title: RNA-Seq-based transcriptome analysis of dormant flower buds of Chinese cherry (Prunus pseudocerasus).
abstract: Bud dormancy is a critical biological process allowing Chinese cherry (Prunus pseudocerasus) to survive in winter. Due to the lake of genomic information, molecular mechanisms triggering endodormancy release in flower buds have remained unclear. Hence, we used Illumina RNA-Seq technology to carry out de novo transcriptome assembly and digital gene expression profiling of flower buds. Approximately 47million clean reads were assembled into 50,604 sequences with an average length of 837bp. A total of 37,650 unigene sequences were successfully annotated. 128 pathways were annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and metabolic, biosynthesis of second metabolite and plant hormone signal transduction accounted for higher percentage in flower bud. In critical period of endodormancy release, 1644, significantly differentially expressed genes (DEGs) were identified from expression profile. DEGs related to oxidoreductase activity were especially abundant in Gene Ontology (GO) molecular function category. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that DEGs were involved in various metabolic processes, including phytohormone metabolism. Quantitative real-time PCR (qRT-PCR) analysis indicated that levels of DEGs for abscisic acid and gibberellin biosynthesis decreased while the abundance of DEGs encoding their degradation enzymes increased and GID1 was down-regulated. Concomitant with endodormancy release, MADS-box transcription factors including P. pseudocerasus dormancy-associated MADS-box (PpcDAM), Agamous-like2, and APETALA3-like genes, shown remarkably epigenetic roles. The newly generated transcriptome and gene expression profiling data provide valuable genetic information for revealing transcriptomic variation during bud dormancy in Chinese cherry. The uncovered data should be useful for future studies of bud dormancy in Prunus fruit trees lacking genomic information.
authors.affiliation: College of Agricultural and Biological Engineering, Jinhua Polytechnic, Jinhua, Zhejiang 321007, China; Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang 321004, China. Electronic address: zhouchen@zjnu.cn.
authors.forename: Youyin
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang 321004, China. Electronic address: lyq@zjnu.cn.
authors.forename: Yongqiang
authors.initials: Y
authors.lastname: Li
authors.affiliation: Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang 321004, China. Electronic address: xindedong@zjnu.cn.
authors.forename: Dedong
authors.initials: D
authors.lastname: Xin
authors.affiliation: Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang 321004, China. Electronic address: cwr@zjnu.cn.
authors.forename: Wenrong
authors.initials: W
authors.lastname: Chen
authors.affiliation: Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang 321004, China. Electronic address: shaoxu0511@126.com.
authors.forename: Xu
authors.initials: X
authors.lastname: Shao
authors.affiliation: Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang 321004, China. Electronic address: yueshizi@163.com.
authors.forename: Yue
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, Zhejiang 321004, China. Electronic address: gwd@zjnu.cn.
authors.forename: Weidong
authors.initials: W
authors.lastname: Guo
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D020451:Contig Mapping; D035264:Flowers / Q000235:genetics* / Q000502:physiology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant; D026161:MADS Domain Proteins / Q000378:metabolism; D057445:Plant Dormancy / Q000235:genetics*; D010937:Plant Growth Regulators / Q000502:physiology; D027861:Prunus / Q000235:genetics* / Q000502:physiology; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA; D013696:Temperature; D059467:Transcriptome
chemical_list: D026161:MADS Domain Proteins; D010937:Plant Growth Regulators; D018749:RNA, Plant
keywords: Bud dormancy; Chinese cherry (Prunus pseudocerasus); Flower buds; RNA-Seq; Transcriptome