Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom.
Identifieur interne : 003680 ( Main/Exploration ); précédent : 003679; suivant : 003681Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom.
Auteurs : Zhanyou Xu [États-Unis] ; Dandan Zhang ; Jun Hu ; Xin Zhou ; Xia Ye ; Kristen L. Reichel ; Nathan R. Stewart ; Ryan D. Syrenne ; Xiaohan Yang ; Peng Gao ; Weibing Shi ; Crissa Doeppke ; Robert W. Sykes ; Jason N. Burris ; Joseph J. Bozell ; Max Zong-Ming Cheng ; Douglas G. Hayes ; Nicole Labbe ; Mark Davis ; C Neal Stewart ; Joshua S. YuanSource :
- BMC bioinformatics [ 1471-2105 ] ; 2009.
Descripteurs français
- KwdFr :
- Arabidopsis (génétique), Duplication de gène (MeSH), Gènes de plante (MeSH), Génome végétal (MeSH), Lignine (biosynthèse), Oryza (génétique), Phylogenèse (MeSH), Plantes (génétique), Poaceae (génétique), Protéines végétales (génétique), Protéines végétales (métabolisme), Régulation de l'expression des gènes végétaux (MeSH), Évolution moléculaire (MeSH).
- MESH :
- biosynthèse : Lignine.
- génétique : Arabidopsis, Oryza, Plantes, Poaceae, Protéines végétales.
- métabolisme : Protéines végétales.
- Duplication de gène, Gènes de plante, Génome végétal, Phylogenèse, Régulation de l'expression des gènes végétaux, Évolution moléculaire.
English descriptors
- KwdEn :
- Arabidopsis (genetics), Evolution, Molecular (MeSH), Gene Duplication (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Genome, Plant (MeSH), Lignin (biosynthesis), Oryza (genetics), Phylogeny (MeSH), Plant Proteins (genetics), Plant Proteins (metabolism), Plants (genetics), Poaceae (genetics).
- MESH :
- chemical , biosynthesis : Lignin.
- genetics : Arabidopsis, Oryza, Plant Proteins, Plants, Poaceae.
- chemical , metabolism : Plant Proteins.
- Evolution, Molecular, Gene Duplication, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Phylogeny.
Abstract
BACKGROUND
As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modification has been a major task for bioenergy feedstock improvement. The study of the evolution and function of lignin biosynthesis genes thus has two-fold implications. First, the lignin biosynthesis pathway provides an excellent model to study the coordinative evolution of a biochemical pathway in plants. Second, understanding the function and evolution of lignin biosynthesis genes will guide us to develop better strategies for bioenergy feedstock improvement.
RESULTS
We analyzed lignin biosynthesis genes from fourteen plant species and one symbiotic fungal species. Comprehensive comparative genome analysis was carried out to study the distribution, relatedness, and family expansion of the lignin biosynthesis genes across the plant kingdom. In addition, we also analyzed the comparative synteny map between rice and sorghum to study the evolution of lignin biosynthesis genes within the Poaceae family and the chromosome evolution between the two species. Comprehensive lignin biosynthesis gene expression analysis was performed in rice, poplar and Arabidopsis. The representative data from rice indicates that different fates of gene duplications exist for lignin biosynthesis genes. In addition, we also carried out the biomass composition analysis of nine Arabidopsis mutants with both MBMS analysis and traditional wet chemistry methods. The results were analyzed together with the genomics analysis.
CONCLUSION
The research revealed that, among the species analyzed, the complete lignin biosynthesis pathway first appeared in moss; the pathway is absent in green algae. The expansion of lignin biosynthesis gene families correlates with substrate diversity. In addition, we found that the expansion of the gene families mostly occurred after the divergence of monocots and dicots, with the exception of the C4H gene family. Gene expression analysis revealed different fates of gene duplications, largely confirming plants are tolerant to gene dosage effects. The rapid expansion of lignin biosynthesis genes indicated that the translation of transgenic lignin modification strategies from model species to bioenergy feedstock might only be successful between the closely relevant species within the same family.
DOI: 10.1186/1471-2105-10-S11-S3
PubMed: 19811687
PubMed Central: PMC3226193
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Reichel</name></author><author><name sortKey="Stewart, Nathan R" sort="Stewart, Nathan R" uniqKey="Stewart N" first="Nathan R" last="Stewart">Nathan R. Stewart</name></author><author><name sortKey="Syrenne, Ryan D" sort="Syrenne, Ryan D" uniqKey="Syrenne R" first="Ryan D" last="Syrenne">Ryan D. Syrenne</name></author><author><name sortKey="Yang, Xiaohan" sort="Yang, Xiaohan" uniqKey="Yang X" first="Xiaohan" last="Yang">Xiaohan Yang</name></author><author><name sortKey="Gao, Peng" sort="Gao, Peng" uniqKey="Gao P" first="Peng" last="Gao">Peng Gao</name></author><author><name sortKey="Shi, Weibing" sort="Shi, Weibing" uniqKey="Shi W" first="Weibing" last="Shi">Weibing Shi</name></author><author><name sortKey="Doeppke, Crissa" sort="Doeppke, Crissa" uniqKey="Doeppke C" first="Crissa" last="Doeppke">Crissa Doeppke</name></author><author><name sortKey="Sykes, Robert W" sort="Sykes, Robert W" uniqKey="Sykes R" first="Robert W" last="Sykes">Robert W. Sykes</name></author><author><name sortKey="Burris, Jason N" sort="Burris, Jason N" uniqKey="Burris J" first="Jason N" last="Burris">Jason N. Burris</name></author><author><name sortKey="Bozell, Joseph J" sort="Bozell, Joseph J" uniqKey="Bozell J" first="Joseph J" last="Bozell">Joseph J. Bozell</name></author><author><name sortKey="Cheng, Max Zong Ming" sort="Cheng, Max Zong Ming" uniqKey="Cheng M" first="Max Zong-Ming" last="Cheng">Max Zong-Ming Cheng</name></author><author><name sortKey="Hayes, Douglas G" sort="Hayes, Douglas G" uniqKey="Hayes D" first="Douglas G" last="Hayes">Douglas G. Hayes</name></author><author><name sortKey="Labbe, Nicole" sort="Labbe, Nicole" uniqKey="Labbe N" first="Nicole" last="Labbe">Nicole Labbe</name></author><author><name sortKey="Davis, Mark" sort="Davis, Mark" uniqKey="Davis M" first="Mark" last="Davis">Mark Davis</name></author><author><name sortKey="Stewart, C Neal" sort="Stewart, C Neal" uniqKey="Stewart C" first="C Neal" last="Stewart">C Neal Stewart</name></author><author><name sortKey="Yuan, Joshua S" sort="Yuan, Joshua S" uniqKey="Yuan J" first="Joshua S" last="Yuan">Joshua S. Yuan</name></author></analytic><series><title level="j">BMC bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Lignin (biosynthesis)</term><term>Oryza (genetics)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Plants (genetics)</term><term>Poaceae (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Arabidopsis (génétique)</term><term>Duplication de gène (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génome végétal (MeSH)</term><term>Lignine (biosynthèse)</term><term>Oryza (génétique)</term><term>Phylogenèse (MeSH)</term><term>Plantes (génétique)</term><term>Poaceae (génétique)</term><term>Protéines végétales (génétique)</term><term>Protéines végétales (métabolisme)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Lignin</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>Lignine</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Oryza</term><term>Plant Proteins</term><term>Plants</term><term>Poaceae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Oryza</term><term>Plantes</term><term>Poaceae</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Gene Duplication</term><term>Gene Expression Regulation, Plant</term><term>Genes, Plant</term><term>Genome, Plant</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Duplication de gène</term><term>Gènes de plante</term><term>Génome végétal</term><term>Phylogenèse</term><term>Régulation de l'expression des gènes végétaux</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modification has been a major task for bioenergy feedstock improvement. The study of the evolution and function of lignin biosynthesis genes thus has two-fold implications. First, the lignin biosynthesis pathway provides an excellent model to study the coordinative evolution of a biochemical pathway in plants. Second, understanding the function and evolution of lignin biosynthesis genes will guide us to develop better strategies for bioenergy feedstock improvement.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We analyzed lignin biosynthesis genes from fourteen plant species and one symbiotic fungal species. Comprehensive comparative genome analysis was carried out to study the distribution, relatedness, and family expansion of the lignin biosynthesis genes across the plant kingdom. In addition, we also analyzed the comparative synteny map between rice and sorghum to study the evolution of lignin biosynthesis genes within the Poaceae family and the chromosome evolution between the two species. Comprehensive lignin biosynthesis gene expression analysis was performed in rice, poplar and Arabidopsis. The representative data from rice indicates that different fates of gene duplications exist for lignin biosynthesis genes. In addition, we also carried out the biomass composition analysis of nine Arabidopsis mutants with both MBMS analysis and traditional wet chemistry methods. The results were analyzed together with the genomics analysis.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>The research revealed that, among the species analyzed, the complete lignin biosynthesis pathway first appeared in moss; the pathway is absent in green algae. The expansion of lignin biosynthesis gene families correlates with substrate diversity. In addition, we found that the expansion of the gene families mostly occurred after the divergence of monocots and dicots, with the exception of the C4H gene family. Gene expression analysis revealed different fates of gene duplications, largely confirming plants are tolerant to gene dosage effects. The rapid expansion of lignin biosynthesis genes indicated that the translation of transgenic lignin modification strategies from model species to bioenergy feedstock might only be successful between the closely relevant species within the same family.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19811687</PMID><DateCompleted><Year>2010</Year><Month>02</Month><Day>12</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN><JournalIssue CitedMedium="Internet"><Volume>10 Suppl 11</Volume><PubDate><Year>2009</Year><Month>Oct</Month><Day>08</Day></PubDate></JournalIssue><Title>BMC bioinformatics</Title><ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom.</ArticleTitle><Pagination><MedlinePgn>S3</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2105-10-S11-S3</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modification has been a major task for bioenergy feedstock improvement. The study of the evolution and function of lignin biosynthesis genes thus has two-fold implications. First, the lignin biosynthesis pathway provides an excellent model to study the coordinative evolution of a biochemical pathway in plants. Second, understanding the function and evolution of lignin biosynthesis genes will guide us to develop better strategies for bioenergy feedstock improvement.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We analyzed lignin biosynthesis genes from fourteen plant species and one symbiotic fungal species. Comprehensive comparative genome analysis was carried out to study the distribution, relatedness, and family expansion of the lignin biosynthesis genes across the plant kingdom. In addition, we also analyzed the comparative synteny map between rice and sorghum to study the evolution of lignin biosynthesis genes within the Poaceae family and the chromosome evolution between the two species. Comprehensive lignin biosynthesis gene expression analysis was performed in rice, poplar and Arabidopsis. The representative data from rice indicates that different fates of gene duplications exist for lignin biosynthesis genes. In addition, we also carried out the biomass composition analysis of nine Arabidopsis mutants with both MBMS analysis and traditional wet chemistry methods. The results were analyzed together with the genomics analysis.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The research revealed that, among the species analyzed, the complete lignin biosynthesis pathway first appeared in moss; the pathway is absent in green algae. The expansion of lignin biosynthesis gene families correlates with substrate diversity. In addition, we found that the expansion of the gene families mostly occurred after the divergence of monocots and dicots, with the exception of the C4H gene family. Gene expression analysis revealed different fates of gene duplications, largely confirming plants are tolerant to gene dosage effects. The rapid expansion of lignin biosynthesis genes indicated that the translation of transgenic lignin modification strategies from model species to bioenergy feedstock might only be successful between the closely relevant species within the same family.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Zhanyou</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Dandan</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Jun</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Xin</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Xia</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Reichel</LastName><ForeName>Kristen L</ForeName><Initials>KL</Initials></Author><Author ValidYN="Y"><LastName>Stewart</LastName><ForeName>Nathan R</ForeName><Initials>NR</Initials></Author><Author ValidYN="Y"><LastName>Syrenne</LastName><ForeName>Ryan D</ForeName><Initials>RD</Initials></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xiaohan</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Peng</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Weibing</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Doeppke</LastName><ForeName>Crissa</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Sykes</LastName><ForeName>Robert W</ForeName><Initials>RW</Initials></Author><Author ValidYN="Y"><LastName>Burris</LastName><ForeName>Jason N</ForeName><Initials>JN</Initials></Author><Author ValidYN="Y"><LastName>Bozell</LastName><ForeName>Joseph J</ForeName><Initials>JJ</Initials></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>Max Zong-Ming</ForeName><Initials>MZ</Initials></Author><Author ValidYN="Y"><LastName>Hayes</LastName><ForeName>Douglas G</ForeName><Initials>DG</Initials></Author><Author ValidYN="Y"><LastName>Labbe</LastName><ForeName>Nicole</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Davis</LastName><ForeName>Mark</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Stewart</LastName><ForeName>C Neal</ForeName><Initials>CN</Initials><Suffix>Jr</Suffix></Author><Author ValidYN="Y"><LastName>Yuan</LastName><ForeName>Joshua S</ForeName><Initials>JS</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2009</Year><Month>10</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Bioinformatics</MedlineTA><NlmUniqueID>100965194</NlmUniqueID><ISSNLinking>1471-2105</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>9005-53-2</RegistryNumber><NameOfSubstance UI="D008031">Lignin</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020440" MajorTopicYN="N">Gene Duplication</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="Y">biosynthesis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant 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