137 lines
19 KiB
XML
137 lines
19 KiB
XML
<document id="8CAAD008AACC1655A905053A2C505A59" ID-DOI="10.1016/j.phytochem.2020.112511" ID-ISSN="1873-3700" ID-Zenodo-Dep="8293258" IM.bibliography_approvedBy="julia" IM.illustrations_approvedBy="julia" IM.materialsCitations_approvedBy="felipe" IM.metadata_approvedBy="felipe" IM.taxonomicNames_approvedBy="julia" IM.treatments_approvedBy="julia" checkinTime="1693251782550" checkinUser="felipe" docAuthor="Costa, Laura S. M., Allan, Pires, S., Damaceno, Neila B., Rigueiras, Pietra O., Maximiano, Mariana R., Franco, Octavio L. & Porto, William F." docDate="2020" docId="442187AFFFCCFFD22869F8D5FA520388" docLanguage="en" docName="Phytochemistry.179.112511.pdf" docOrigin="Phytochemistry (112511) 179" docSource="http://dx.doi.org/10.1016/j.phytochem.2020.112511" docStyle="DocumentStyle:F36D69FC8B198FBE91029DF9C24697D3.5:Phytochemistry.2020-.journal_article" docStyleId="F36D69FC8B198FBE91029DF9C24697D3" docStyleName="Phytochemistry.2020-.journal_article" docStyleVersion="5" docTitle="Arabidopsis thaliana subsp. defensins" docType="treatment" docVersion="3" lastPageNumber="2" masterDocId="B818FFD7FFCDFFD3280DFFD6FF980741" masterDocTitle="In silico characterization of class II plant defensins from Arabidopsis thaliana" masterLastPageNumber="8" masterPageNumber="1" pageNumber="2" updateTime="1693404443183" updateUser="julia">
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<mods:title id="12A0BB15CE238A162536836BFF599E20">In silico characterization of class II plant defensins from Arabidopsis thaliana</mods:title>
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<mods:namePart id="C10463A70AA77BAC4D6C8E6D3775ED61">Costa, Laura S. M.</mods:namePart>
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<mods:affiliation id="BB78ABCD51B4EEF42DDC2F71F9D31068">Centro de An´alises Proteˆomicas e Bioquímicas. Programa de P´os-Graduaç ˜ ao em Ciˆencias Genˆomicas e Biotecnologia, Universidade Cat´olica de Brasília, Brasília, DF, & Departamento de Biologia, Programa de P´os-Graduaç ˜ ao em Gen´etica e Biotecnologia, Universidade Federal de Juiz de Fora, Campus Universit´ario, Juiz de Fora, MG,</mods:affiliation>
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<mods:namePart id="58FE6BD1CD9BDBA67DF072736096F394">Pires, S.</mods:namePart>
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<mods:affiliation id="868C6776E1141D9373FFD9B63572F494">Centro de An´alises Proteˆomicas e Bioquímicas. Programa de P´os-Graduaç ˜ ao em Ciˆencias Genˆomicas e Biotecnologia, Universidade Cat´olica de Brasília, Brasília, DF,</mods:affiliation>
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<mods:namePart id="A666593F47A69C13F11EDF78D6B83CB3">Damaceno, Neila B.</mods:namePart>
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<mods:namePart id="C18C201A57A8FD4DCA8B7197867FCBAF">Rigueiras, Pietra O.</mods:namePart>
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<mods:namePart id="ABE1799158C94C33F7BE0FB119E84E77">Maximiano, Mariana R.</mods:namePart>
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<mods:namePart id="D463C01AC0426D75FF568DD93BF542CF">Franco, Octavio L.</mods:namePart>
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<mods:namePart id="458E20C82D076CCE5B9FABF6BADF8F37">Porto, William F.</mods:namePart>
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<mods:title id="7EBB360964FA374D48116218E66257D7">Phytochemistry</mods:title>
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<mods:date id="75964AB77AFA0DED3BD59FBCCC4FEF9D">2020</mods:date>
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<subSubSection id="84926532FFCCFFD22869F8D5FD410057" box="[100,729,1795,1814]" pageId="1" pageNumber="2" type="nomenclature">
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<paragraph id="CC3736B9FFCCFFD22869F8D5FD410057" blockId="1.[100,729,1795,1814]" box="[100,729,1795,1814]" pageId="1" pageNumber="2">
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<heading id="977F81D5FFCCFFD22869F8D5FD410057" bold="true" box="[100,729,1795,1814]" fontSize="36" level="1" pageId="1" pageNumber="2" reason="1">
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<emphasis id="FEFCEAABFFCCFFD22869F8D5FD410057" bold="true" box="[100,729,1795,1814]" italics="true" pageId="1" pageNumber="2">
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2.1. The majority of
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<taxonomicName id="0B884D3AFFCCFFD2292AF8D5FE140057" ID-CoL="G26R" ID-ENA="3702" authority="L." box="[295,396,1795,1814]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="1" pageNumber="2" phylum="Tracheophyta" rank="species" species="thaliana">A. thaliana</taxonomicName>
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defensins belongs to class I defensins
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<paragraph id="CC3736B9FFCCFFD22889F8EDFA520388" blockId="1.[100,770,1851,1982]" lastBlockId="1.[818,1488,955,1225]" pageId="1" pageNumber="2">
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<materialsCitation id="7CE03CE4FFCCFFD22889F8EDFB9B0347" collectingDate="2017-03" collectionCode="PERL" pageId="1" pageNumber="2" specimenCount="1">
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In order to identify class II defensin sequences, we designed a semiautomatic pipeline (
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<figureCitation id="54B32A3CFFCCFFD22942F881FE1C002B" box="[335,388,1879,1898]" captionStart="Fig" captionStartId="1.[818,848,616,633]" captionTargetBox="[824,1480,149,588]" captionTargetId="figure-1044@1.[823,1481,148,589]" captionTargetPageId="1" captionText="Fig. 1. Flowchart of identification of class II defensins. The indigo boxes indicated steps performed by Perl scripts and the red boxes, steps curated by hand. The white boxes indicated the number of sequences for each respective step. The sequences from A. thaliana were retrieved from UniProt database; the defensin RegEx “CX2-18CX3CX2-10[GAPSIDERYW]XCX4-17CXC” was determined by Zhu (Zhu, 2008). The complete sequences were retrieved according the UniProt annotations; and the sequences predicted to be secreted were selected according to the Phobius prediction, presenting signal peptide and no transmembrane domains. The selected sequences at the end of the process represented less than 1% of all defensin sequences from A. thaliana. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)" figureDoi="http://doi.org/10.5281/zenodo.8293260" httpUri="https://zenodo.org/record/8293260/files/figure.png" pageId="1" pageNumber="2">Fig. 1</figureCitation>
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). For that, initially all proteins from the
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<taxonomicName id="0B884D3AFFCCFFD22869F8A5FE8D00C7" authority="Uniprot" authorityName="Uniprot" box="[100,277,1906,1926]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="1" pageNumber="2" phylum="Tracheophyta" rank="species" species="thaliana">
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<emphasis id="FEFCEAABFFCCFFD22869F8A5FF5F00C4" bold="true" box="[100,199,1906,1926]" italics="true" pageId="1" pageNumber="2">A. thaliana</emphasis>
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Uniprot
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</taxonomicName>
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database were downloaded. The dataset consisted of 86,486 sequences (
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<date id="B8361079FFCCFFD22918F859FE1400E3" box="[277,396,1935,1954]" pageId="1" pageNumber="2" value="2017-03">
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<collectingDate id="A872E991FFCCFFD22918F859FE1400E3" box="[277,396,1935,1954]" pageId="1" pageNumber="2" value="2017-03">March 2017</collectingDate>
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</date>
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). From this dataset, 387 sequences were retrieved by using regular expression (RegEx) search (step 2,
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<figureCitation id="54B32A3CFFCCFFD22AB1F87DFD6C00FF" box="[700,756,1963,1982]" captionStart="Fig" captionStartId="1.[818,848,616,633]" captionTargetBox="[824,1480,149,588]" captionTargetId="figure-1044@1.[823,1481,148,589]" captionTargetPageId="1" captionText="Fig. 1. Flowchart of identification of class II defensins. The indigo boxes indicated steps performed by Perl scripts and the red boxes, steps curated by hand. The white boxes indicated the number of sequences for each respective step. The sequences from A. thaliana were retrieved from UniProt database; the defensin RegEx “CX2-18CX3CX2-10[GAPSIDERYW]XCX4-17CXC” was determined by Zhu (Zhu, 2008). The complete sequences were retrieved according the UniProt annotations; and the sequences predicted to be secreted were selected according to the Phobius prediction, presenting signal peptide and no transmembrane domains. The selected sequences at the end of the process represented less than 1% of all defensin sequences from A. thaliana. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)" figureDoi="http://doi.org/10.5281/zenodo.8293260" httpUri="https://zenodo.org/record/8293260/files/figure.png" pageId="1" pageNumber="2">Fig. 1</figureCitation>
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). From these, 285 had up to 130 amino acid residues (step 3,
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<figureCitation id="54B32A3CFFCCFFD22D52FC6DFA0C048F" box="[1375,1428,955,974]" captionStart="Fig" captionStartId="1.[818,848,616,633]" captionTargetBox="[824,1480,149,588]" captionTargetId="figure-1044@1.[823,1481,148,589]" captionTargetPageId="1" captionText="Fig. 1. Flowchart of identification of class II defensins. The indigo boxes indicated steps performed by Perl scripts and the red boxes, steps curated by hand. The white boxes indicated the number of sequences for each respective step. The sequences from A. thaliana were retrieved from UniProt database; the defensin RegEx “CX2-18CX3CX2-10[GAPSIDERYW]XCX4-17CXC” was determined by Zhu (Zhu, 2008). The complete sequences were retrieved according the UniProt annotations; and the sequences predicted to be secreted were selected according to the Phobius prediction, presenting signal peptide and no transmembrane domains. The selected sequences at the end of the process represented less than 1% of all defensin sequences from A. thaliana. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)" figureDoi="http://doi.org/10.5281/zenodo.8293260" httpUri="https://zenodo.org/record/8293260/files/figure.png" pageId="1" pageNumber="2">Fig. 1</figureCitation>
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). This criterion allows eventual larger C-terminal prodomains to be identified. Then, we used a
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</materialsCitation>
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<materialsCitation id="7CE03CE4FFCCFFD22C04FC25FA5E0388" collectionCode="A, REG" pageId="1" pageNumber="2" specimenCode="A7, REG2, REG4" specimenCount="1">
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script to select the sequences with the following flags: hypothetical, unknown, unnamed and/or uncharacterized (step 4,
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<figureCitation id="54B32A3CFFCCFFD22B3FFBFCFCF4037F" box="[818,876,1066,1086]" captionStart="Fig" captionStartId="1.[818,848,616,633]" captionTargetBox="[824,1480,149,588]" captionTargetId="figure-1044@1.[823,1481,148,589]" captionTargetPageId="1" captionText="Fig. 1. Flowchart of identification of class II defensins. The indigo boxes indicated steps performed by Perl scripts and the red boxes, steps curated by hand. The white boxes indicated the number of sequences for each respective step. The sequences from A. thaliana were retrieved from UniProt database; the defensin RegEx “CX2-18CX3CX2-10[GAPSIDERYW]XCX4-17CXC” was determined by Zhu (Zhu, 2008). The complete sequences were retrieved according the UniProt annotations; and the sequences predicted to be secreted were selected according to the Phobius prediction, presenting signal peptide and no transmembrane domains. The selected sequences at the end of the process represented less than 1% of all defensin sequences from A. thaliana. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)" figureDoi="http://doi.org/10.5281/zenodo.8293260" httpUri="https://zenodo.org/record/8293260/files/figure.png" pageId="1" pageNumber="2">Fig. 1</figureCitation>
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), resulting in 15 sequences. From 15 sequences, seven were incomplete and therefore were discarded, (step 5,
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<figureCitation id="54B32A3CFFCCFFD22D28FB90FAC60318" box="[1317,1374,1094,1113]" captionStart="Fig" captionStartId="1.[818,848,616,633]" captionTargetBox="[824,1480,149,588]" captionTargetId="figure-1044@1.[823,1481,148,589]" captionTargetPageId="1" captionText="Fig. 1. Flowchart of identification of class II defensins. The indigo boxes indicated steps performed by Perl scripts and the red boxes, steps curated by hand. The white boxes indicated the number of sequences for each respective step. The sequences from A. thaliana were retrieved from UniProt database; the defensin RegEx “CX2-18CX3CX2-10[GAPSIDERYW]XCX4-17CXC” was determined by Zhu (Zhu, 2008). The complete sequences were retrieved according the UniProt annotations; and the sequences predicted to be secreted were selected according to the Phobius prediction, presenting signal peptide and no transmembrane domains. The selected sequences at the end of the process represented less than 1% of all defensin sequences from A. thaliana. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)" figureDoi="http://doi.org/10.5281/zenodo.8293260" httpUri="https://zenodo.org/record/8293260/files/figure.png" pageId="1" pageNumber="2">Fig. 1</figureCitation>
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). From the remaining sequences, two sequences without signal peptide or with transmembrane domains were discarded (step 6,
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<figureCitation id="54B32A3CFFCCFFD22D05FBA8FAA703D0" box="[1288,1343,1150,1169]" captionStart="Fig" captionStartId="1.[818,848,616,633]" captionTargetBox="[824,1480,149,588]" captionTargetId="figure-1044@1.[823,1481,148,589]" captionTargetPageId="1" captionText="Fig. 1. Flowchart of identification of class II defensins. The indigo boxes indicated steps performed by Perl scripts and the red boxes, steps curated by hand. The white boxes indicated the number of sequences for each respective step. The sequences from A. thaliana were retrieved from UniProt database; the defensin RegEx “CX2-18CX3CX2-10[GAPSIDERYW]XCX4-17CXC” was determined by Zhu (Zhu, 2008). The complete sequences were retrieved according the UniProt annotations; and the sequences predicted to be secreted were selected according to the Phobius prediction, presenting signal peptide and no transmembrane domains. The selected sequences at the end of the process represented less than 1% of all defensin sequences from A. thaliana. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)" figureDoi="http://doi.org/10.5281/zenodo.8293260" httpUri="https://zenodo.org/record/8293260/files/figure.png" pageId="1" pageNumber="2">Fig. 1</figureCitation>
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). Finally, from six remaining sequences, two sequences with a potential C-Terminal prodomain were selected, with accession codes
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<specimenCode id="9C2E9EC2FFCCFFD22CF9FB60FA960388" box="[1268,1294,1206,1225]" collectionCode="A" country="USA" lsid="urn:lsid:biocol.org:col:15406" name="Harvard University - Arnold Arboretum" pageId="1" pageNumber="2" type="Herbarium">A7</specimenCode>
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<specimenCode id="9C2E9EC2FFCCFFD22D00FB60FADB0388" box="[1293,1347,1206,1225]" collectionCode="REG" country="Germany" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15512" lsid="urn:lsid:biocol.org:col:15512" name="Universität Regensburg" pageId="1" pageNumber="2" type="Herbarium">REG2</specimenCode>
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and
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<specimenCode id="9C2E9EC2FFCCFFD22D80FB60FA5E0388" box="[1421,1478,1206,1225]" collectionCode="REG" country="Germany" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15512" lsid="urn:lsid:biocol.org:col:15512" name="Universität Regensburg" pageId="1" pageNumber="2" type="Herbarium">REG4</specimenCode>
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.
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</paragraph>
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</treatment>
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