB1FF25FA509593" ID-DOI="http://doi.org/10.5281/zenodo.8293822" ID-Zenodo-Dep="8293822" httpUri="https://zenodo.org/record/8293822/files/figure.png" pageId="4" pageNumber="5" startId="4.[1151,1181,152,169]" targetBox="[100,1151,151,1058]" targetPageId="4" targetType="figure">
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<paragraph id="8B8636F0FF94FF96FBB1FF25FA509593" blockId="4.[1151,1489,152,934]" pageId="4" pageNumber="5">
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<emphasis id="B94DEAE2FF94FF96FBB1FF25FB64969C" bold="true" box="[1151,1209,152,169]" pageId="4" pageNumber="5">Fig. 2.</emphasis>
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Chromosomal gene arrangement around SerR homologous genes (a) and phylogenetic tree based on the nucleotide sequence of SerR homologous genes (b) from
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<taxonomicName id="4C394D73FF94FF96FB1FFF43FAC2973A" box="[1233,1311,254,271]" class="Magnoliopsida" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="order">Solanales</taxonomicName>
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species. (a) The arrows indicate the direction of transcription. The genome sequences were obtained from GenBank and the accession numbers are as follows: CP025656,
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<taxonomicName id="4C394D73FF94FF96FBB1FEC3FAC497BB" box="[1151,1305,381,398]" class="Magnoliopsida" family="Convolvulaceae" genus="Ipomoea" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="trifida">
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<emphasis id="B94DEAE2FF94FF96FBB1FEC3FAC497BB" bold="true" box="[1151,1305,381,398]" italics="true" pageId="4" pageNumber="5">Ipomoea trifida</emphasis>
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</taxonomicName>
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; NW_015850497,
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<taxonomicName id="4C394D73FF94FF96FBB1FE2AFACE979D" box="[1151,1299,407,424]" class="Magnoliopsida" family="Solanaceae" genus="Nicotiana" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="tabacum">
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<emphasis id="B94DEAE2FF94FF96FBB1FE2AFACE979D" bold="true" box="[1151,1299,407,424]" italics="true" pageId="4" pageNumber="5">Nicotiana tabacum</emphasis>
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</taxonomicName>
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; CM008450,
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<taxonomicName id="4C394D73FF94FF96FA4AFE2AFB1797F4" class="Magnoliopsida" family="Solanaceae" genus="Capsicum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="baccatum">
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<emphasis id="B94DEAE2FF94FF96FA4AFE2AFB1797F4" bold="true" italics="true" pageId="4" pageNumber="5">Capsicum baccatum</emphasis>
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</taxonomicName>
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; NC_015445,
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<taxonomicName id="4C394D73FF94FF96FA9AFE0DFB1997EE" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="lycopersicum">
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<emphasis id="B94DEAE2FF94FF96FA9AFE0DFB1997EE" bold="true" italics="true" pageId="4" pageNumber="5">Solanum lycopersicum</emphasis>
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</taxonomicName>
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; NC_028644,
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<taxonomicName id="4C394D73FF94FF96FAF3FE77FA1797EE" box="[1341,1482,458,475]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="pennellii">
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<emphasis id="B94DEAE2FF94FF96FAF3FE77FA1797EE" bold="true" box="[1341,1482,458,475]" italics="true" pageId="4" pageNumber="5">Solanum pennellii</emphasis>
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</taxonomicName>
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; NW_006239070,
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<taxonomicName id="4C394D73FF94FF96FAD1FE5EFA1797C1" box="[1311,1482,483,500]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="tuberosum">
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<emphasis id="B94DEAE2FF94FF96FAD1FE5EFA1797C1" bold="true" box="[1311,1482,483,500]" italics="true" pageId="4" pageNumber="5">Solanum tuberosum</emphasis>
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</taxonomicName>
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; FYAA01000154,
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<taxonomicName id="4C394D73FF94FF96FAD4FE40FA179438" box="[1306,1482,509,526]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="verrucosum">
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<emphasis id="B94DEAE2FF94FF96FAD4FE40FA179438" bold="true" box="[1306,1482,509,526]" italics="true" pageId="4" pageNumber="5">Solanum verrucosum</emphasis>
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</taxonomicName>
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; NC_039913,
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<taxonomicName id="4C394D73FF94FF96FB20FDABFABA9412" box="[1262,1383,534,551]" class="Magnoliopsida" family="Rubiaceae" genus="Coffea" kingdom="Plantae" order="Gentianales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="arabica">
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<emphasis id="B94DEAE2FF94FF96FB20FDABFABA9412" bold="true" box="[1262,1383,534,551]" italics="true" pageId="4" pageNumber="5">Coffea arabica</emphasis>
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</taxonomicName>
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. Each SerR homologous gene was predicted as AspR or SerR based on the amino acid sequence of the triple serine loop region. AHL5, AT-hook motif nuclear-localized protein 5; FTIP1, FT-interacting protein 1; NOB1, RNA-binding protein NOB1; LOR, LURP-one-related. (b) The nucleotide sequence of SerR homologous genes was obtained from genome sequences. The ML tree was constructed using the MEGA 7 (
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<bibRefCitation id="EFA84B01FF94FF96FB16FC8DFAA09575" author="Kumar, S. & Stecher, G. & Tamura, K." box="[1240,1405,815,832]" pageId="4" pageNumber="5" pagination="1870 - 1874" refId="ref8807" 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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) and the ML bootstrap values are shown at the branching point. The symbols (A) to (D) before sequence name correspond to the gene arrangement shown in (a).
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</paragraph>
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</caption>
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<paragraph id="8B8636F0FF94FF96FFAAFBE0FD1E92F1" blockId="4.[100,771,1117,1974]" pageId="4" pageNumber="5">
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GenBank SRA database (Accession No. SRP068096). The numbers of RNA-Seq reads for
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<taxonomicName id="4C394D73FF94FF96FEDAFBC4FE3592B9" box="[276,488,1145,1164]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="lycopersicum">Solanum lycopersicum</taxonomicName>
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SerR, AspR1, and AspR2 were counted at seven mature organs (flesh, peel, seed, leaf, petals, buds and root) and calculated the RPKM values (Supplemental
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<tableCitation id="C6BB034BFF94FF96FDADFB0CFD6892F1" box="[611,693,1201,1220]" captionStart="Table 2" captionStartId="2.[100,150,161,177]" captionTargetPageId="2" captionText="Table 2 Comparison of kinetic constants of plant AspRs and SerRs." httpUri="http://table.plazi.org/id/DF466678FF92FF90FFAAFF1CFD8796FE" pageId="4" pageNumber="5" tableUuid="DF466678FF92FF90FFAAFF1CFD8796FE">Table S2</tableCitation>
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).
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</paragraph>
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</subSubSection>
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<subSubSection id="C323657BFF94FF97FF4BFB70FDF49542" lastPageId="5" lastPageNumber="6" pageId="4" pageNumber="5" type="discussion">
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<paragraph id="8B8636F0FF94FF97FF4BFB70FDF49542" blockId="4.[100,771,1117,1974]" lastBlockId="5.[100,770,813,888]" lastPageId="5" lastPageNumber="6" pageId="4" pageNumber="5">
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The
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<taxonomicName id="4C394D73FF94FF96FF7AFB70FEA292D5" box="[180,383,1229,1248]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="lycopersicum">
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<emphasis id="B94DEAE2FF94FF96FF7AFB70FEA292D5" bold="true" box="[180,383,1229,1248]" italics="true" pageId="4" pageNumber="5">Solanum lycopersicum</emphasis>
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</taxonomicName>
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SerR and AspR1 genes are constantly expressed throughout all mature organs suggesting that these proteins may have an essential function involved in D- amino acid metabolism. The expression level of the SerR is about twice that of the AspR1 except in seed, which may be related to the fact that the enzyme activity of the AspR is more than 1000 times higher than that of the SerR (
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<tableCitation id="C6BB034BFF94FF96FD5AFAE5FD04935E" box="[660,729,1368,1387]" captionStart="Table 2" captionStartId="2.[100,150,161,177]" captionTargetPageId="2" captionText="Table 2 Comparison of kinetic constants of plant AspRs and SerRs." httpUri="http://table.plazi.org/id/DF466678FF92FF90FFAAFF1CFD8796FE" pageId="4" pageNumber="5" tableUuid="DF466678FF92FF90FFAAFF1CFD8796FE">Table 2</tableCitation>
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and Supplemental
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<tableCitation id="C6BB034BFF94FF96FF22FAC9FEE393B2" box="[236,318,1396,1415]" captionStart="Table 2" captionStartId="2.[100,150,161,177]" captionTargetPageId="2" captionText="Table 2 Comparison of kinetic constants of plant AspRs and SerRs." httpUri="http://table.plazi.org/id/DF466678FF92FF90FFAAFF1CFD8796FE" pageId="4" pageNumber="5" tableUuid="DF466678FF92FF90FFAAFF1CFD8796FE">Table S2</tableCitation>
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). In contrast to the SerR and AspR1 genes, the RNA-Seq reads corresponding to the AspR2 gene are hardly detected in any of the mature organs, suggesting the AspR2 gene may be expressed under limiting conditions or may have become a pseudogene in the recent past (Supplemental
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<tableCitation id="C6BB034BFF94FF96FEA9FA59FE6793C2" box="[359,442,1508,1527]" captionStart="Table 2" captionStartId="2.[100,150,161,177]" captionTargetPageId="2" captionText="Table 2 Comparison of kinetic constants of plant AspRs and SerRs." httpUri="http://table.plazi.org/id/DF466678FF92FF90FFAAFF1CFD8796FE" pageId="4" pageNumber="5" tableUuid="DF466678FF92FF90FFAAFF1CFD8796FE">Table S2</tableCitation>
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). In order to further examine the gene expression of SerR and AspRs in different plant organs and tissues, we use the TomExpress (http://tomexpress.toulouse.inra.fr/ aboutTomExpress;
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<bibRefCitation id="EFA84B01FF94FF96FED0F985FE39907E" author="Zouine, M. & Maza, E. & Djari, A. & Lauvernier, M. & Frasse, P. & Smouni, A. & Pirrello, J. & Bouzayen, M." box="[286,484,1592,1611]" pageId="4" pageNumber="5" pagination="727 - 735" refId="ref10761" refString="Zouine, M., Maza, E., Djari, A., Lauvernier, M., Frasse, P., Smouni, A., Pirrello, J., Bouzayen, M., 2017. TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks. Plant J. 92, 727 - 735. https: // doi. org / 10.1111 / tpj. 13711." type="journal article" year="2017">Zouine et al., 2017</bibRefCitation>
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) and the tomato functional genomic database (TFGD; http://ted.bti.cornell.edu/cgi-bin/TFGD/ digital/home.cgi;
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<bibRefCitation id="EFA84B01FF94FF96FEDCF9D2FE6D90B6" author="Fei, Z. & Joung, J. - G. & Tang, X. & Zheng, Y. & Huang, M. & Lee, J. M. & McQuinn, R. & Tieman, D. M. & Alba, R. & Klee, H. J. & Giovannoni, J. J." box="[274,432,1647,1667]" pageId="4" pageNumber="5" pagination="1163" refId="ref7977" refString="Fei, Z., Joung, J. - G., Tang, X., Zheng, Y., Huang, M., Lee, J. M., McQuinn, R., Tieman, D. M., Alba, R., Klee, H. J., Giovannoni, J. J., 2011. Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. Nucleic Acids Res. 39, D 1156 - D 1163. https: // doi. org / 10.1093 / nar / gkq 991." type="journal article" year="2011">Fei et al., 2011</bibRefCitation>
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). These web-based transcriptomic platforms are using the publicly available RNA-Seq data sets and provide the gene expression profile discriminated by Solyc ID which is based on the gene locus in
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<taxonomicName id="4C394D73FF94FF96FEA8F97EFDF190E3" box="[358,556,1731,1750]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="lycopersicum">
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<emphasis id="B94DEAE2FF94FF96FEA8F97EFDF190E3" bold="true" box="[358,556,1731,1750]" italics="true" pageId="4" pageNumber="5">Solanum lycopersicum</emphasis>
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</taxonomicName>
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genome. The Solyc ID of Solyc08g008010 precisely corresponded to the SerR gene, while Solyc08g008000 corresponded to both adjacent genes AspR1 and AspR2. Therefore, it is not possible to distinguish the gene expression level of AspR1 and AspR
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<quantity id="4CC19B15FF94FF96FE9FF88EFEA99173" box="[337,372,1843,1862]" metricMagnitude="-2" metricUnit="m" metricValue="5.08" pageId="4" pageNumber="5" unit="in" value="2.0">2 in</quantity>
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TomExpress and TFGD, so we referred to the expression level of Solyc08g008000 as that of AspRs. However, gene expression level of the Solyc08g008000 is expected to be mainly due to the AspR1 gene, on the basis of above-mentioned data analysis using RNA-Seq data of seven mature organs (Supplemental
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<tableCitation id="C6BB034BFF94FF96FD6FF81FFD2E9180" box="[673,755,1954,1973]" captionStart="Table 2" captionStartId="2.[100,150,161,177]" captionTargetPageId="2" captionText="Table 2 Comparison of kinetic constants of plant AspRs and SerRs." httpUri="http://table.plazi.org/id/DF466678FF92FF90FFAAFF1CFD8796FE" pageId="4" pageNumber="5" tableUuid="DF466678FF92FF90FFAAFF1CFD8796FE">Table S2</tableCitation>
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). The gene expression pattern of
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<taxonomicName id="4C394D73FF94FF96FBABFBE0FAF39245" box="[1125,1326,1117,1136]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="lycopersicum">
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<emphasis id="B94DEAE2FF94FF96FBABFBE0FAF39245" bold="true" box="[1125,1326,1117,1136]" italics="true" pageId="4" pageNumber="5">Solanum lycopersicum</emphasis>
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</taxonomicName>
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SerR and AspRs from RNA-Seq data (Supplemental
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<tableCitation id="C6BB034BFF94FF96FB5DFBC4FB3792B9" box="[1171,1258,1145,1164]" captionStart="Table 2" captionStartId="2.[100,150,161,177]" captionTargetPageId="2" captionText="Table 2 Comparison of kinetic constants of plant AspRs and SerRs." httpUri="http://table.plazi.org/id/DF466678FF92FF90FFAAFF1CFD8796FE" pageId="4" pageNumber="5" tableUuid="DF466678FF92FF90FFAAFF1CFD8796FE">Table S2</tableCitation>
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) and results from TomExperss and TFGD do not always agree with each other. For example, TomExpress (Supplemental Table S3) and TFGD (Supplemental Table S4) show that AspR expression is predominantly in seeds but AspR expression seems to be quite uniform among different tissues (Supplemental
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<tableCitation id="C6BB034BFF94FF96FC0DFAB8FBCB932D" box="[963,1046,1285,1304]" captionStart="Table 2" captionStartId="2.[100,150,161,177]" captionTargetPageId="2" captionText="Table 2 Comparison of kinetic constants of plant AspRs and SerRs." httpUri="http://table.plazi.org/id/DF466678FF92FF90FFAAFF1CFD8796FE" pageId="4" pageNumber="5" tableUuid="DF466678FF92FF90FFAAFF1CFD8796FE">Table S2</tableCitation>
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). The AspRs expression in seeds tends to decrease as the fruit matures (Supplemental Tables S3 and S4). However, the seeds used for RNA-Seq analysis in the Supplemental
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<tableCitation id="C6BB034BFF94FF96FA9DFA81FA799365" box="[1363,1444,1340,1360]" captionStart="Table 2" captionStartId="2.[100,150,161,177]" captionTargetPageId="2" captionText="Table 2 Comparison of kinetic constants of plant AspRs and SerRs." httpUri="http://table.plazi.org/id/DF466678FF92FF90FFAAFF1CFD8796FE" pageId="4" pageNumber="5" tableUuid="DF466678FF92FF90FFAAFF1CFD8796FE">Table S2</tableCitation>
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was derived from red ripe fruit. We thought that the expression level of the AspRs in seeds is low in the Supplemental
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<tableCitation id="C6BB034BFF94FF96FB19FAC9FAF793B2" box="[1239,1322,1396,1415]" captionStart="Table 2" captionStartId="2.[100,150,161,177]" captionTargetPageId="2" captionText="Table 2 Comparison of kinetic constants of plant AspRs and SerRs." httpUri="http://table.plazi.org/id/DF466678FF92FF90FFAAFF1CFD8796FE" pageId="4" pageNumber="5" tableUuid="DF466678FF92FF90FFAAFF1CFD8796FE">Table S2</tableCitation>
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. There are some other differences in gene expression level, because different development stage samples were used in each database. Thus, we only describe the gene expression patterns supported by a large number of datasets. A comparison of gene expression level of
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<taxonomicName id="4C394D73FF94FF96FB65FA5EFAAF93C3" box="[1195,1394,1507,1526]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="lycopersicum">
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<emphasis id="B94DEAE2FF94FF96FB65FA5EFAAF93C3" bold="true" box="[1195,1394,1507,1526]" italics="true" pageId="4" pageNumber="5">Solanum lycopersicum</emphasis>
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</taxonomicName>
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SerR and AspRs using 95 RNA-Seq data points from TomExpress (Supplemental Tables S3) and 90 RNA-Seq data points from TFGD (Supplemental Table S4) revealed the following findings (
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<figureCitation id="13022A75FF94FF96FB42F985FB1F907E" box="[1164,1218,1592,1611]" captionStart="Fig" captionStartId="5.[1151,1181,152,169]" captionTargetBox="[100,1121,151,753]" captionTargetId="graphics-671@5.[151,1087,156,753]" captionTargetPageId="5" captionText="Fig. 3. Gene expression level of Solanum lycopersicum SerR, AspRs (AspR1 and AspR2) genes using the TomExpress and TFGD. Gene expression level of Solanum lycopersicum SerR (Solyc ID: Solyc08g008010) and AspRs (Solyc ID: Solyc08g008000) was analyzed by the TomExpress (Zouine et al., 2017) and the tomato functional genomic database (TFGD; Fei et al., 2011). Data in their entirety are shown in Supplemental Tables S3 and S4 while pertinent data are shown in this figure. The gene expression level using TomExpress and TFGD showed by RPKM (Reads Per Kilobase per Million mapped reads) and Normalized mean counts per base, respectively. DPA, days post anthesis; DAP, days after planting." figureDoi="http://doi.org/10.5281/zenodo.8293824" httpUri="https://zenodo.org/record/8293824/files/figure.png" pageId="4" pageNumber="5">Fig. 3</figureCitation>
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).
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<taxonomicName id="4C394D73FF94FF96FB18F98AFA40907F" box="[1238,1437,1591,1610]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="lycopersicum">
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<emphasis id="B94DEAE2FF94FF96FB18F98AFA40907F" bold="true" box="[1238,1437,1591,1610]" italics="true" pageId="4" pageNumber="5">Solanum lycopersicum</emphasis>
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</taxonomicName>
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SerR is expressed in all investigated samples, and its expression level is significantly higher in the shoot apical meristem and leaf primordium, which are both active cell division tissues (
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<figureCitation id="13022A75FF94FF96FB1EF936FADB90AB" box="[1232,1286,1675,1694]" captionStart="Fig" captionStartId="5.[1151,1181,152,169]" captionTargetBox="[100,1121,151,753]" captionTargetId="graphics-671@5.[151,1087,156,753]" captionTargetPageId="5" captionText="Fig. 3. Gene expression level of Solanum lycopersicum SerR, AspRs (AspR1 and AspR2) genes using the TomExpress and TFGD. Gene expression level of Solanum lycopersicum SerR (Solyc ID: Solyc08g008010) and AspRs (Solyc ID: Solyc08g008000) was analyzed by the TomExpress (Zouine et al., 2017) and the tomato functional genomic database (TFGD; Fei et al., 2011). Data in their entirety are shown in Supplemental Tables S3 and S4 while pertinent data are shown in this figure. The gene expression level using TomExpress and TFGD showed by RPKM (Reads Per Kilobase per Million mapped reads) and Normalized mean counts per base, respectively. DPA, days post anthesis; DAP, days after planting." figureDoi="http://doi.org/10.5281/zenodo.8293824" httpUri="https://zenodo.org/record/8293824/files/figure.png" pageId="4" pageNumber="5">Fig. 3</figureCitation>
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; Supplemental Table S3). The ubiquitous expression of the SerR gene and its increased expression level in active cell division tissues has also been reported in
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<taxonomicName id="4C394D73FF94FF96FCFCF962FC3490C7" box="[818,1001,1759,1778]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="thaliana">
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<emphasis id="B94DEAE2FF94FF96FCFCF962FC3490C7" bold="true" box="[818,1001,1759,1778]" italics="true" pageId="4" pageNumber="5">Arabidopsis thaliana</emphasis>
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</taxonomicName>
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(
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<bibRefCitation id="EFA84B01FF94FF96FC37F962FB6A90C7" author="Fujitani, Y. & Nakajima, N. & Ishihara, K. & Oikawa, T. & Ito, K. & Sugimoto, M." box="[1017,1207,1759,1778]" pageId="4" pageNumber="5" pagination="668 - 674" refId="ref8127" refString="Fujitani, Y., Nakajima, N., Ishihara, K., Oikawa, T., Ito, K., Sugimoto, M., 2006. Molecular and biochemical characterization of a serine racemase from Arabidopsis thaliana. Phytochemistry 67, 668 - 674. https: // doi. org / 10.1016 / j. phytochem. 2006.01.003." type="journal article" year="2006">Fujitani et al., 2006</bibRefCitation>
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;
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<bibRefCitation id="EFA84B01FF94FF96FB0AF962FA4F90C7" author="Sugimoto, M. & Sakamoto, W. & Fujitani, Y." box="[1220,1426,1759,1778]" pageId="4" pageNumber="5" pagination="587 - 590" refId="ref9532" refString="Sugimoto, M., Sakamoto, W., Fujitani, Y., 2009. Localization and expression of serine racemase in Arabidopsis thaliana. Amino Acids 36, 587 - 590. https: // doi. org / 10. 1007 / s 00726 - 008 - 0112 - z." type="journal article" year="2009">Sugimoto et al., 2009</bibRefCitation>
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). This expression pattern suggests that plant SerR has multiple roles, and it might be related to the fact that SerR is a bifunctional enzyme, producing both
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<subScript id="17BD34B5FF94FF96FC7FF88AFC1C9173" attach="right" box="[945,961,1843,1862]" fontSize="6" pageId="4" pageNumber="5">D-</subScript>
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serine and pyruvate. The expression of
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<taxonomicName id="4C394D73FF94FF96FA82F88FFC1D9157" authority="AspRs" authorityName="AspRs" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="lycopersicum">
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<emphasis id="B94DEAE2FF94FF96FA82F88FFC5D9154" bold="true" italics="true" pageId="4" pageNumber="5">Solanum lycopersicum</emphasis>
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AspRs
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</taxonomicName>
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is detected in all tissues, similar to SerR, but AspR expression level is much lower than that of SerR in all tissues except seed, ovule, and the surrounding ovule tissues (
|
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<figureCitation id="13022A75FF94FF96FB02F83BFADE91AC" box="[1228,1283,1926,1945]" captionStart="Fig" captionStartId="5.[1151,1181,152,169]" captionTargetBox="[100,1121,151,753]" captionTargetId="graphics-671@5.[151,1087,156,753]" captionTargetPageId="5" captionText="Fig. 3. Gene expression level of Solanum lycopersicum SerR, AspRs (AspR1 and AspR2) genes using the TomExpress and TFGD. Gene expression level of Solanum lycopersicum SerR (Solyc ID: Solyc08g008010) and AspRs (Solyc ID: Solyc08g008000) was analyzed by the TomExpress (Zouine et al., 2017) and the tomato functional genomic database (TFGD; Fei et al., 2011). Data in their entirety are shown in Supplemental Tables S3 and S4 while pertinent data are shown in this figure. The gene expression level using TomExpress and TFGD showed by RPKM (Reads Per Kilobase per Million mapped reads) and Normalized mean counts per base, respectively. DPA, days post anthesis; DAP, days after planting." figureDoi="http://doi.org/10.5281/zenodo.8293824" httpUri="https://zenodo.org/record/8293824/files/figure.png" pageId="4" pageNumber="5">Fig. 3</figureCitation>
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; Supplemental Table S4). The expression level of AspRs increased sharply in ovule after anthesis and became 20 times higher, especially in embryo, compared to that of SerR, suggesting that D- aspartate is synthesized by AspR and it may be involved in plant embryo development.
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</paragraph>
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</subSubSection>
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</treatment>
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</document> |