title: Profiling microRNA expression during multi-staged date palm (Phoenix dactylifera L.) fruit development.
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.
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China.
authors: Chengqi
authors: C
authors: Xin
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
authors: Wanfei
authors: W
authors: Liu
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
authors: Qiang
authors: Q
authors: Lin
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
authors: Xiaowei
authors: X
authors: Zhang
authors: Biological and Environmental Sciences and Engineering Division, King Abdullah University of Sciences and Technology, Thuwal 23955-6900, Saudi Arabia.
authors: Peng
authors: P
authors: Cui
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
authors: Fusen
authors: F
authors: Li
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
authors: Guangyu
authors: G
authors: Zhang
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
authors: Linlin
authors: L
authors: Pan
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia.
authors: Ali
authors: A
authors: Al-Amer
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, China.
authors: Hailiang
authors: H
authors: Mei
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia; Department of Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Hofuf, Saudi Arabia. Electronic address: imssallem@gmail.com.
authors: Ibrahim S
authors: IS
authors: Al-Mssallem
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China. Electronic address: husn@big.ac.cn.
authors: Songnian
authors: S
authors: Hu
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia. Electronic address: haljohi@kacst.edu.sa.
authors: Hasan Awad
authors: HA
authors: Al-Johi
authors: Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh 11442, Saudi Arabia; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China. Electronic address: junyu@big.ac.cn.
authors: Jun
authors: J
authors: Yu
mesh_terms: D050260:Carbohydrate Metabolism / Q000235:genetics; D005638:Fruit / Q000235:genetics* / Q000254:growth & development; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D053858:Metabolic Networks and Pathways / Q000235:genetics; D035683:MicroRNAs / Q000378:metabolism*; D065749:Phoeniceae / Q000235:genetics* / Q000254:growth & development
chemical_list: D035683:MicroRNAs
keywords: Fruit development; Gene regulation; MiRNA; MiRNA target; Phoenix dactylifera