Evolution and Functional Divergence of the Fructokinase Gene Family in Populus.
Identifieur interne : 000415 ( Main/Exploration ); précédent : 000414; suivant : 000416Evolution and Functional Divergence of the Fructokinase Gene Family in Populus.
Auteurs : Weijie Xu [République populaire de Chine] ; Yiyang Zhao [République populaire de Chine] ; Sisi Chen [République populaire de Chine] ; Jianbo Xie [République populaire de Chine] ; Deqiang Zhang [République populaire de Chine]Source :
- Frontiers in plant science [ 1664-462X ] ; 2020.
Abstract
New kinase has emerged throughout evolution, but how new kinase evolve while maintaining their functions and acquiring new functions remains unclear. Fructokinase (FRK), the gateway kinase to fructose metabolism, plays essential roles in plant development, and stress tolerance. Here, we explored the evolution of FRK gene family in 20 plant species (from green algae to angiosperms) and their functional roles in Populus. We identified 125 putative FRK genes in the 20 plant species with an average of 6 members per species. Phylogenetic analysis separated these 125 genes into 8 clades including 3 conserved clades and 5 specific clades, the 5 of which only exist in green algae or angiosperms. Evolutionary analysis revealed that FRK genes in ancient land plants have the largest number of functional domains with the longest amino acid sequences, and the length of FRK genes became shorter during the transition to vascular plants. This was accompanied by loss, acquisition, and diversification of functional domains. In Populus, segmental duplication appears to be the main mechanism for the expansion of FRK genes. Specially, most FRK genes duplicated in salicoids are regulated by Populus-specific microRNAs. Furthermore, compared with common FRKs, Populus-specific FRKs have showed higher expression specificity and are associated with fewer growth and wood property traits, which suggests that these FRKs may have undergone functional divergence. Our study explores the specific roles of FRKs in the Populus genome and provides new insights for functional investigation of this gene family.
DOI: 10.3389/fpls.2020.00484
PubMed: 32499793
PubMed Central: PMC7243158
Affiliations:
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type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhao, Yiyang" sort="Zhao, Yiyang" uniqKey="Zhao Y" first="Yiyang" last="Zhao">Yiyang Zhao</name><affiliation wicri:level="3"><nlm:affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de 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and Technology, Beijing Forestry University, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name><affiliation wicri:level="3"><nlm:affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">New kinase has emerged throughout evolution, but how new kinase evolve while maintaining their functions and acquiring new functions remains unclear. Fructokinase (FRK), the gateway kinase to fructose metabolism, plays essential roles in plant development, and stress tolerance. Here, we explored the evolution of <i>FRK</i> gene family in 20 plant species (from green algae to angiosperms) and their functional roles in <i>Populus</i>. We identified 125 putative <i>FRK</i> genes in the 20 plant species with an average of 6 members per species. Phylogenetic analysis separated these 125 genes into 8 clades including 3 conserved clades and 5 specific clades, the 5 of which only exist in green algae or angiosperms. Evolutionary analysis revealed that <i>FRK</i> genes in ancient land plants have the largest number of functional domains with the longest amino acid sequences, and the length of <i>FRK</i> genes became shorter during the transition to vascular plants. This was accompanied by loss, acquisition, and diversification of functional domains. In <i>Populus</i>, segmental duplication appears to be the main mechanism for the expansion of <i>FRK</i> genes. Specially, most <i>FRK</i> genes duplicated in salicoids are regulated by <i>Populus</i>-specific microRNAs. Furthermore, compared with common <i>FRKs, Populus</i>-specific <i>FRK</i>s have showed higher expression specificity and are associated with fewer growth and wood property traits, which suggests that these <i>FRKs</i> may have undergone functional divergence. Our study explores the specific roles of <i>FRKs</i> in the <i>Populus</i> genome and provides new insights for functional investigation of this gene family.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32499793</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>11</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Evolution and Functional Divergence of the <i>Fructokinase</i> Gene Family in <i>Populus</i>.</ArticleTitle><Pagination><MedlinePgn>484</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2020.00484</ELocationID><Abstract><AbstractText>New kinase has emerged throughout evolution, but how new kinase evolve while maintaining their functions and acquiring new functions remains unclear. Fructokinase (FRK), the gateway kinase to fructose metabolism, plays essential roles in plant development, and stress tolerance. Here, we explored the evolution of <i>FRK</i> gene family in 20 plant species (from green algae to angiosperms) and their functional roles in <i>Populus</i>. We identified 125 putative <i>FRK</i> genes in the 20 plant species with an average of 6 members per species. Phylogenetic analysis separated these 125 genes into 8 clades including 3 conserved clades and 5 specific clades, the 5 of which only exist in green algae or angiosperms. Evolutionary analysis revealed that <i>FRK</i> genes in ancient land plants have the largest number of functional domains with the longest amino acid sequences, and the length of <i>FRK</i> genes became shorter during the transition to vascular plants. This was accompanied by loss, acquisition, and diversification of functional domains. In <i>Populus</i>, segmental duplication appears to be the main mechanism for the expansion of <i>FRK</i> genes. Specially, most <i>FRK</i> genes duplicated in salicoids are regulated by <i>Populus</i>-specific microRNAs. Furthermore, compared with common <i>FRKs, Populus</i>-specific <i>FRK</i>s have showed higher expression specificity and are associated with fewer growth and wood property traits, which suggests that these <i>FRKs</i> may have undergone functional divergence. Our study explores the specific roles of <i>FRKs</i> in the <i>Populus</i> genome and provides new insights for functional investigation of this gene family.</AbstractText><CopyrightInformation>Copyright © 2020 Xu, Zhao, Chen, Xie and Zhang.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Weijie</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Yiyang</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Sisi</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xie</LastName><ForeName>Jianbo</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Deqiang</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Ministry of Education, Beijing, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>05</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">FRK gene family</Keyword><Keyword MajorTopicYN="N">Populus tomentosa</Keyword><Keyword MajorTopicYN="N">adaptation</Keyword><Keyword MajorTopicYN="N">functional novelty</Keyword><Keyword MajorTopicYN="N">lineage-specific gene</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>10</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>03</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>6</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>6</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>6</Month><Day>6</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32499793</ArticleId><ArticleId IdType="doi">10.3389/fpls.2020.00484</ArticleId><ArticleId 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sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name><name sortKey="Zhao, Yiyang" sort="Zhao, Yiyang" uniqKey="Zhao Y" first="Yiyang" last="Zhao">Yiyang Zhao</name><name sortKey="Zhao, Yiyang" sort="Zhao, Yiyang" uniqKey="Zhao Y" first="Yiyang" last="Zhao">Yiyang Zhao</name><name sortKey="Zhao, Yiyang" sort="Zhao, Yiyang" uniqKey="Zhao Y" first="Yiyang" last="Zhao">Yiyang Zhao</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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