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Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis.

Identifieur interne : 000E25 ( Main/Exploration ); précédent : 000E24; suivant : 000E26

Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis.

Auteurs : Jack P. Wang [République populaire de Chine, États-Unis] ; Megan L. Matthews [États-Unis] ; Cranos M. Williams [États-Unis] ; Rui Shi [États-Unis] ; Chenmin Yang [États-Unis] ; Sermsawat Tunlaya-Anukit [États-Unis] ; Hsi-Chuan Chen [États-Unis] ; Quanzi Li [République populaire de Chine] ; Jie Liu [États-Unis] ; Chien-Yuan Lin [États-Unis] ; Punith Naik [États-Unis] ; Ying-Hsuan Sun [Taïwan] ; Philip L. Loziuk [États-Unis] ; Ting-Feng Yeh [Taïwan] ; Hoon Kim [États-Unis] ; Erica Gjersing [États-Unis] ; Todd Shollenberger [États-Unis] ; Christopher M. Shuford [États-Unis] ; Jina Song [États-Unis] ; Zachary Miller [États-Unis] ; Yung-Yun Huang [États-Unis] ; Charles W. Edmunds [États-Unis] ; Baoguang Liu [République populaire de Chine] ; Yi Sun [République populaire de Chine] ; Ying-Chung Jimmy Lin [République populaire de Chine, États-Unis, Taïwan] ; Wei Li [République populaire de Chine, États-Unis] ; Hao Chen [États-Unis] ; Ilona Peszlen [États-Unis] ; Joel J. Ducoste [États-Unis] ; John Ralph [États-Unis] ; Hou-Min Chang [États-Unis] ; David C. Muddiman [États-Unis] ; Mark F. Davis [États-Unis] ; Chris Smith [États-Unis] ; Fikret Isik [États-Unis] ; Ronald Sederoff [États-Unis] ; Vincent L. Chiang [République populaire de Chine, États-Unis]

Source :

RBID : pubmed:29679008

Descripteurs français

English descriptors

Abstract

A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in wood formation of Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 reactions on 24 metabolites, leading to lignin and affecting wood properties. We perturb these 21 pathway genes and integrate transcriptomic, proteomic, fluxomic and phenomic data from 221 lines selected from ~2000 transgenics (6-month-old). The integrative analysis estimates how changing expression of pathway gene or gene combination affects protein abundance, metabolic-flux, metabolite concentrations, and 25 wood traits, including lignin, tree-growth, density, strength, and saccharification. The analysis then predicts improvements in any of these 25 traits individually or in combinations, through engineering expression of specific monolignol genes. The analysis may lead to greater understanding of other pathways for improved growth and adaptation.

DOI: 10.1038/s41467-018-03863-z
PubMed: 29679008
PubMed Central: PMC5910405


Affiliations:


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Le document en format XML

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<name sortKey="Kim, Hoon" sort="Kim, Hoon" uniqKey="Kim H" first="Hoon" last="Kim">Hoon Kim</name>
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<name sortKey="Gjersing, Erica" sort="Gjersing, Erica" uniqKey="Gjersing E" first="Erica" last="Gjersing">Erica Gjersing</name>
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<name sortKey="Song, Jina" sort="Song, Jina" uniqKey="Song J" first="Jina" last="Song">Jina Song</name>
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<name sortKey="Miller, Zachary" sort="Miller, Zachary" uniqKey="Miller Z" first="Zachary" last="Miller">Zachary Miller</name>
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<name sortKey="Huang, Yung Yun" sort="Huang, Yung Yun" uniqKey="Huang Y" first="Yung-Yun" last="Huang">Yung-Yun Huang</name>
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<wicri:regionArea>Department of Operations Research, North Carolina State University, Raleigh, NC, 27695</wicri:regionArea>
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<name sortKey="Edmunds, Charles W" sort="Edmunds, Charles W" uniqKey="Edmunds C" first="Charles W" last="Edmunds">Charles W. Edmunds</name>
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<nlm:affiliation>Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, 27695, USA.</nlm:affiliation>
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<name sortKey="Liu, Baoguang" sort="Liu, Baoguang" uniqKey="Liu B" first="Baoguang" last="Liu">Baoguang Liu</name>
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<nlm:affiliation>Department of Forestry, Beihua University, Jilin, 132013, China.</nlm:affiliation>
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<name sortKey="Sun, Yi" sort="Sun, Yi" uniqKey="Sun Y" first="Yi" last="Sun">Yi Sun</name>
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<name sortKey="Lin, Ying Chung Jimmy" sort="Lin, Ying Chung Jimmy" uniqKey="Lin Y" first="Ying-Chung Jimmy" last="Lin">Ying-Chung Jimmy Lin</name>
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<nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.</nlm:affiliation>
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<name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name>
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<name sortKey="Chen, Hao" sort="Chen, Hao" uniqKey="Chen H" first="Hao" last="Chen">Hao Chen</name>
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<name sortKey="Peszlen, Ilona" sort="Peszlen, Ilona" uniqKey="Peszlen I" first="Ilona" last="Peszlen">Ilona Peszlen</name>
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<name sortKey="Ducoste, Joel J" sort="Ducoste, Joel J" uniqKey="Ducoste J" first="Joel J" last="Ducoste">Joel J. Ducoste</name>
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<name sortKey="Ralph, John" sort="Ralph, John" uniqKey="Ralph J" first="John" last="Ralph">John Ralph</name>
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<nlm:affiliation>Department of Biochemistry, and the DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53726, USA.</nlm:affiliation>
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<wicri:regionArea>Department of Biochemistry, and the DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53726</wicri:regionArea>
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<name sortKey="Chang, Hou Min" sort="Chang, Hou Min" uniqKey="Chang H" first="Hou-Min" last="Chang">Hou-Min Chang</name>
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<nlm:affiliation>Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, 27695, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, 27695</wicri:regionArea>
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<name sortKey="Muddiman, David C" sort="Muddiman, David C" uniqKey="Muddiman D" first="David C" last="Muddiman">David C. Muddiman</name>
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<nlm:affiliation>Department of Chemistry, W.M. Keck Fourier Transform Mass Spectrometry Laboratory, North Carolina State University, Raleigh, NC, 27695, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemistry, W.M. Keck Fourier Transform Mass Spectrometry Laboratory, North Carolina State University, Raleigh, NC, 27695</wicri:regionArea>
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<name sortKey="Davis, Mark F" sort="Davis, Mark F" uniqKey="Davis M" first="Mark F" last="Davis">Mark F. Davis</name>
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<nlm:affiliation>Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
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<name sortKey="Smith, Chris" sort="Smith, Chris" uniqKey="Smith C" first="Chris" last="Smith">Chris Smith</name>
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<nlm:affiliation>Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
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<name sortKey="Isik, Fikret" sort="Isik, Fikret" uniqKey="Isik F" first="Fikret" last="Isik">Fikret Isik</name>
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<name sortKey="Sederoff, Ronald" sort="Sederoff, Ronald" uniqKey="Sederoff R" first="Ronald" last="Sederoff">Ronald Sederoff</name>
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<name sortKey="Chiang, Vincent L" sort="Chiang, Vincent L" uniqKey="Chiang V" first="Vincent L" last="Chiang">Vincent L. Chiang</name>
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<nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China. vchiang@ncsu.edu.</nlm:affiliation>
<country xml:lang="fr">République populaire de Chine</country>
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<nlm:affiliation>Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA. vchiang@ncsu.edu.</nlm:affiliation>
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<affiliation wicri:level="1">
<nlm:affiliation>Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, 27695, USA. vchiang@ncsu.edu.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, 27695</wicri:regionArea>
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<series>
<title level="j">Nature communications</title>
<idno type="eISSN">2041-1723</idno>
<imprint>
<date when="2018" type="published">2018</date>
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<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Lignin (biosynthesis)</term>
<term>Lignin (genetics)</term>
<term>Plants, Genetically Modified (genetics)</term>
<term>Populus (genetics)</term>
<term>Populus (metabolism)</term>
<term>Transcriptome (genetics)</term>
<term>Trees (genetics)</term>
<term>Trees (metabolism)</term>
<term>Wood (chemistry)</term>
<term>Wood (physiology)</term>
<term>Xylem (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Arbres (génétique)</term>
<term>Arbres (métabolisme)</term>
<term>Bois (composition chimique)</term>
<term>Bois (physiologie)</term>
<term>Lignine (biosynthèse)</term>
<term>Lignine (génétique)</term>
<term>Populus (génétique)</term>
<term>Populus (métabolisme)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Transcriptome (génétique)</term>
<term>Végétaux génétiquement modifiés (génétique)</term>
<term>Xylème (métabolisme)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en">
<term>Lignin</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en">
<term>Lignin</term>
</keywords>
<keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr">
<term>Lignine</term>
</keywords>
<keywords scheme="MESH" qualifier="chemistry" xml:lang="en">
<term>Wood</term>
</keywords>
<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr">
<term>Bois</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Plants, Genetically Modified</term>
<term>Populus</term>
<term>Transcriptome</term>
<term>Trees</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Arbres</term>
<term>Lignine</term>
<term>Populus</term>
<term>Transcriptome</term>
<term>Végétaux génétiquement modifiés</term>
</keywords>
<keywords scheme="MESH" qualifier="metabolism" xml:lang="en">
<term>Populus</term>
<term>Trees</term>
<term>Xylem</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr">
<term>Arbres</term>
<term>Populus</term>
<term>Xylème</term>
</keywords>
<keywords scheme="MESH" qualifier="physiologie" xml:lang="fr">
<term>Bois</term>
</keywords>
<keywords scheme="MESH" qualifier="physiology" xml:lang="en">
<term>Wood</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Gene Expression Regulation, Plant</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Régulation de l'expression des gènes végétaux</term>
</keywords>
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<front>
<div type="abstract" xml:lang="en">A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in wood formation of Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 reactions on 24 metabolites, leading to lignin and affecting wood properties. We perturb these 21 pathway genes and integrate transcriptomic, proteomic, fluxomic and phenomic data from 221 lines selected from ~2000 transgenics (6-month-old). The integrative analysis estimates how changing expression of pathway gene or gene combination affects protein abundance, metabolic-flux, metabolite concentrations, and 25 wood traits, including lignin, tree-growth, density, strength, and saccharification. The analysis then predicts improvements in any of these 25 traits individually or in combinations, through engineering expression of specific monolignol genes. The analysis may lead to greater understanding of other pathways for improved growth and adaptation.</div>
</front>
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<DateCompleted>
<Year>2018</Year>
<Month>12</Month>
<Day>11</Day>
</DateCompleted>
<DateRevised>
<Year>2019</Year>
<Month>04</Month>
<Day>20</Day>
</DateRevised>
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<Journal>
<ISSN IssnType="Electronic">2041-1723</ISSN>
<JournalIssue CitedMedium="Internet">
<Volume>9</Volume>
<Issue>1</Issue>
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<Year>2018</Year>
<Month>04</Month>
<Day>20</Day>
</PubDate>
</JournalIssue>
<Title>Nature communications</Title>
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<ArticleTitle>Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis.</ArticleTitle>
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<Abstract>
<AbstractText>A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in wood formation of Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 reactions on 24 metabolites, leading to lignin and affecting wood properties. We perturb these 21 pathway genes and integrate transcriptomic, proteomic, fluxomic and phenomic data from 221 lines selected from ~2000 transgenics (6-month-old). The integrative analysis estimates how changing expression of pathway gene or gene combination affects protein abundance, metabolic-flux, metabolite concentrations, and 25 wood traits, including lignin, tree-growth, density, strength, and saccharification. The analysis then predicts improvements in any of these 25 traits individually or in combinations, through engineering expression of specific monolignol genes. The analysis may lead to greater understanding of other pathways for improved growth and adaptation.</AbstractText>
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<ForeName>Jack P</ForeName>
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</AffiliationInfo>
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<LastName>Matthews</LastName>
<ForeName>Megan L</ForeName>
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<ForeName>Chenmin</ForeName>
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</AffiliationInfo>
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<LastName>Tunlaya-Anukit</LastName>
<ForeName>Sermsawat</ForeName>
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<LastName>Loziuk</LastName>
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<LastName>Yeh</LastName>
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<Affiliation>Department of Biochemistry, and the DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53726, USA.</Affiliation>
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<LastName>Gjersing</LastName>
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<AffiliationInfo>
<Affiliation>Department of Biochemistry, and the DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53726, USA.</Affiliation>
</AffiliationInfo>
</Author>
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<LastName>Chang</LastName>
<ForeName>Hou-Min</ForeName>
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</AffiliationInfo>
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<LastName>Muddiman</LastName>
<ForeName>David C</ForeName>
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</AffiliationInfo>
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<LastName>Davis</LastName>
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<LastName>Smith</LastName>
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<ForeName>Ronald</ForeName>
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<LastName>Chiang</LastName>
<ForeName>Vincent L</ForeName>
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<Affiliation>Department of Forest Biomaterials, North Carolina State University, Raleigh, NC, 27695, USA. vchiang@ncsu.edu.</Affiliation>
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<Month>04</Month>
<Day>20</Day>
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<RegistryNumber>9005-53-2</RegistryNumber>
<NameOfSubstance UI="D008031">Lignin</NameOfSubstance>
</Chemical>
</ChemicalList>
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<MeshHeading>
<DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName>
<QualifierName UI="Q000096" MajorTopicYN="Y">biosynthesis</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D030821" MajorTopicYN="N">Plants, Genetically Modified</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D014197" MajorTopicYN="N">Trees</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D052584" MajorTopicYN="N">Xylem</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
</MeshHeadingList>
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<Year>2017</Year>
<Month>07</Month>
<Day>14</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted">
<Year>2018</Year>
<Month>03</Month>
<Day>16</Day>
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<PubMedPubDate PubStatus="entrez">
<Year>2018</Year>
<Month>4</Month>
<Day>22</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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