Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions.
Identifieur interne : 000977 ( Main/Exploration ); précédent : 000976; suivant : 000978Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions.
Auteurs : Jiadai He [République populaire de Chine] ; Hua Zhao [République populaire de Chine] ; Zhilu Cheng [République populaire de Chine] ; Yuwei Ke [République populaire de Chine] ; Jiaxi Liu [République populaire de Chine] ; Haoli Ma [République populaire de Chine]Source :
- International journal of molecular sciences [ 1422-0067 ] ; 2019.
Descripteurs français
- KwdFr :
- Domaines protéiques (MeSH), Duplication de gène (MeSH), Génome végétal (MeSH), Mucoprotéines (composition chimique), Mucoprotéines (génétique), Phylogenèse (MeSH), Plantes (génétique), Plantes (métabolisme), Protéines végétales (composition chimique), Protéines végétales (génétique), Séquence d'acides aminés (MeSH), Taille du génome (MeSH), Évolution moléculaire (MeSH).
- MESH :
- composition chimique : Mucoprotéines, Protéines végétales.
- génétique : Mucoprotéines, Plantes, Protéines végétales.
- métabolisme : Plantes.
- Domaines protéiques, Duplication de gène, Génome végétal, Phylogenèse, Séquence d'acides aminés, Taille du génome, Évolution moléculaire.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Evolution, Molecular (MeSH), Gene Duplication (MeSH), Genome Size (MeSH), Genome, Plant (MeSH), Mucoproteins (chemistry), Mucoproteins (genetics), Phylogeny (MeSH), Plant Proteins (chemistry), Plant Proteins (genetics), Plants (genetics), Plants (metabolism), Protein Domains (MeSH).
- MESH :
- chemical , chemistry : Mucoproteins, Plant Proteins.
- chemical , genetics : Mucoproteins, Plant Proteins.
- genetics : Plants.
- metabolism : Plants.
- Amino Acid Sequence, Evolution, Molecular, Gene Duplication, Genome Size, Genome, Plant, Phylogeny, Protein Domains.
Abstract
The fasciclin-like arabinogalactan proteins (FLAs) play important roles in plant development and adaptation to the environment. FLAs contain both fasciclin domains and arabinogalactan protein (AGP) regions, which have been identified in several plants. The evolutionary history of this gene family in plants is still undiscovered. In this study, we identified the FLA gene family in 13 plant species covering major lineages of plants using bioinformatics methods. A total of 246 FLA genes are identified with gene copy numbers ranging from one (Chondrus crispus) to 49 (Populus trichocarpa). These FLAs are classified into seven groups, mainly based on the phylogenetic analysis of plant FLAs. All FLAs in land plants contain one or two fasciclin domains, while in algae, several FLAs contain four or six fasciclin domains. It has been proposed that there was a divergence event, represented by the reduced number of fasciclin domains from algae to land plants in evolutionary history. Furthermore, introns in FLA genes are lost during plant evolution, especially from green algae to land plants. Moreover, it is found that gene duplication events, including segmental and tandem duplications are essential for the expansion of FLA gene families. The duplicated gene pairs in FLA gene family mainly evolve under purifying selection. Our findings give insight into the origin and expansion of the FLA gene family and help us understand their functions during the process of evolution.
DOI: 10.3390/ijms20081945
PubMed: 31010036
PubMed Central: PMC6514703
Affiliations:
Links toward previous steps (curation, corpus...)
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mahaoli@nwsuaf.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi</wicri:regionArea><wicri:noRegion>Shaanxi</wicri:noRegion></affiliation></author></analytic><series><title level="j">International journal of molecular sciences</title><idno type="eISSN">1422-0067</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Genome Size (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Mucoproteins (chemistry)</term><term>Mucoproteins (genetics)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (chemistry)</term><term>Plant Proteins (genetics)</term><term>Plants (genetics)</term><term>Plants 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moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The fasciclin-like arabinogalactan proteins (FLAs) play important roles in plant development and adaptation to the environment. FLAs contain both fasciclin domains and arabinogalactan protein (AGP) regions, which have been identified in several plants. The evolutionary history of this gene family in plants is still undiscovered. In this study, we identified the <i>FLA</i> gene family in 13 plant species covering major lineages of plants using bioinformatics methods. A total of 246 <i>FLA</i> genes are identified with gene copy numbers ranging from one (<i>Chondrus crispus</i>) to 49 (<i>Populus trichocarpa</i>). These FLAs are classified into seven groups, mainly based on the phylogenetic analysis of plant FLAs. All FLAs in land plants contain one or two fasciclin domains, while in algae, several FLAs contain four or six fasciclin domains. It has been proposed that there was a divergence event, represented by the reduced number of fasciclin domains from algae to land plants in evolutionary history. Furthermore, introns in <i>FLA</i> genes are lost during plant evolution, especially from green algae to land plants. Moreover, it is found that gene duplication events, including segmental and tandem duplications are essential for the expansion of <i>FLA</i> gene families. The duplicated gene pairs in <i>FLA</i> gene family mainly evolve under purifying selection. Our findings give insight into the origin and expansion of the <i>FLA</i> gene family and help us understand their functions during the process of evolution.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31010036</PMID><DateCompleted><Year>2019</Year><Month>08</Month><Day>12</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1422-0067</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>8</Issue><PubDate><Year>2019</Year><Month>Apr</Month><Day>20</Day></PubDate></JournalIssue><Title>International journal of molecular sciences</Title><ISOAbbreviation>Int J Mol Sci</ISOAbbreviation></Journal><ArticleTitle>Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E1945</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/ijms20081945</ELocationID><Abstract><AbstractText>The fasciclin-like arabinogalactan proteins (FLAs) play important roles in plant development and adaptation to the environment. FLAs contain both fasciclin domains and arabinogalactan protein (AGP) regions, which have been identified in several plants. The evolutionary history of this gene family in plants is still undiscovered. In this study, we identified the <i>FLA</i> gene family in 13 plant species covering major lineages of plants using bioinformatics methods. A total of 246 <i>FLA</i> genes are identified with gene copy numbers ranging from one (<i>Chondrus crispus</i>) to 49 (<i>Populus trichocarpa</i>). These FLAs are classified into seven groups, mainly based on the phylogenetic analysis of plant FLAs. All FLAs in land plants contain one or two fasciclin domains, while in algae, several FLAs contain four or six fasciclin domains. It has been proposed that there was a divergence event, represented by the reduced number of fasciclin domains from algae to land plants in evolutionary history. Furthermore, introns in <i>FLA</i> genes are lost during plant evolution, especially from green algae to land plants. Moreover, it is found that gene duplication events, including segmental and tandem duplications are essential for the expansion of <i>FLA</i> gene families. The duplicated gene pairs in <i>FLA</i> gene family mainly evolve under purifying selection. Our findings give insight into the origin and expansion of the <i>FLA</i> gene family and help us understand their functions during the process of evolution.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>He</LastName><ForeName>Jiadai</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China. 2015014922@nwsuaf.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Hua</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China. zhaohua362@nwsuaf.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>Zhilu</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>College of Landscape Architecture and Arts, Northwest A&F University, Xianyang 712100, Shaanxi, China. czl980525@163.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ke</LastName><ForeName>Yuwei</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Northwest A&F University, Xianyang 712100, Shaanxi, China. keyuwei98@163.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Jiaxi</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China. 2015014872@nwsuaf.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Haoli</ForeName><Initials>H</Initials><Identifier Source="ORCID">0000-0003-4689-1489</Identifier><AffiliationInfo><Affiliation>College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China. mahaoli@nwsuaf.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>31500212</GrantID><Agency>National Natural Science Foundation of China</Agency><Country></Country></Grant><Grant><GrantID>2015JQ3090</GrantID><Agency>Natural Science Foundation of Shaanxi Province</Agency><Country></Country></Grant><Grant><GrantID>No. 1201610712119</GrantID><Agency>Undergraduate Innovation Foundation of Northwest A&F University</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>04</Month><Day>20</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Int J Mol Sci</MedlineTA><NlmUniqueID>101092791</NlmUniqueID><ISSNLinking>1422-0067</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009088">Mucoproteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C006619">arabinogalactan proteins</NameOfSubstance></Chemical></ChemicalList><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020440" MajorTopicYN="N">Gene Duplication</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059646" MajorTopicYN="N">Genome Size</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009088" MajorTopicYN="N">Mucoproteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000072417" MajorTopicYN="N">Protein Domains</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">FLA</Keyword><Keyword MajorTopicYN="N">evolution</Keyword><Keyword MajorTopicYN="N">fasciclin-like AGP</Keyword><Keyword MajorTopicYN="N">phylogeny</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>02</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>04</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>04</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>4</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>4</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>8</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31010036</ArticleId><ArticleId IdType="pii">ijms20081945</ArticleId><ArticleId 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