167 lines
19 KiB
XML
167 lines
19 KiB
XML
<document id="2999CC04066D63AD85DA27314F84868F" ID-DOI="10.1016/j.phytochem.2021.112932" ID-ISSN="1873-3700" ID-Zenodo-Dep="8258180" IM.bibliography_approvedBy="juliana" IM.illustrations_approvedBy="juliana" IM.materialsCitations_approvedBy="juliana" IM.metadata_approvedBy="felipe" IM.tables_approvedBy="juliana" IM.taxonomicNames_approvedBy="juliana" IM.treatments_approvedBy="juliana" checkinTime="1692305192677" checkinUser="felipe" docAuthor="Zhang, Haihua, Xu, Jinfeng, Chen, Haimin, Jin, Weibo & Liang, Zongsuo" docDate="2021" docId="03F987D2FFF8FFF3AE7BFE06FF01FE27" docLanguage="en" docName="Phytochemistry.191.112932.pdf" docOrigin="Phytochemistry (112932) 191" docSource="http://dx.doi.org/10.1016/j.phytochem.2021.112932" docStyle="DocumentStyle:F36D69FC8B198FBE91029DF9C24697D3.5:Phytochemistry.2020-.journal_article" docStyleId="F36D69FC8B198FBE91029DF9C24697D3" docStyleName="Phytochemistry.2020-.journal_article" docStyleVersion="5" docTitle="Salvia miltiorrhiza Bunge" docType="treatment" docVersion="1" lastPageNumber="2" masterDocId="FFC0FFAAFFF9FFF1AD49FFADFFA1FFD1" masterDocTitle="Characterization of NAC family genes in Salvia miltiorrhiza and NAC 2 potentially involved in the biosynthesis of tanshinones" masterLastPageNumber="8" masterPageNumber="1" pageNumber="2" updateTime="1692630214032" updateUser="juliana">
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<mods:title id="446DE6AE8EC60F7CEE98112C3B13C3B4">Characterization of NAC family genes in Salvia miltiorrhiza and NAC 2 potentially involved in the biosynthesis of tanshinones</mods:title>
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<mods:namePart id="56400506457B8269F55C1C4B3B0D7955">Zhang, Haihua</mods:namePart>
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<mods:namePart id="7B999D61D73578DC50965FC7DC1D42CD">Xu, Jinfeng</mods:namePart>
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<mods:namePart id="89BEA78E3E720F8E566F4A7E3B2DC3E8">Chen, Haimin</mods:namePart>
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<mods:namePart id="81B66F5E6B87A197F108489548148E00">Jin, Weibo</mods:namePart>
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<mods:namePart id="A67217B50E701464CFE0EC3867E1E355">Liang, Zongsuo</mods:namePart>
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<mods:title id="65A4245F48A4779F94CDEDCC41176008">Phytochemistry</mods:title>
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<mods:date id="4551C177E2A3973C09D65A1326FFA7B1">2021</mods:date>
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<paragraph id="8BEF36C4FFF8FFF0AE7BFE06FC13FE08" blockId="1.[818,1434,426,473]" pageId="1" pageNumber="2">
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<emphasis id="B924EAD6FFF8FFF0AE7BFE06FA3BFE6F" bold="true" box="[818,1434,426,446]" italics="true" pageId="1" pageNumber="2">
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2.1. Identification of
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family genes and phylogenetic analysis in
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</emphasis>
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<taxonomicName id="4C504D47FFF8FFF0AE7BFE6BFC13FE08" ID-CoL="6XH2C" ID-ENA="226208" authority="Bunge" authorityName="Bunge" box="[818,946,454,473]" class="Magnoliopsida" family="Lamiaceae" genus="Salvia" kingdom="Plantae" order="Lamiales" pageId="1" pageNumber="6" phylum="Tracheophyta" rank="species" species="miltiorrhiza">
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<emphasis id="B924EAD6FFF8FFF0AE7BFE6BFC13FE08" bold="true" box="[818,946,454,473]" italics="true" pageId="1" pageNumber="2">S. miltiorrhiza</emphasis>
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<paragraph id="8BEF36C4FFF8FFF3AE18FE52FF01FE27" blockId="1.[818,1487,510,920]" lastBlockId="2.[100,771,147,502]" lastPageId="2" lastPageNumber="3" pageId="1" pageNumber="2">
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In this study, BLASTP and HMM searches using the
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protein sequences of
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<taxonomicName id="4C504D47FFF8FFF0AEFBFDB7FBB8FDFC" box="[946,1049,538,557]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="1" pageNumber="2" phylum="Tracheophyta" rank="genus">
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<emphasis id="B924EAD6FFF8FFF0AEFBFDB7FBB8FDFC" bold="true" box="[946,1049,538,557]" italics="true" pageId="1" pageNumber="2">Arabidopsis</emphasis>
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</taxonomicName>
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as query were performed to broadly identify
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<taxonomicName id="4C504D47FFF8FFF0AE7BFD9BFC12FD98" authority="NAC" authorityName="NAC" box="[818,947,566,585]" class="Magnoliopsida" family="Lamiaceae" genus="Salvia" kingdom="Plantae" order="Lamiales" pageId="1" pageNumber="2" phylum="Tracheophyta" rank="species" species="miltiorrhiza">
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<emphasis id="B924EAD6FFF8FFF0AE7BFD9BFC12FD98" bold="true" box="[818,947,566,585]" italics="true" pageId="1" pageNumber="2">S. miltiorrhiza</emphasis>
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</taxonomicName>
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NAC family members. A total of 84
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proteins were identified in the
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<taxonomicName id="4C504D47FFF8FFF0AE9AFDFFFBF5FDB4" box="[979,1108,594,613]" class="Magnoliopsida" family="Lamiaceae" genus="Salvia" kingdom="Plantae" order="Lamiales" pageId="1" pageNumber="2" phylum="Tracheophyta" rank="species" species="miltiorrhiza">
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<emphasis id="B924EAD6FFF8FFF0AE9AFDFFFBF5FDB4" bold="true" box="[979,1108,594,613]" italics="true" pageId="1" pageNumber="2">S. miltiorrhiza</emphasis>
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</taxonomicName>
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genome. They were named Sm-
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<emphasis id="B924EAD6FFF8FFF0A8C3FDFFFA60FDB4" bold="true" box="[1418,1473,594,613]" italics="true" pageId="1" pageNumber="2">
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<collectionCode id="ED41AE01FFF8FFF0A8C3FDFFFA17FDB4" box="[1418,1462,594,613]" country="Japan" httpUri="http://biocol.org/urn:lsid:biocol.org:col:13686" lsid="urn:lsid:biocol.org:col:13686" name="Nagano Environmental Conservation Research Institute" pageId="1" pageNumber="2" type="Herbarium">NAC</collectionCode>
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4
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- Sm-
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<emphasis id="B924EAD6FFF8FFF0AE1FFDC3FC39FD50" bold="true" box="[854,920,622,641]" italics="true" pageId="1" pageNumber="2">
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<collectionCode id="ED41AE01FFF8FFF0AE1FFDC3FC22FD50" box="[854,899,622,641]" country="Japan" httpUri="http://biocol.org/urn:lsid:biocol.org:col:13686" lsid="urn:lsid:biocol.org:col:13686" name="Nagano Environmental Conservation Research Institute" pageId="1" pageNumber="2" type="Herbarium">NAC</collectionCode>
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84
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</emphasis>
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is based in accordance with gene IDs in the newly sequenced genome. Sm-
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<emphasis id="B924EAD6FFF8FFF0AEE7FD27FC45FD4C" bold="true" box="[942,996,650,669]" italics="true" pageId="1" pageNumber="2">
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<collectionCode id="ED41AE01FFF8FFF0AEE7FD27FC7DFD4C" box="[942,988,650,669]" country="Japan" httpUri="http://biocol.org/urn:lsid:biocol.org:col:13686" lsid="urn:lsid:biocol.org:col:13686" name="Nagano Environmental Conservation Research Institute" pageId="1" pageNumber="2" type="Herbarium">NAC</collectionCode>
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1
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</emphasis>
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- Sm-
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<emphasis id="B924EAD6FFF8FFF0A969FD27FBF7FD4C" bold="true" box="[1056,1110,650,669]" italics="true" pageId="1" pageNumber="2">
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<collectionCode id="ED41AE01FFF8FFF0A969FD27FBECFD4C" box="[1056,1101,650,669]" country="Japan" httpUri="http://biocol.org/urn:lsid:biocol.org:col:13686" lsid="urn:lsid:biocol.org:col:13686" name="Nagano Environmental Conservation Research Institute" pageId="1" pageNumber="2" type="Herbarium">NAC</collectionCode>
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3
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</emphasis>
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had been identified previously (
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<bibRefCitation id="EFC14B35FFF8FFF0A8DCFD27FC6FFD68" author="Zhang, H. & Liang, Z." pageId="1" pageNumber="2" refId="ref11210" refString="Zhang, H., Liang, Z., 2019. The studies on miRNA responding to Salvia miltiorrhiza continuous cropping problem and its role in secondary metabolic regulation. Northwest A & F University." type="book" year="2019">Zhang and Liang, 2019</bibRefCitation>
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||
;
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||
<bibRefCitation id="EFC14B35FFF8FFF0AE95FD0BFBD2FD68" author="Yin, X. & Fan, H. & Chen, Y. & Li, L. Z. & Song, W. & Fan, Y. & Zhou, W. & Ma, G. & Alolga, R. N. & Li, W. & Zhang, B. & Li, P. & Tran, L. P. & Lu, X. & Qi, L. W." box="[988,1139,678,697]" pageId="1" pageNumber="2" pagination="781 - 799" refId="ref11072" refString="Yin, X., Fan, H., Chen, Y., Li, L. Z., Song, W., Fan, Y., Zhou, W., Ma, G., Alolga, R. N., Li, W., Zhang, B., Li, P., Tran, L. P., Lu, X., Qi, L. W., 2020. Integrative omic and transgenic analyses reveal the positive effect of ultraviolet-B irradiation on salvianolic acid biosynthesis through upregulation of SmNAC 1. Plant J.: Cell Mol. Biol. 104 (3), 781 - 799. https: // doi. org / 10.1111 / tpj. 14952." type="journal article" year="2020">Yin et al., 2020</bibRefCitation>
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||
;
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||
<bibRefCitation id="EFC14B35FFF8FFF0A9C8FD0BFA88FD68" author="Zhu, B. & Huo, D. A. & Hong, X. X. & Guo, J. & Peng, T. & Liu, J. & Huang, X. L. & Yan, H. Q. & Weng, Q. B. & Zhang, X. C. & Du, X. Y." box="[1153,1321,678,697]" pageId="1" pageNumber="2" pagination="54 - 61" refId="ref11621" refString="Zhu, B., Huo, D. A., Hong, X. X., Guo, J., Peng, T., Liu, J., Huang, X. L., Yan, H. Q., Weng, Q. B., Zhang, X. C., Du, X. Y., 2019 b. The Salvia miltiorrhiza NAC transcription factor SmNAC 1 enhances zinc content in transgenic Arabidopsis. Gene 688, 54 - 61. https: // doi. org / 10.1016 / j. gene. 2018.11.076." type="journal article" year="2019">Zhu et al., 2019b</bibRefCitation>
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); therefore, their names were maintained (Supplementary
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<tableCitation id="C6D2037FFFF8FFF0A9E4FD6CFB5CFD04" box="[1197,1277,705,725]" captionStart="Table 1" captionStartId="3.[100,150,1651,1667]" captionTargetPageId="3" captionText="Table 1 FPKM values of 10 significantly different genes after MeJA treatment." pageId="1" pageNumber="2">Table S1</tableCitation>
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). The coding DNA and protein sequences of Sm-NAC gene family members are given in Supplementary Files S1–S2. The protein sequence lengths of the 84 Sm-NACs are quite different (Supplementary
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<tableCitation id="C6D2037FFFF8FFF0A9AAFCB8FA94FCF9" box="[1251,1333,789,808]" captionStart="Table 1" captionStartId="3.[100,150,1651,1667]" captionTargetPageId="3" captionText="Table 1 FPKM values of 10 significantly different genes after MeJA treatment." pageId="1" pageNumber="2">Table S1</tableCitation>
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). The longest is 794 bp (Sm-NAC79), and the shortest is only 120 bp (Sm-NAC27). The molecular weights range from 14.01 kDa (Sm-NAC27) to 89.74 kDa (Sm-NAC79), and the isoelectric points (pI) range from 4.53 (Sm-NAC83) to 9.73 (Sm-NAC4). The locations of the 84 Sm
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||
<emphasis id="B924EAD6FFF8FFF0A82DFC28FA34FC49" bold="true" box="[1380,1429,901,920]" italics="true" pageId="1" pageNumber="2">
|
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-
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<collectionCode id="ED41AE01FFF8FFF0A820FC28FA34FC49" box="[1385,1429,901,920]" country="Japan" httpUri="http://biocol.org/urn:lsid:biocol.org:col:13686" lsid="urn:lsid:biocol.org:col:13686" name="Nagano Environmental Conservation Research Institute" pageId="1" pageNumber="2" type="Herbarium">NAC</collectionCode>
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</emphasis>
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genes on the chromosomes of
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<taxonomicName id="4C504D47FFFBFFF3AC11FF39FE7DFF77" box="[344,476,147,167]" class="Magnoliopsida" family="Lamiaceae" genus="Salvia" kingdom="Plantae" order="Lamiales" pageId="2" pageNumber="3" phylum="Tracheophyta" rank="species" species="miltiorrhiza">
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<emphasis id="B924EAD6FFFBFFF3AC11FF39FE7DFF77" bold="true" box="[344,476,147,167]" italics="true" pageId="2" pageNumber="3">S. miltiorrhiza</emphasis>
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||
</taxonomicName>
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are shown in Supplementary
|
||
<figureCitation id="136B2A41FFFBFFF3AD2DFF1DFF1CFF12" box="[100,189,176,195]" captionStart="Fig" captionStartId="1.[100,130,1913,1930]" captionTargetBox="[340,1246,979,1884]" captionTargetId="figure-537@1.[339,1249,978,1886]" captionTargetPageId="1" captionText="Fig. 1. Phylogenetic relationship among the NAC family members of S. miltiorrhiza and Arabidopsis. Full-length amino acid sequences were aligned using ClustalW, and the phylogenetic tree was constructed using the MEGA7 method. The tree clustered the NAC proteins into different groups, which are indicated by different colors within the clades. (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.8258182" httpUri="https://zenodo.org/record/8258182/files/figure.png" pageId="2" pageNumber="3">Figure S1</figureCitation>
|
||
, and all 84 Sm
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||
<emphasis id="B924EAD6FFFBFFF3AC03FF1DFEDDFF12" bold="true" box="[330,380,176,195]" italics="true" pageId="2" pageNumber="3">
|
||
-
|
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<collectionCode id="ED41AE01FFFBFFF3AC19FF1DFEDDFF12" box="[336,380,176,195]" country="Japan" httpUri="http://biocol.org/urn:lsid:biocol.org:col:13686" lsid="urn:lsid:biocol.org:col:13686" name="Nagano Environmental Conservation Research Institute" pageId="2" pageNumber="3" type="Herbarium">NAC</collectionCode>
|
||
</emphasis>
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||
genes, except for Sm
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<emphasis id="B924EAD6FFFBFFF3AF0AFF1DFD21FF12" bold="true" box="[579,640,176,195]" italics="true" pageId="2" pageNumber="3">
|
||
-
|
||
<collectionCode id="ED41AE01FFFBFFF3AF00FF1DFDD7FF12" box="[585,630,176,195]" country="Japan" httpUri="http://biocol.org/urn:lsid:biocol.org:col:13686" lsid="urn:lsid:biocol.org:col:13686" name="Nagano Environmental Conservation Research Institute" pageId="2" pageNumber="3" type="Herbarium">NAC</collectionCode>
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||
4
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||
</emphasis>
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||
that is on the scaffold, are distributed among the eight chromosomes. There was no significant correlation between the number of Sm
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<emphasis id="B924EAD6FFFBFFF3AF0FFF4AFDD9FF2B" bold="true" box="[582,632,231,250]" italics="true" pageId="2" pageNumber="3">
|
||
-
|
||
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||
</emphasis>
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||
genes present per chromosome and the chromosomal length. To investigate the phylogenetic relationships among the 84 Sm-NACs, a phylogenetic tree was constructed by combining Sm-NACs with
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<taxonomicName id="4C504D47FFFBFFF3AF5EFE96FDDFFE9F" authority="NAC" authorityName="NAC" box="[535,638,315,334]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="2" pageNumber="3" phylum="Tracheophyta" rank="genus">
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||
<emphasis id="B924EAD6FFFBFFF3AF5EFE96FDDFFE9F" bold="true" box="[535,638,315,334]" italics="true" pageId="2" pageNumber="3">Arabidopsis</emphasis>
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</taxonomicName>
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NAC proteins (AtNACs). The 84 Sm-NACs were divided into nine families (Groups 1–9) (
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<figureCitation id="136B2A41FFFBFFF3ADD5FEDEFF70FE57" box="[156,209,371,390]" captionStart="Fig" captionStartId="1.[100,130,1913,1930]" captionTargetBox="[340,1246,979,1884]" captionTargetId="figure-537@1.[339,1249,978,1886]" captionTargetPageId="1" captionText="Fig. 1. Phylogenetic relationship among the NAC family members of S. miltiorrhiza and Arabidopsis. Full-length amino acid sequences were aligned using ClustalW, and the phylogenetic tree was constructed using the MEGA7 method. The tree clustered the NAC proteins into different groups, which are indicated by different colors within the clades. (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.8258182" httpUri="https://zenodo.org/record/8258182/files/figure.png" pageId="2" pageNumber="3">Fig. 1</figureCitation>
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||
). There was an unequal distribution of Sm-NACs among the groups, with the Group 9 subfamily, containing 22 genes, having the most members, followed by Groups 7 and 6, each containing 15 proteins. The Group 3 subfamily had the least members, containing only two genes.
|
||
</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |