Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)
Identifieur interne : 001155 ( Pmc/Curation ); précédent : 001154; suivant : 001156Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)
Auteurs : Yong Xiao [République populaire de Chine] ; Wei Xia [République populaire de Chine] ; Yaodong Yang [République populaire de Chine] ; Annaliese S. Mason [Australie] ; Xintao Lei [République populaire de Chine] ; Zilong Ma [République populaire de Chine]Source :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (
Url:
DOI: 10.1371/journal.pone.0071435
PubMed: 23951162
PubMed Central: 3738527
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :001156
Links to Exploration step
PMC:3738527Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (<italic>Phoenix dactylifera</italic>)</title><author><name sortKey="Xiao, Yong" sort="Xiao, Yong" uniqKey="Xiao Y" first="Yong" last="Xiao">Yong Xiao</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan</wicri:regionArea></affiliation></author><author><name sortKey="Xia, Wei" sort="Xia, Wei" uniqKey="Xia W" first="Wei" last="Xia">Wei Xia</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan</wicri:regionArea></affiliation></author><author><name sortKey="Yang, Yaodong" sort="Yang, Yaodong" uniqKey="Yang Y" first="Yaodong" last="Yang">Yaodong Yang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan</wicri:regionArea></affiliation></author><author><name sortKey="Mason, Annaliese S" sort="Mason, Annaliese S" uniqKey="Mason A" first="Annaliese S." last="Mason">Annaliese S. Mason</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane</wicri:regionArea></affiliation></author><author><name sortKey="Lei, Xintao" sort="Lei, Xintao" uniqKey="Lei X" first="Xintao" last="Lei">Xintao Lei</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan</wicri:regionArea></affiliation></author><author><name sortKey="Ma, Zilong" sort="Ma, Zilong" uniqKey="Ma Z" first="Zilong" last="Ma">Zilong Ma</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23951162</idno><idno type="pmc">3738527</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738527</idno><idno type="RBID">PMC:3738527</idno><idno type="doi">10.1371/journal.pone.0071435</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">001156</idno><idno type="wicri:Area/Pmc/Curation">001155</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (<italic>Phoenix dactylifera</italic>)</title><author><name sortKey="Xiao, Yong" sort="Xiao, Yong" uniqKey="Xiao Y" first="Yong" last="Xiao">Yong Xiao</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan</wicri:regionArea></affiliation></author><author><name sortKey="Xia, Wei" sort="Xia, Wei" uniqKey="Xia W" first="Wei" last="Xia">Wei Xia</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan</wicri:regionArea></affiliation></author><author><name sortKey="Yang, Yaodong" sort="Yang, Yaodong" uniqKey="Yang Y" first="Yaodong" last="Yang">Yaodong Yang</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan</wicri:regionArea></affiliation></author><author><name sortKey="Mason, Annaliese S" sort="Mason, Annaliese S" uniqKey="Mason A" first="Annaliese S." last="Mason">Annaliese S. Mason</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane</wicri:regionArea></affiliation></author><author><name sortKey="Lei, Xintao" sort="Lei, Xintao" uniqKey="Lei X" first="Xintao" last="Lei">Xintao Lei</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan</wicri:regionArea></affiliation></author><author><name sortKey="Ma, Zilong" sort="Ma, Zilong" uniqKey="Ma Z" first="Zilong" last="Ma">Zilong Ma</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan, China</addr-line></nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (<italic>Phoenix dactylifera</italic>). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in <italic>Arabidopsis</italic>, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Carthew, Rw" uniqKey="Carthew R">RW Carthew</name></author><author><name sortKey="Sontheimer, Ej" uniqKey="Sontheimer E">EJ Sontheimer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Voinnet, O" uniqKey="Voinnet O">O Voinnet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shabalina, Sa" uniqKey="Shabalina S">SA Shabalina</name></author><author><name sortKey="Koonin, Ev" uniqKey="Koonin E">EV Koonin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fujii, H" uniqKey="Fujii H">H Fujii</name></author><author><name sortKey="Chiou, Tj" uniqKey="Chiou T">TJ Chiou</name></author><author><name sortKey="Lin, Si" uniqKey="Lin S">SI Lin</name></author><author><name sortKey="Aung, K" uniqKey="Aung K">K Aung</name></author><author><name sortKey="Zhu, Jk" uniqKey="Zhu J">JK Zhu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Garcia, D" uniqKey="Garcia D">D Garcia</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Palatnik, Jf" uniqKey="Palatnik J">JF Palatnik</name></author><author><name sortKey="Allen, E" uniqKey="Allen E">E Allen</name></author><author><name sortKey="Wu, X" uniqKey="Wu X">X Wu</name></author><author><name sortKey="Schommer, C" uniqKey="Schommer C">C Schommer</name></author><author><name sortKey="Schwab, R" uniqKey="Schwab R">R Schwab</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mallory, Ac" uniqKey="Mallory A">AC Mallory</name></author><author><name sortKey="Vaucheret, H" uniqKey="Vaucheret H">H Vaucheret</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zeng, C" uniqKey="Zeng C">C Zeng</name></author><author><name sortKey="Wang, W" uniqKey="Wang W">W Wang</name></author><author><name sortKey="Zheng, Y" uniqKey="Zheng Y">Y Zheng</name></author><author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name></author><author><name sortKey="Bo, W" uniqKey="Bo W">W Bo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sunkar, R" uniqKey="Sunkar R">R Sunkar</name></author><author><name sortKey="Jagadeeswaran, G" uniqKey="Jagadeeswaran G">G Jagadeeswaran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cuperus, Jt" uniqKey="Cuperus J">JT Cuperus</name></author><author><name sortKey="Fahlgren, N" uniqKey="Fahlgren N">N Fahlgren</name></author><author><name sortKey="Carrington, Jc" uniqKey="Carrington J">JC Carrington</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Al Dous, Ek" uniqKey="Al Dous E">EK Al-Dous</name></author><author><name sortKey="George, B" uniqKey="George B">B George</name></author><author><name sortKey="Al Mahmoud, Me" uniqKey="Al Mahmoud M">ME Al-Mahmoud</name></author><author><name sortKey="Al Jaber, My" uniqKey="Al Jaber M">MY Al-Jaber</name></author><author><name sortKey="Wang, H" uniqKey="Wang H">H Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nozawa, M" uniqKey="Nozawa M">M Nozawa</name></author><author><name sortKey="Miura, S" uniqKey="Miura S">S Miura</name></author><author><name sortKey="Nei, M" uniqKey="Nei M">M Nei</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sun, J" uniqKey="Sun J">J Sun</name></author><author><name sortKey="Zhou, M" uniqKey="Zhou M">M Zhou</name></author><author><name sortKey="Mao, Z" uniqKey="Mao Z">Z Mao</name></author><author><name sortKey="Li, C" uniqKey="Li C">C Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kozomara, A" uniqKey="Kozomara A">A Kozomara</name></author><author><name sortKey="Griffiths Jones, S" uniqKey="Griffiths Jones S">S Griffiths-Jones</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hofacker, Il" uniqKey="Hofacker I">IL Hofacker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rhoades, Mw" uniqKey="Rhoades M">MW Rhoades</name></author><author><name sortKey="Reinhart, Bj" uniqKey="Reinhart B">BJ Reinhart</name></author><author><name sortKey="Lim, Lp" uniqKey="Lim L">LP Lim</name></author><author><name sortKey="Burge, Cb" uniqKey="Burge C">CB Burge</name></author><author><name sortKey="Bartel, B" uniqKey="Bartel B">B Bartel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meyers, Bc" uniqKey="Meyers B">BC Meyers</name></author><author><name sortKey="Axtell, Mj" uniqKey="Axtell M">MJ Axtell</name></author><author><name sortKey="Bartel, B" uniqKey="Bartel B">B Bartel</name></author><author><name sortKey="Bartel, Dp" uniqKey="Bartel D">DP Bartel</name></author><author><name sortKey="Baulcombe, D" uniqKey="Baulcombe D">D Baulcombe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cs S, M" uniqKey="Cs S M">M Csűös</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meunier, J" uniqKey="Meunier J">J Meunier</name></author><author><name sortKey="Lemoine, F" uniqKey="Lemoine F">F Lemoine</name></author><author><name sortKey="Soumillon, M" uniqKey="Soumillon M">M Soumillon</name></author><author><name sortKey="Liechti, A" uniqKey="Liechti A">A Liechti</name></author><author><name sortKey="Weier, M" uniqKey="Weier M">M Weier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bourgis, F" uniqKey="Bourgis F">F Bourgis</name></author><author><name sortKey="Kilaru, A" uniqKey="Kilaru A">A Kilaru</name></author><author><name sortKey="Cao, X" uniqKey="Cao X">X Cao</name></author><author><name sortKey="Ngando Ebongue, G F" uniqKey="Ngando Ebongue G">G-F Ngando-Ebongue</name></author><author><name sortKey="Drira, N" uniqKey="Drira N">N Drira</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Allen, E" uniqKey="Allen E">E Allen</name></author><author><name sortKey="Xie, Z" uniqKey="Xie Z">Z Xie</name></author><author><name sortKey="Gustafson, Am" uniqKey="Gustafson A">AM Gustafson</name></author><author><name sortKey="Carrington, Jc" uniqKey="Carrington J">JC Carrington</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fahlgren, N" uniqKey="Fahlgren N">N Fahlgren</name></author><author><name sortKey="Howell, Md" uniqKey="Howell M">MD Howell</name></author><author><name sortKey="Kasschau, Kd" uniqKey="Kasschau K">KD Kasschau</name></author><author><name sortKey="Chapman, Ej" uniqKey="Chapman E">EJ Chapman</name></author><author><name sortKey="Sullivan, Cm" uniqKey="Sullivan C">CM Sullivan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kozik, A" uniqKey="Kozik A">A Kozik</name></author><author><name sortKey="Kochetkova, E" uniqKey="Kochetkova E">E Kochetkova</name></author><author><name sortKey="Michelmore, R" uniqKey="Michelmore R">R Michelmore</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schmutz, J" uniqKey="Schmutz J">J Schmutz</name></author><author><name sortKey="Cannon, Sb" uniqKey="Cannon S">SB Cannon</name></author><author><name sortKey="Schlueter, J" uniqKey="Schlueter J">J Schlueter</name></author><author><name sortKey="Ma, J" uniqKey="Ma J">J Ma</name></author><author><name sortKey="Mitros, T" uniqKey="Mitros T">T Mitros</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, A" uniqKey="Li A">A Li</name></author><author><name sortKey="Mao, L" uniqKey="Mao L">L Mao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bonnet, E" uniqKey="Bonnet E">E Bonnet</name></author><author><name sortKey="Wuyts, J" uniqKey="Wuyts J">J Wuyts</name></author><author><name sortKey="Rouze, P" uniqKey="Rouze P">P Rouzé</name></author><author><name sortKey="Van De Peer, Y" uniqKey="Van De Peer Y">Y Van de Peer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Maher, C" uniqKey="Maher C">C Maher</name></author><author><name sortKey="Stein, L" uniqKey="Stein L">L Stein</name></author><author><name sortKey="Ware, D" uniqKey="Ware D">D Ware</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Blanc, G" uniqKey="Blanc G">G Blanc</name></author><author><name sortKey="Hokamp, K" uniqKey="Hokamp K">K Hokamp</name></author><author><name sortKey="Wolfe, Kh" uniqKey="Wolfe K">KH Wolfe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jaillon, O" uniqKey="Jaillon O">O Jaillon</name></author><author><name sortKey="Aury, Jm" uniqKey="Aury J">JM Aury</name></author><author><name sortKey="Noel, B" uniqKey="Noel B">B Noel</name></author><author><name sortKey="Policriti, A" uniqKey="Policriti A">A Policriti</name></author><author><name sortKey="Clepet, C" uniqKey="Clepet C">C Clepet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Velasco, R" uniqKey="Velasco R">R Velasco</name></author><author><name sortKey="Zharkikh, A" uniqKey="Zharkikh A">A Zharkikh</name></author><author><name sortKey="Affourtit, J" uniqKey="Affourtit J">J Affourtit</name></author><author><name sortKey="Dhingra, A" uniqKey="Dhingra A">A Dhingra</name></author><author><name sortKey="Cestaro, A" uniqKey="Cestaro A">A Cestaro</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tuskan, Ga" uniqKey="Tuskan G">GA Tuskan</name></author><author><name sortKey="Difazio, S" uniqKey="Difazio S">S Difazio</name></author><author><name sortKey="Jansson, S" uniqKey="Jansson S">S Jansson</name></author><author><name sortKey="Bohlmann, J" uniqKey="Bohlmann J">J Bohlmann</name></author><author><name sortKey="Grigoriev, I" uniqKey="Grigoriev I">I Grigoriev</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name></author><author><name sortKey="Jiang, Wk" uniqKey="Jiang W">WK Jiang</name></author><author><name sortKey="Gao, Lz" uniqKey="Gao L">LZ Gao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Turner, M" uniqKey="Turner M">M Turner</name></author><author><name sortKey="Yu, O" uniqKey="Yu O">O Yu</name></author><author><name sortKey="Subramanian, S" uniqKey="Subramanian S">S Subramanian</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jones Rhoades, Mw" uniqKey="Jones Rhoades M">MW Jones-Rhoades</name></author><author><name sortKey="Bartel, Dp" uniqKey="Bartel D">DP Bartel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guddeti, S" uniqKey="Guddeti S">S Guddeti</name></author><author><name sortKey="Zhang, Dc" uniqKey="Zhang D">DC Zhang</name></author><author><name sortKey="Li, Al" uniqKey="Li A">AL Li</name></author><author><name sortKey="Leseberg, Ch" uniqKey="Leseberg C">CH Leseberg</name></author><author><name sortKey="Kang, H" uniqKey="Kang H">H Kang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, B" uniqKey="Zhang B">B Zhang</name></author><author><name sortKey="Pan, X" uniqKey="Pan X">X Pan</name></author><author><name sortKey="Cannon, Ch" uniqKey="Cannon C">CH Cannon</name></author><author><name sortKey="Cobb, Gp" uniqKey="Cobb G">GP Cobb</name></author><author><name sortKey="Anderson, Ta" uniqKey="Anderson T">TA Anderson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fahlgren, N" uniqKey="Fahlgren N">N Fahlgren</name></author><author><name sortKey="Jogdeo, S" uniqKey="Jogdeo S">S Jogdeo</name></author><author><name sortKey="Kasschau, Kd" uniqKey="Kasschau K">KD Kasschau</name></author><author><name sortKey="Sullivan, Cm" uniqKey="Sullivan C">CM Sullivan</name></author><author><name sortKey="Chapman, Ej" uniqKey="Chapman E">EJ Chapman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ellis, Cm" uniqKey="Ellis C">CM Ellis</name></author><author><name sortKey="Nagpal, P" uniqKey="Nagpal P">P Nagpal</name></author><author><name sortKey="Young, Jc" uniqKey="Young J">JC Young</name></author><author><name sortKey="Hagen, G" uniqKey="Hagen G">G Hagen</name></author><author><name sortKey="Guilfoyle, Tj" uniqKey="Guilfoyle T">TJ Guilfoyle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Guilfoyle, Tj" uniqKey="Guilfoyle T">TJ Guilfoyle</name></author><author><name sortKey="Hagen, G" uniqKey="Hagen G">G Hagen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Varaud, E" uniqKey="Varaud E">E Varaud</name></author><author><name sortKey="Brioudes, F" uniqKey="Brioudes F">F Brioudes</name></author><author><name sortKey="Szecsi, J" uniqKey="Szecsi J">J Szecsi</name></author><author><name sortKey="Leroux, J" uniqKey="Leroux J">J Leroux</name></author><author><name sortKey="Brown, S" uniqKey="Brown S">S Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Djerbi, S" uniqKey="Djerbi S">S Djerbi</name></author><author><name sortKey="Lindskog, M" uniqKey="Lindskog M">M Lindskog</name></author><author><name sortKey="Arvestad, L" uniqKey="Arvestad L">L Arvestad</name></author><author><name sortKey="Sterky, F" uniqKey="Sterky F">F Sterky</name></author><author><name sortKey="Teeri, Tt" uniqKey="Teeri T">TT Teeri</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23951162</article-id><article-id pub-id-type="pmc">3738527</article-id><article-id pub-id-type="publisher-id">PONE-D-13-02142</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0071435</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Genomics</subject><subj-group><subject>Genome Analysis Tools</subject><subject>Genome Databases</subject></subj-group></subj-group><subj-group><subject>Sequence Analysis</subject></subj-group></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Gene Expression</subject></subj-group></subj-group><subj-group><subject>Genomics</subject><subj-group><subject>Genome Databases</subject><subj-group><subject>Sequence Databases</subject></subj-group></subj-group><subj-group><subject>Genome Evolution</subject><subject>Genome Sequencing</subject></subj-group></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Computer Science</subject><subj-group><subject>Algorithms</subject></subj-group><subj-group><subject>Information Technology</subject><subj-group><subject>Databases</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (<italic>Phoenix dactylifera</italic>)</article-title><alt-title alt-title-type="running-head">Conserved miRNA in Date Palm (<italic>Phoenix dactylifera</italic>)</alt-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Xiao</surname><given-names>Yong</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author" equal-contrib="yes"><name><surname>Xia</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Yaodong</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mason</surname><given-names>Annaliese S.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lei</surname><given-names>Xintao</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ma</surname><given-names>Zilong</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China</addr-line></aff><aff id="aff2"><label>2</label><addr-line>School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane, Australia</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan, China</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Robinson-Rechavi</surname><given-names>Marc</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>University of Lausanne, Switzerland</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>ydyang@tocri.com</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: YX WX YY. Performed the experiments: YX WX. Analyzed the data: YX WX. Contributed reagents/materials/analysis tools: YY XL ZM. Wrote the paper: YX WX ASM.</p></fn></author-notes><pub-date pub-type="collection"><year>2013</year></pub-date><pub-date pub-type="epub"><day>8</day><month>8</month><year>2013</year></pub-date><volume>8</volume><issue>8</issue><elocation-id>e71435</elocation-id><history><date date-type="received"><day>10</day><month>1</month><year>2013</year></date><date date-type="accepted"><day>1</day><month>7</month><year>2013</year></date></history><permissions><copyright-year>2013</copyright-year><copyright-holder>Xiao et al</copyright-holder><license><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><p>MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (<italic>Phoenix dactylifera</italic>). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in <italic>Arabidopsis</italic>, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.</p></abstract><funding-group><funding-statement>This work was supported by grants from the National Natural Science Foundation of China (No. 31101179), the Project for High-Level Returned Scholar of Ministry of Human Resources and Social Security of P.R. China (2011), the National Nonprofit Institute Research Grant of CATAS- ITBB120506, and Australian Research Council Early Career Researcher Award (DE120100668). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="10"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/OrangerV1/Data/Pmc/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001155 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd -nk 001155 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Bois
|area= OrangerV1
|flux= Pmc
|étape= Curation
|type= RBID
|clé= PMC:3738527
|texte= Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:23951162" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \
| NlmPubMed2Wicri -a OrangerV1
| This area was generated with Dilib version V0.6.25. |  |