Profiling microRNA expression during multi-staged date palm (Phoenix dactylifera L.) fruit development

Handle URI:
http://hdl.handle.net/10754/552308
Title:
Profiling microRNA expression during multi-staged date palm (Phoenix dactylifera L.) fruit development
Authors:
Xin, Chengqi; Liu, Wanfei; Lin, Qiang; Zhang, Xiaowei; Cui, Peng; Li, Fusen; Zhang, Guangyu; Pan, Linlin; Al-Amer, Ali; Mei, Hailiang; Al-Mssallem, Ibrahim S.; Hu, Songnian; Al-Johi, Hasan Awad; Yu, Jun
Abstract:
MicroRNAs (miRNAs) play crucial roles in multiple stages of plant development and regulate gene expression at posttranscriptional and translational levels. In this study, we first identified 238 conserved miRNAs in date palm (Phoenix dactylifera) based on a high-quality genome assembly and defined 78 fruit-development-associated (FDA) miRNAs, whose expression profiles are variable at different fruit development stages. Using experimental data, we subsequently detected 276 novel P. dactylifera-specific FDA miRNAs and predicted their targets. We also revealed that FDA miRNAs function mainly in regulating genes involved in starch/sucrose metabolisms and other carbon metabolic pathways; among them, 221 FDA miRNAs exhibit negative correlation with their corresponding targets, which suggests their direct regulatory roles on mRNA targets. Our data define a comprehensive set of conserved and novel FDA miRNAs along with their expression profiles, which provide a basis for further experimentation in assigning discrete functions of these miRNAs in P. dactylifera fruit development.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Profiling microRNA expression during multi-staged date palm (Phoenix dactylifera L.) fruit development 2015, 105 (4):242 Genomics
Journal:
Genomics
Issue Date:
29-Jan-2015
DOI:
10.1016/j.ygeno.2015.01.004
Type:
Article
ISSN:
08887543
Additional Links:
http://linkinghub.elsevier.com/retrieve/pii/S088875431500021X
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorXin, Chengqien
dc.contributor.authorLiu, Wanfeien
dc.contributor.authorLin, Qiangen
dc.contributor.authorZhang, Xiaoweien
dc.contributor.authorCui, Pengen
dc.contributor.authorLi, Fusenen
dc.contributor.authorZhang, Guangyuen
dc.contributor.authorPan, Linlinen
dc.contributor.authorAl-Amer, Alien
dc.contributor.authorMei, Hailiangen
dc.contributor.authorAl-Mssallem, Ibrahim S.en
dc.contributor.authorHu, Songnianen
dc.contributor.authorAl-Johi, Hasan Awaden
dc.contributor.authorYu, Junen
dc.date.accessioned2015-05-05T14:41:26Zen
dc.date.available2015-05-05T14:41:26Zen
dc.date.issued2015-01-29en
dc.identifier.citationProfiling microRNA expression during multi-staged date palm (Phoenix dactylifera L.) fruit development 2015, 105 (4):242 Genomicsen
dc.identifier.issn08887543en
dc.identifier.doi10.1016/j.ygeno.2015.01.004en
dc.identifier.urihttp://hdl.handle.net/10754/552308en
dc.description.abstractMicroRNAs (miRNAs) play crucial roles in multiple stages of plant development and regulate gene expression at posttranscriptional and translational levels. In this study, we first identified 238 conserved miRNAs in date palm (Phoenix dactylifera) based on a high-quality genome assembly and defined 78 fruit-development-associated (FDA) miRNAs, whose expression profiles are variable at different fruit development stages. Using experimental data, we subsequently detected 276 novel P. dactylifera-specific FDA miRNAs and predicted their targets. We also revealed that FDA miRNAs function mainly in regulating genes involved in starch/sucrose metabolisms and other carbon metabolic pathways; among them, 221 FDA miRNAs exhibit negative correlation with their corresponding targets, which suggests their direct regulatory roles on mRNA targets. Our data define a comprehensive set of conserved and novel FDA miRNAs along with their expression profiles, which provide a basis for further experimentation in assigning discrete functions of these miRNAs in P. dactylifera fruit development.en
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S088875431500021Xen
dc.rightsArchived with thanks to Genomics .http://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectPhoenix dactyliferaen
dc.subjectMiRNAen
dc.subjectFruit developmenten
dc.subjectMiRNA targeten
dc.subjectGene regulationen
dc.titleProfiling microRNA expression during multi-staged date palm (Phoenix dactylifera L.) fruit developmenten
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalGenomicsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, Chinaen
dc.contributor.institutionUniversity of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, Chinaen
dc.contributor.institutionJoint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabiaen
dc.contributor.institutionDepartment of Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Hofuf, Saudi Arabiaen
kaust.authorCui, Pengen
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