title: Whole-transcriptome analysis of differentially expressed genes in the ray florets and disc florets of Chrysanthemum morifolium.
abstract: Chrysanthemum morifolium is one of the most important global cut flower and pot plants, and has been cultivated worldwide. However, limited genomic resources are available and the molecular mechanisms involved in the two morphologically distinct floret developmental cycles in chrysanthemum remain unclear.
  
  
  
  The transcriptomes of chrysanthemum ray florets, disc florets and leaves were sequenced using Illumina paired-end sequencing technology. In total, 16.9 G reads were assembled into 93,138 unigenes with an average length of 738 bp, of which 44,364 unigenes showed similarity to known proteins in the Swissprot or NCBI non-redundant protein databases. Additionally, 26,320, 22,304 and 13,949 unigenes were assigned to 54 gene ontology (GO) categories, 25 EuKaryotic Orthologous Groups (KOG) categories, and 280 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 1863 differentially expressed genes (DEGs) (1210 up-regulated and 653 down-regulated) were identified between ray florets and disc florets, including genes encoding transcription factors and protein kinases. GO and KEGG pathway enrichment analyses were performed on the DEGs to identify differences in the biological processes and pathways between ray florets and disc florets. The important regulatory genes controlling flower development and flower organ determination, as well as important functional genes in the anthocyanin biosynthetic pathway, were identified, of which two leucoanthocyanidin dioxygenase-encoding genes showed specific expression in ray florets. Lastly, reverse transcription quantitative PCR was conducted to validate the DEGs identified in our study.
  
  
  
  Comparative transcriptome analysis revealed significant differences in patterns of gene expression and signaling pathways between ray florets and disc florets in Chrysanthemum morifolium. This study provided the first step to understanding the molecular mechanism of the differential development of ray florets and disc florets in chrysanthemum, and also provided valuable genomic resources for candidate genes applicable for the breeding of novel varieties in chrysanthemum.
authors.affiliation: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Liu
authors.affiliation: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Sun
authors.affiliation: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
authors.forename: Dongliang
authors.initials: D
authors.lastname: Du
authors.affiliation: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
authors.forename: Huitang
authors.initials: H
authors.lastname: Pan
authors.affiliation: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
authors.forename: Tangren
authors.initials: T
authors.lastname: Cheng
authors.affiliation: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Wang
authors.affiliation: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China. zqxbjfu@126.com.
authors.forename: Qixiang
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
authors.forename: Yike
authors.initials: Y
authors.lastname: Gao
mesh_terms: D031202:Chrysanthemum / Q000235:genetics / Q000254:growth & development*; D035264:Flowers / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D058977:Molecular Sequence Annotation; D000069600:Plant Breeding; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D010940:Plant Proteins / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D010940:Plant Proteins
keywords: Anthocyanin biosynthetic pathway; Chrysanthemum morifolium; Differentially expressed genes; Disc florets; Flower development; RNA-seq; Ray florets; Transcriptome