259 lines
38 KiB
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259 lines
38 KiB
XML
<document id="A09791ED357FED6E53A4AAE5F90B5164" ID-DOI="10.1016/j.phytochem.2020.112590" ID-ISSN="1873-3700" ID-Zenodo-Dep="8290677" IM.bibliography_approvedBy="juliana" IM.illustrations_approvedBy="juliana" IM.materialsCitations_approvedBy="felipe" IM.metadata_approvedBy="juliana" IM.tables_approvedBy="juliana" IM.taxonomicNames_approvedBy="juliana" IM.treatments_approvedBy="juliana" checkinTime="1693243682909" checkinUser="felipe" docAuthor="Mehmood, Nasir, Yuan, Yuan, Ali, Mohammed, Ali, Muhammad, Iftikhar, Junaid, Cheng, Chunzhen, Lyu, Meiling & Wu, Binghua" docDate="2021" docId="038E87B0CA4AFFE5FF9CFAC9FAC70DF2" docLanguage="en" docName="Phytochemistry.181.112590.pdf" docOrigin="Phytochemistry (112590) 181" docSource="http://dx.doi.org/10.1016/j.phytochem.2020.112590" docStyle="DocumentStyle:F36D69FC8B198FBE91029DF9C24697D3.5:Phytochemistry.2020-.journal_article" docStyleId="F36D69FC8B198FBE91029DF9C24697D3" docStyleName="Phytochemistry.2020-.journal_article" docStyleVersion="5" docTitle="Fragaria nilgerrensis subsp. leaf" docType="treatment" docVersion="4" lastPageNumber="4" masterDocId="FFB7FFC8CA48FFE6FFF8FFE0FFCC0B64" masterDocTitle="Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis" masterLastPageNumber="12" masterPageNumber="1" pageNumber="3" updateTime="1693400242790" updateUser="juliana">
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<mods:title id="5EED57BF0EA3C427208DB8C07192491E">Early transcriptional response of terpenoid metabolism to Colletotrichum gloeosporioides in a resistant wild strawberry Fragaria nilgerrensis</mods:title>
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<mods:namePart id="18DE13D2903974EC898D57FA9DF864D1">Mehmood, Nasir</mods:namePart>
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<mods:affiliation id="F0A6A86A7FBC1AAB33D173AFBBE2F39F">* & College of Horticulture and the Fujian provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China</mods:affiliation>
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<mods:namePart id="EC56EE58F2BEDE3D4BA7E04900CE2974">Yuan, Yuan</mods:namePart>
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<mods:affiliation id="95E521693879B842812C0E35AC30011D">* & College of Horticulture and the Fujian provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China</mods:affiliation>
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<mods:namePart id="6E75C3D367151609FC5C6A8D8993926A">Ali, Mohammed</mods:namePart>
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<mods:affiliation id="5A1863B679A6A7386792F0343746056F">Egyptian Deserts Gene Bank, Department of Genetic Resources, Desert Research Center, Egypt</mods:affiliation>
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<mods:namePart id="91D09ACF0B4013688C4CA078F1B875DC">Ali, Muhammad</mods:namePart>
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<mods:affiliation id="4B8502ACED7956B5FA9DD1A78CEEC02A">College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China</mods:affiliation>
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<mods:namePart id="E4414D92D8A4F780CD9500DBCE0C1D40">Iftikhar, Junaid</mods:namePart>
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<mods:affiliation id="F7A88D0428997CBCE76612C123D16A32">* & College of Horticulture and the Fujian provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China</mods:affiliation>
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<mods:namePart id="B0AAC39204E86E84A548515216D119AD">Cheng, Chunzhen</mods:namePart>
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<mods:namePart id="F288407F822EAC65876B67925E8E0B8D">Wu, Binghua</mods:namePart>
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<mods:affiliation id="DABEC4328FAE7A3A5B7505B92A43A4B0">* & College of Horticulture and the Fujian provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China</mods:affiliation>
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<mods:date id="42D06E0980A26277184182ECAF878893">2021</mods:date>
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<treatment id="038E87B0CA4AFFE5FF9CFAC9FAC70DF2" LSID="urn:lsid:plazi:treatment:038E87B0CA4AFFE5FF9CFAC9FAC70DF2" httpUri="http://treatment.plazi.org/id/038E87B0CA4AFFE5FF9CFAC9FAC70DF2" lastPageId="3" lastPageNumber="4" pageId="2" pageNumber="3">
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<subSubSection id="C33D652DCA4AFFE4FF9CFAC9FD3E0E58" box="[100,754,1321,1340]" pageId="2" pageNumber="3" type="nomenclature">
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<paragraph id="8B9836A6CA4AFFE4FF9CFAC9FD3E0E58" blockId="2.[100,754,1321,1340]" box="[100,754,1321,1340]" pageId="2" pageNumber="3">
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<heading id="D0D081CACA4AFFE4FF9CFAC9FD3E0E58" bold="true" box="[100,754,1321,1340]" centered="true" fontSize="36" level="1" pageId="2" pageNumber="3" reason="1">
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<emphasis id="B953EAB4CA4AFFE4FF9CFAC9FD3E0E58" bold="true" box="[100,754,1321,1340]" italics="true" pageId="2" pageNumber="3">
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2.3. Isoprenoid biosynthesis genes from
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<taxonomicName id="4C274D25CA4AFFE4FE37FAC9FD860E58" ID-CoL="6JJST" ID-ENA="64941" authority="Schltdl. ex J.Gay" box="[463,586,1321,1340]" class="Magnoliopsida" family="Rosaceae" genus="Fragaria" kingdom="Plantae" order="Rosales" pageId="2" pageNumber="3" phylum="Tracheophyta" rank="species" species="nilgerrensis">F. nilgerrensis</taxonomicName>
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leaf transcriptome
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</emphasis>
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</heading>
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<paragraph id="8B9836A6CA4AFFE4FF7CFA81FE510DA6" blockId="2.[100,770,1377,1982]" pageId="2" pageNumber="3">
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Fruits of wild and cultivated varieties of strawberry contains numerous
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<typeStatus id="549C8804CA4AFFE4FF32FA9DFF370EF4" box="[202,251,1405,1424]" pageId="2" pageNumber="3">types</typeStatus>
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of terpenoids as the major components of the aroma essential oils, represented mainly by myrtenol, α- pinene, β- pinene, myrtenyl acetate, sabinene, β- myrcene, α- phellandrene, β- phellandrene, dihydromyrcenol, α- terpinolene, α- terpineol, linalool, nerolidol, ()-limonene and (+)-limonene (
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<bibRefCitation id="EFB64B57CA4AFFE4FE5EFA0CFDA60E9B" author="Aharoni, A. & Giri, A. P. & Verstappen, F. W. & Bertea, C. M. & Sevenier, R. & Sun, Z. & Jongsma, M. A. & Schwab, W. & Bouwmeester, H. J." box="[422,618,1516,1536]" pageId="2" pageNumber="3" pagination="3110 - 3131" refId="ref9579" refString="Aharoni, A., Giri, A. P., Verstappen, F. W., Bertea, C. M., Sevenier, R., Sun, Z., Jongsma, M. A., Schwab, W., Bouwmeester, H. J., 2004. Gain and loss of fruit flavor compounds produced by wild and cultivated strawberry species. Plant Cell 16, 3110 - 3131." type="journal article" year="2004">Aharoni et al., 2004</bibRefCitation>
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). However, the composition of terpenoids in leave are rarely reported. Our GC/MS profile unveils that the leaf contained low amount (less than 2% of total extracts) of terpenoids in total. However, upon challenged with
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<taxonomicName id="4C274D25CA4AFFE4FF9CF9BCFECB0D0B" authority="(Penz.) Penz. & Sacc." box="[100,263,1628,1647]" class="Dothideomycetes" family="Botryosphaeriaceae" genus="Colletotrichum" kingdom="Fungi" order="Botryosphaeriales" pageId="2" pageNumber="3" phylum="Ascomycota" rank="species" species="gloeosporioides">
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<emphasis id="B953EAB4CA4AFFE4FF9CF9BCFECB0D0B" bold="true" box="[100,263,1628,1647]" italics="true" pageId="2" pageNumber="3">C. gloeosporioides</emphasis>
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</taxonomicName>
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, rapid induction in terpenoid biosynthesis is quite impressed. Thus, we played particular attention to the fungus-elicited transcriptional regulation of terpenoid biosynthesis network in the leaf based on our transcriptome data.
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</paragraph>
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<paragraph id="8B9836A6CA4AFFE4FF7CF92BFA030EA1" blockId="2.[100,770,1377,1982]" lastBlockId="2.[818,1488,1123,1980]" pageId="2" pageNumber="3">
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Plant terpenoids biosynthesis are initiated from the plastidial MEP (methylerythritol phosphate) and the cytosolic/peroxisomal MVA (mevalonic acid) pathways that generate the building blocks isopentyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) for diverse downstream conversions (
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<figureCitation id="131C2A23CA4AFFE4FEA0F8DBFE400C2A" box="[344,396,1851,1870]" captionStart="Fig" captionStartId="6.[100,130,1054,1071]" captionTargetBox="[264,1323,150,1025]" captionTargetId="figure-424@6.[263,1324,148,1027]" captionTargetPageId="6" captionText="Fig. 4. Schematic illustration of general terpenoid biosynthesis pathways showing identified unigenes from F. nilgerrensis leaf transcriptome data. The interconvertible precursors IPP and DMAPP, two phosphorylated C5 unites, are produced by the MVA and MEP pathways which are exchangeable from both compartmentations. The chloroplast is a major site for synthesis of hemiterpene (C5), monoterpenoids (C10), diterpenoids (C20) carotenoids (C40) and chlorophyll, while the cytosol and other organelle are responsible for synthesis of monoterpenoids (C10), sesquiterpene (C15) and triterpene (C30). But that is not strictly conclusive. Arrow with lines indicate reactions catalyzed by enzymes and the encoding genes, with unigenes identified in this experiment boxed. The color highlights are for better visualization. Abbreviations: AACT, acetoacetyl-CoA thiolase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; DXR, 1-deoxy-D-xylulose 5-phosphate reductase; DXS, 1-deoxy-D-xylulose 5-phosphate synthase; HDR, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3- methyl-but-2-enyl diphosphate synthase; HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase; HMGS, 3-hydroxy-3-methylglutaryl-CoA synthase; IDI, isopentenyl diphosphate isomerase; MCT, MEP cytidyltransferase; MDC, mevalonate-5-diphosphate decarboxylase; MDS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; MVK, mevalonate kinase. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)" figureDoi="http://doi.org/10.5281/zenodo.8290688" httpUri="https://zenodo.org/record/8290688/files/figure.png" pageId="2" pageNumber="3">Fig. 4</figureCitation>
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). Therefore, we first identified unigenes coding for enzymes in various steps of terpenoid biosynthesis pathways in the transcriptome, such as isopentyl diphosphate synthases (IPPS), dimethylallyl diphosphate synthases (DMADPS), geranyl diphosphate synthases (GPPS), farnesyl diphosphate synthases (FPPS) and geranylgeranyl diphosphate synthases (GGPPS). In addition, most unigenes associated with biosynthesis of isoprenoid in both MEP and MVA pathways were found, including
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<emphasis id="B953EAB4CA4AFFE4FB57FB7BFB230FCA" bold="true" box="[1199,1263,1179,1198]" italics="true" pageId="2" pageNumber="3">FnDXR</emphasis>
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(1-deoxy-D-xylulose-5- phosphate reductoisomerase),
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<emphasis id="B953EAB4CA4AFFE4FB93FB57FB660FAE" bold="true" box="[1131,1194,1207,1226]" italics="true" pageId="2" pageNumber="3">FnISPF</emphasis>
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(2-C-methyl-D-erythritol-2,4- cyclodiphosphate synthase),
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<emphasis id="B953EAB4CA4AFFE4FBB5FB33FB540F82" bold="true" box="[1101,1176,1235,1254]" italics="true" pageId="2" pageNumber="3">FnHDS1</emphasis>
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((E)-4-hydroxy-3-methylbut- 2- enyl-diphosphate synthase 1),
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<emphasis id="B953EAB4CA4AFFE4FBA7FB0FFB6C0E66" bold="true" box="[1119,1184,1263,1282]" italics="true" pageId="2" pageNumber="3">FnHDR</emphasis>
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(4-hydroxy-3-methylbut-2-enyl diphosphate reductase),
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<emphasis id="B953EAB4CA4AFFE4FBC5FAEBFBB70E7A" bold="true" box="[1085,1147,1291,1310]" italics="true" pageId="2" pageNumber="3">FnIDI1</emphasis>
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(isopentenyl-diphosphate deltaisomerase 1),
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<emphasis id="B953EAB4CA4AFFE4FC47FAC7FBDB0E5E" bold="true" box="[959,1047,1319,1338]" italics="true" pageId="2" pageNumber="3">FnAACT1</emphasis>
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(acetyl-CoA C-acetyltransferase 1),
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<emphasis id="B953EAB4CA4AFFE4FA86FAC7FA1C0E5E" bold="true" box="[1406,1488,1319,1338]" italics="true" pageId="2" pageNumber="3">FnHMGS</emphasis>
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(hydroxylmethylglutaryl-CoA synthase),
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<emphasis id="B953EAB4CA4AFFE4FB3BFAA2FAEF0E31" bold="true" box="[1219,1315,1346,1365]" italics="true" pageId="2" pageNumber="3">FnHMGR4</emphasis>
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and 5 (hydroxymethylglutaryl-CoA reductase (NADPH) 4 and 5),
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<emphasis id="B953EAB4CA4AFFE4FACBFABEFABB0E15" bold="true" box="[1331,1399,1374,1393]" italics="true" pageId="2" pageNumber="3">FnMDC</emphasis>
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(diphosphomevalonate decarboxylase). In total 57 unigenes related to MEP, MVA and other terpenoid backbone biosynthesis pathway were identified and assigned gene names based on homology (Table S4 and
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<figureCitation id="131C2A23CA4AFFE4FA75FA52FA0D0EA1" box="[1421,1473,1458,1477]" captionStart="Fig" captionStartId="6.[100,130,1054,1071]" captionTargetBox="[264,1323,150,1025]" captionTargetId="figure-424@6.[263,1324,148,1027]" captionTargetPageId="6" captionText="Fig. 4. Schematic illustration of general terpenoid biosynthesis pathways showing identified unigenes from F. nilgerrensis leaf transcriptome data. The interconvertible precursors IPP and DMAPP, two phosphorylated C5 unites, are produced by the MVA and MEP pathways which are exchangeable from both compartmentations. The chloroplast is a major site for synthesis of hemiterpene (C5), monoterpenoids (C10), diterpenoids (C20) carotenoids (C40) and chlorophyll, while the cytosol and other organelle are responsible for synthesis of monoterpenoids (C10), sesquiterpene (C15) and triterpene (C30). But that is not strictly conclusive. Arrow with lines indicate reactions catalyzed by enzymes and the encoding genes, with unigenes identified in this experiment boxed. The color highlights are for better visualization. Abbreviations: AACT, acetoacetyl-CoA thiolase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; DXR, 1-deoxy-D-xylulose 5-phosphate reductase; DXS, 1-deoxy-D-xylulose 5-phosphate synthase; HDR, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3- methyl-but-2-enyl diphosphate synthase; HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase; HMGS, 3-hydroxy-3-methylglutaryl-CoA synthase; IDI, isopentenyl diphosphate isomerase; MCT, MEP cytidyltransferase; MDC, mevalonate-5-diphosphate decarboxylase; MDS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; MVK, mevalonate kinase. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)" figureDoi="http://doi.org/10.5281/zenodo.8290688" httpUri="https://zenodo.org/record/8290688/files/figure.png" pageId="2" pageNumber="3">Fig. 4</figureCitation>
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).
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</paragraph>
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<paragraph id="8B9836A6CA4AFFE4FCA9FA2FFAE60CDF" blockId="2.[818,1488,1123,1980]" pageId="2" pageNumber="3">
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Terpene synthase (TPS) catalysis the final step for various terpenoid molecules. In total 59 homologous
|
||
<emphasis id="B953EAB4CA4AFFE4FB84FA0AFB6C0E99" bold="true" box="[1148,1184,1514,1533]" italics="true" pageId="2" pageNumber="3">TPS</emphasis>
|
||
unigenes from our dataset were identified and determined on the basis of TPS sequence resemblances that were discovered in the reference of canonical annotation database (Table S5 and
|
||
<figureCitation id="131C2A23CA4AFFE4FC3FF9DEFBCD0D35" box="[967,1025,1598,1617]" captionStart="Fig" captionStartId="6.[100,130,1054,1071]" captionTargetBox="[264,1323,150,1025]" captionTargetId="figure-424@6.[263,1324,148,1027]" captionTargetPageId="6" captionText="Fig. 4. Schematic illustration of general terpenoid biosynthesis pathways showing identified unigenes from F. nilgerrensis leaf transcriptome data. The interconvertible precursors IPP and DMAPP, two phosphorylated C5 unites, are produced by the MVA and MEP pathways which are exchangeable from both compartmentations. The chloroplast is a major site for synthesis of hemiterpene (C5), monoterpenoids (C10), diterpenoids (C20) carotenoids (C40) and chlorophyll, while the cytosol and other organelle are responsible for synthesis of monoterpenoids (C10), sesquiterpene (C15) and triterpene (C30). But that is not strictly conclusive. Arrow with lines indicate reactions catalyzed by enzymes and the encoding genes, with unigenes identified in this experiment boxed. The color highlights are for better visualization. Abbreviations: AACT, acetoacetyl-CoA thiolase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; DXR, 1-deoxy-D-xylulose 5-phosphate reductase; DXS, 1-deoxy-D-xylulose 5-phosphate synthase; HDR, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3- methyl-but-2-enyl diphosphate synthase; HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase; HMGS, 3-hydroxy-3-methylglutaryl-CoA synthase; IDI, isopentenyl diphosphate isomerase; MCT, MEP cytidyltransferase; MDC, mevalonate-5-diphosphate decarboxylase; MDS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; MVK, mevalonate kinase. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)" figureDoi="http://doi.org/10.5281/zenodo.8290688" httpUri="https://zenodo.org/record/8290688/files/figure.png" pageId="2" pageNumber="3">Fig. 4</figureCitation>
|
||
). Fifteen of these unigenes were annotated as monoterpenes, limonene and pinene degradation biosynthesis, such as (3 S)-linalool synthase, (+)-neomenthol dehydrogenase, ()-alphaterpineol synthase, ()-camphene/tricyclene synthase and aldehyde dehydrogenase (NAD
|
||
<superScript id="7C529BEECA4AFFE4FBF9F948FBC10DD2" attach="left" box="[1025,1037,1704,1718]" fontSize="6" pageId="2" pageNumber="3">+</superScript>
|
||
). Twenty-three unigenes were annotated as sesquiterpene biosynthesis, such as farnesyl-diphosphate farnesyltransferase, NAD
|
||
<superScript id="7C529BEECA4AFFE4FC29F93FFC110D89" attach="left" box="[977,989,1759,1773]" fontSize="6" pageId="2" pageNumber="3">+</superScript>
|
||
-dependent farnesol dehydrogenase, alpha-farnesene synthase, ()-germacrene D synthase and beta-amyrin synthase. Also, twelve unigenes were annotated as diterpene biosynthesis, such as ent-copalyl diphosphate synthase, ent-kaurene synthase, ent-kaurene oxidase, ent-kaurenoic acid monooxygenase, gibberellin-44 dioxygenase, gibberellin 3 beta-dioxygenase and gibberellin 2 beta-dioxygenase. Finally, nine unigenes related to squalene monooxygenase were annotated as triterpene biosynthesis (Table S5 and
|
||
<figureCitation id="131C2A23CA4AFFE4FB1FF848FAD00CDF" box="[1255,1308,1960,1979]" captionStart="Fig" captionStartId="6.[100,130,1054,1071]" captionTargetBox="[264,1323,150,1025]" captionTargetId="figure-424@6.[263,1324,148,1027]" captionTargetPageId="6" captionText="Fig. 4. Schematic illustration of general terpenoid biosynthesis pathways showing identified unigenes from F. nilgerrensis leaf transcriptome data. The interconvertible precursors IPP and DMAPP, two phosphorylated C5 unites, are produced by the MVA and MEP pathways which are exchangeable from both compartmentations. The chloroplast is a major site for synthesis of hemiterpene (C5), monoterpenoids (C10), diterpenoids (C20) carotenoids (C40) and chlorophyll, while the cytosol and other organelle are responsible for synthesis of monoterpenoids (C10), sesquiterpene (C15) and triterpene (C30). But that is not strictly conclusive. Arrow with lines indicate reactions catalyzed by enzymes and the encoding genes, with unigenes identified in this experiment boxed. The color highlights are for better visualization. Abbreviations: AACT, acetoacetyl-CoA thiolase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; DXR, 1-deoxy-D-xylulose 5-phosphate reductase; DXS, 1-deoxy-D-xylulose 5-phosphate synthase; HDR, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3- methyl-but-2-enyl diphosphate synthase; HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase; HMGS, 3-hydroxy-3-methylglutaryl-CoA synthase; IDI, isopentenyl diphosphate isomerase; MCT, MEP cytidyltransferase; MDC, mevalonate-5-diphosphate decarboxylase; MDS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; MVK, mevalonate kinase. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)" figureDoi="http://doi.org/10.5281/zenodo.8290688" httpUri="https://zenodo.org/record/8290688/files/figure.png" pageId="2" pageNumber="3">Fig. 4</figureCitation>
|
||
).
|
||
</paragraph>
|
||
<caption id="DF58662ECA4BFFE5FBAFFF75FAD109B3" ID-DOI="http://doi.org/10.5281/zenodo.8290681" ID-Zenodo-Dep="8290681" httpUri="https://zenodo.org/record/8290681/files/figure.png" pageId="3" pageNumber="4" startId="3.[1111,1141,149,166]" targetBox="[102,1085,149,1344]" targetPageId="3" targetType="figure">
|
||
<paragraph id="8B9836A6CA4BFFE5FBAFFF75FAD109B3" blockId="3.[1111,1488,149,727]" pageId="3" pageNumber="4">
|
||
<emphasis id="B953EAB4CA4BFFE5FBAFFF75FB430BC2" bold="true" box="[1111,1167,149,166]" pageId="3" pageNumber="4">Fig. 2.</emphasis>
|
||
Global differentially-expressed-genes (DEG) in leaves of
|
||
<taxonomicName id="4C274D25CA4BFFE5FB07FF4FFAA30BA4" authority="Schltdl. ex J.Gay" box="[1279,1391,175,192]" class="Magnoliopsida" family="Rosaceae" genus="Fragaria" kingdom="Plantae" order="Rosales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="nilgerrensis">
|
||
<emphasis id="B953EAB4CA4BFFE5FB07FF4FFAA30BA4" bold="true" box="[1279,1391,175,192]" italics="true" pageId="3" pageNumber="4">F. nilgerrensis</emphasis>
|
||
</taxonomicName>
|
||
after challenged by
|
||
<taxonomicName id="4C274D25CA4BFFE5FB4CFF28FA8A0BBD" authority="(Penz.) Penz. & Sacc." box="[1204,1350,200,217]" class="Dothideomycetes" family="Botryosphaeriaceae" genus="Colletotrichum" kingdom="Fungi" order="Botryosphaeriales" pageId="3" pageNumber="4" phylum="Ascomycota" rank="species" species="gloeosporioides">
|
||
<emphasis id="B953EAB4CA4BFFE5FB4CFF28FA8A0BBD" bold="true" box="[1204,1350,200,217]" italics="true" pageId="3" pageNumber="4">C. gloeosporioides</emphasis>
|
||
</taxonomicName>
|
||
. (A) DEG heatmap depicts clustering of the early upregulated genes (up to 18-h post challenge) and the late respondents (
|
||
<emphasis id="B953EAB4CA4BFFE5FAB3FEF5FA960A42" box="[1355,1370,277,294]" italics="true" pageId="3" pageNumber="4">></emphasis>
|
||
24 h) in the upper and lower parts, respectively, with top GO terms indicated. (B) Major GO term enrichment in an early responsive gene cluster 7 showing that terpenoid biosynthesis genes are co-expressed with antipathogen immune-responsive pathway genes. Each time-point contains 2 biological replications and the expression data was zero-normalized before hierarchical clustering is performed (Pearson uncentered metric, average linkage ordering) using Cluster 3.0 version 1.58. Heatmap was examined and generated using Java Tree- View version 1.1.6r4. Gene Ontology (GO) enrichment analysis of the DEGs is implemented by the topGO R package-based Kolmogorov–Smirnov test.
|
||
</paragraph>
|
||
</caption>
|
||
<paragraph id="8B9836A6CA4BFFE5FF7CFA68FE1B0D1E" blockId="3.[100,770,1416,1965]" pageId="3" pageNumber="4">
|
||
Based on the transcript sequences, we also detected simple sequence repeat (SSR) motifs in the identified unigenes associating with terpenoid biosynthesis, e.g.
|
||
<emphasis id="B953EAB4CA4BFFE5FEF2FA20FE100E8A" bold="true" italics="true" pageId="3" pageNumber="4">Hmgcr 4, FnDXS 3, FnDXR, FnMCT, FnIDI 1, FnFPPS 1, FnGGPPS 1, FnCMT, FnFNTB 2, FnSPS 1</emphasis>
|
||
, and unigenes related to (3 S)- linalool synthase, aldehyde dehydrogenase (NAD
|
||
<superScript id="7C529BEECA4BFFE5FDC9FA12FDF10D64" attach="left" box="[561,573,1522,1536]" fontSize="6" pageId="3" pageNumber="4">+</superScript>
|
||
), 3, 4, 6, ent-copalyl diphosphate synthase, ent-kaurene synthase 1, ent-karene oxidase, ent-kaurenoic acid monooxygenase 2, gibberellin-3-beta dioxygenase, farnesyl-diphosphate, farnesyltransferase, squalene monooxygenase 2, and beta-amyrin synthase 3 (Table S6).
|
||
</paragraph>
|
||
<paragraph id="8B9836A6CA4BFFE5FF7CF963FCCE0CC9" blockId="3.[100,770,1416,1965]" pageId="3" pageNumber="4">
|
||
The identified homologous genes provide an overview for further deciphering terpenoid biosynthesis in leaves of the
|
||
<taxonomicName id="4C274D25CA4BFFE5FDAFF97FFD1B0DD5" box="[599,727,1694,1714]" class="Magnoliopsida" family="Rosaceae" genus="Fragaria" kingdom="Plantae" order="Rosales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="nilgerrensis">
|
||
<emphasis id="B953EAB4CA4BFFE5FDAFF97FFD1B0DD5" bold="true" box="[599,727,1694,1714]" italics="true" pageId="3" pageNumber="4">N. nilgerrensis</emphasis>
|
||
</taxonomicName>
|
||
and may be a reference for other strawberry cultivars as well (
|
||
<figureCitation id="131C2A23CA4BFFE5FD7FF95AFD700DAA" box="[647,700,1722,1742]" captionStart="Fig" captionStartId="6.[100,130,1054,1071]" captionTargetBox="[264,1323,150,1025]" captionTargetId="figure-424@6.[263,1324,148,1027]" captionTargetPageId="6" captionText="Fig. 4. Schematic illustration of general terpenoid biosynthesis pathways showing identified unigenes from F. nilgerrensis leaf transcriptome data. The interconvertible precursors IPP and DMAPP, two phosphorylated C5 unites, are produced by the MVA and MEP pathways which are exchangeable from both compartmentations. The chloroplast is a major site for synthesis of hemiterpene (C5), monoterpenoids (C10), diterpenoids (C20) carotenoids (C40) and chlorophyll, while the cytosol and other organelle are responsible for synthesis of monoterpenoids (C10), sesquiterpene (C15) and triterpene (C30). But that is not strictly conclusive. Arrow with lines indicate reactions catalyzed by enzymes and the encoding genes, with unigenes identified in this experiment boxed. The color highlights are for better visualization. Abbreviations: AACT, acetoacetyl-CoA thiolase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; DXR, 1-deoxy-D-xylulose 5-phosphate reductase; DXS, 1-deoxy-D-xylulose 5-phosphate synthase; HDR, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3- methyl-but-2-enyl diphosphate synthase; HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase; HMGS, 3-hydroxy-3-methylglutaryl-CoA synthase; IDI, isopentenyl diphosphate isomerase; MCT, MEP cytidyltransferase; MDC, mevalonate-5-diphosphate decarboxylase; MDS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; MVK, mevalonate kinase. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)" figureDoi="http://doi.org/10.5281/zenodo.8290688" httpUri="https://zenodo.org/record/8290688/files/figure.png" pageId="3" pageNumber="4">Fig. 4</figureCitation>
|
||
). Next, we examined the expression profiles of these unigenes during the timecourse after fungal challenge. In the general terpenoid biosynthesis pathways, more unigenes from the MVA, MEP and those related to diphosphate synthases (PPS) showed up-regulation as early at 3 hpi with various fold-change levels, while only a few unigenes were repressed, especially
|
||
<emphasis id="B953EAB4CA4BFFE5FF2CF882FE4C0C11" bold="true" box="[212,384,1890,1909]" italics="true" pageId="3" pageNumber="4">c27310. graph_c0</emphasis>
|
||
(
|
||
<emphasis id="B953EAB4CA4BFFE5FE64F882FDCF0C11" bold="true" box="[412,515,1890,1909]" italics="true" pageId="3" pageNumber="4">FnDHDDS4</emphasis>
|
||
) and
|
||
<emphasis id="B953EAB4CA4BFFE5FDAEF882FCCD0C11" bold="true" box="[598,769,1890,1909]" italics="true" pageId="3" pageNumber="4">c15242. graph_c0</emphasis>
|
||
(
|
||
<emphasis id="B953EAB4CA4BFFE5FF94F89EFF180CF5" bold="true" box="[108,212,1918,1937]" italics="true" pageId="3" pageNumber="4">FnDHDDS1</emphasis>
|
||
) (
|
||
<figureCitation id="131C2A23CA4BFFE5FF15F89EFEFB0CF5" box="[237,311,1918,1937]" captionStart="Fig" captionStartId="7.[100,130,1060,1077]" captionTargetBox="[227,1361,150,1032]" captionTargetId="figure-577@7.[225,1362,148,1033]" captionTargetPageId="7" captionText="Fig. 5. Heat maps depicting the transcript levels of terpenoid biosynthesis genes from F. nilgerrensis leaf transcriptome in response to C. gloeosporioides. (A) Fifty-six MVA and MEP pathway-associated genes. Annotation of the unigenes by homologous are listed in Table S4. (B) Fifty-nine terpene synthase-like or related genes. Annotation of the unigenes by homologous are listed in Table S5. Average FPKM (n = 2) were log2 transformed. The heatmap was generated by Prism GraphPad version 7.04." figureDoi="http://doi.org/10.5281/zenodo.8290690" httpUri="https://zenodo.org/record/8290690/files/figure.png" pageId="3" pageNumber="4">Fig. 5A</figureCitation>
|
||
). For
|
||
<emphasis id="B953EAB4CA4BFFE5FE8BF89EFE5B0CF5" bold="true" box="[371,407,1918,1937]" italics="true" pageId="3" pageNumber="4">TPS</emphasis>
|
||
-like unigenes, ten unigenes (
|
||
<emphasis id="B953EAB4CA4BFFE5FD40F89EFF7D0CC8" bold="true" italics="true" pageId="3" pageNumber="4">c26859. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FF45F87AFE960CC8" bold="true" box="[189,346,1945,1965]" italics="true" pageId="3" pageNumber="4">c23001. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FE9EF87AFDC80CC8" bold="true" box="[358,516,1945,1965]" italics="true" pageId="3" pageNumber="4">c26382. graph_c2</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FDF7F87AFD600CC8" bold="true" box="[527,684,1945,1965]" italics="true" pageId="3" pageNumber="4">c24450. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FD4FF87AFCCE0CC9" bold="true" box="[695,770,1946,1965]" italics="true" pageId="3" pageNumber="4">c34218.</emphasis>
|
||
</paragraph>
|
||
<paragraph id="8B9836A6CA4BFFE5FCCAFA67FAC70DF2" blockId="3.[818,1488,1415,1686]" pageId="3" pageNumber="4">
|
||
<emphasis id="B953EAB4CA4BFFE5FCCAFA67FCB30EFE" bold="true" box="[818,895,1415,1434]" italics="true" pageId="3" pageNumber="4">graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FC73FA68FBEB0EFE" bold="true" box="[907,1063,1415,1435]" italics="true" pageId="3" pageNumber="4">c34395. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FBCBFA68FB1C0EFE" bold="true" box="[1075,1232,1415,1435]" italics="true" pageId="3" pageNumber="4">c39471. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FB24FA68FAB50EFE" bold="true" box="[1244,1401,1415,1435]" italics="true" pageId="3" pageNumber="4">c31932. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FA7DFA68FCB30ED2" bold="true" italics="true" pageId="3" pageNumber="4">c24276. graph_c0</emphasis>
|
||
and
|
||
<emphasis id="B953EAB4CA4BFFE5FC4CFA44FB980ED2" bold="true" box="[948,1108,1443,1463]" italics="true" pageId="3" pageNumber="4">c27886. graph_c0</emphasis>
|
||
) were up-regulated remarkedly at 3–6 hpi, and further fourteen unigenes (
|
||
<emphasis id="B953EAB4CA4BFFE5FB7AFA20FAEC0EB6" bold="true" box="[1154,1312,1471,1491]" italics="true" pageId="3" pageNumber="4">c24788. graph_c1</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FAD3FA20FA050EB6" bold="true" box="[1323,1481,1471,1491]" italics="true" pageId="3" pageNumber="4">c27601. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FCCAFA3BFC0A0E8A" bold="true" box="[818,966,1499,1518]" italics="true" pageId="3" pageNumber="4">c9433. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FC2DFA3BFBBA0E8A" bold="true" box="[981,1142,1499,1518]" italics="true" pageId="3" pageNumber="4">c26113. graph_c2</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FB7DFA3BFAD50E8A" bold="true" box="[1157,1305,1499,1518]" italics="true" pageId="3" pageNumber="4">c8446. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FAD0FA3BFA050E8A" bold="true" box="[1320,1481,1499,1518]" italics="true" pageId="3" pageNumber="4">c26141. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FCCAFA17FC1E0D6E" bold="true" box="[818,978,1527,1546]" italics="true" pageId="3" pageNumber="4">c13323. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FC18FA17FB4C0D6E" bold="true" box="[992,1152,1527,1546]" italics="true" pageId="3" pageNumber="4">c11811. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FB77FA17FAEF0D6E" bold="true" box="[1167,1315,1527,1546]" italics="true" pageId="3" pageNumber="4">c9937. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FACAFA17FA050D6E" bold="true" box="[1330,1481,1527,1546]" italics="true" pageId="3" pageNumber="4">18669. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FCCAF9F3FC1D0D42" bold="true" box="[818,977,1555,1574]" italics="true" pageId="3" pageNumber="4">c28365. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FC27F9F3FBBF0D42" bold="true" box="[991,1139,1555,1574]" italics="true" pageId="3" pageNumber="4">c1733. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FB79F9F3FAED0D42" bold="true" box="[1153,1313,1555,1574]" italics="true" pageId="3" pageNumber="4">c45499. graph_c0</emphasis>
|
||
,
|
||
<emphasis id="B953EAB4CA4BFFE5FAD7F9F3FA030D42" bold="true" box="[1327,1487,1555,1574]" italics="true" pageId="3" pageNumber="4">c19725. graph_c0</emphasis>
|
||
and
|
||
<emphasis id="B953EAB4CA4BFFE5FCA1F9CFFC3A0D26" bold="true" box="[857,1014,1583,1602]" italics="true" pageId="3" pageNumber="4">c19236. graph_c0</emphasis>
|
||
) were induced significantly at 12–18 hpi (
|
||
<figureCitation id="131C2A23CA4BFFE5FA78F9CFFA080D26" box="[1408,1476,1583,1602]" captionStart="Fig" captionStartId="7.[100,130,1060,1077]" captionTargetBox="[227,1361,150,1032]" captionTargetId="figure-577@7.[225,1362,148,1033]" captionTargetPageId="7" captionText="Fig. 5. Heat maps depicting the transcript levels of terpenoid biosynthesis genes from F. nilgerrensis leaf transcriptome in response to C. gloeosporioides. (A) Fifty-six MVA and MEP pathway-associated genes. Annotation of the unigenes by homologous are listed in Table S4. (B) Fifty-nine terpene synthase-like or related genes. Annotation of the unigenes by homologous are listed in Table S5. Average FPKM (n = 2) were log2 transformed. The heatmap was generated by Prism GraphPad version 7.04." figureDoi="http://doi.org/10.5281/zenodo.8290690" httpUri="https://zenodo.org/record/8290690/files/figure.png" pageId="3" pageNumber="4">Fig. 5B</figureCitation>
|
||
). These results indicate that in response to
|
||
<taxonomicName id="4C274D25CA4BFFE5FB3FF9ABFAAB0D3A" authority="(Penz.) Penz. & Sacc." box="[1223,1383,1611,1630]" class="Dothideomycetes" family="Botryosphaeriaceae" genus="Colletotrichum" kingdom="Fungi" order="Botryosphaeriales" pageId="3" pageNumber="4" phylum="Ascomycota" rank="species" species="gloeosporioides">
|
||
<emphasis id="B953EAB4CA4BFFE5FB3FF9ABFAAB0D3A" bold="true" box="[1223,1383,1611,1630]" italics="true" pageId="3" pageNumber="4">C. gloeosporioides</emphasis>
|
||
</taxonomicName>
|
||
challenge, terpenoid biosynthesis genes are among the most active transcripts of the specialised metabolism during the early stage.
|
||
</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |