title: Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome.
abstract: Cymbidium ensifolium is a Chinese Cymbidium with an elegant shape, beautiful appearance, and a fragrant aroma. C. ensifolium has a long history of cultivation in China and it has excellent commercial value as a potted plant and cut flower. The development of C. ensifolium genomic resources has been delayed because of its large genome size. Taking advantage of technical and cost improvement of RNA-Seq, we extracted total mRNA from flower buds and mature flowers and obtained a total of 9.52 Gb of filtered nucleotides comprising 98,819,349 filtered reads. The filtered reads were assembled into 101,423 isotigs, representing 51,696 genes. Of the 101,423 isotigs, 41,873 were putative homologs of annotated sequences in the public databases, of which 158 were associated with floral development and 119 were associated with flowering. The isotigs were categorized according to their putative functions. In total, 10,212 of the isotigs were assigned into 25 eukaryotic orthologous groups (KOGs), 41,690 into 58 gene ontology (GO) terms, and 9,830 into 126 Arabidopsis Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 9,539 isotigs into 123 rice pathways. Comparison of the isotigs with those of the two related orchid species P. equestris and C. sinense showed that 17,906 isotigs are unique to C. ensifolium. In addition, a total of 7,936 SSRs and 16,676 putative SNPs were identified. To our knowledge, this transcriptome database is the first major genomic resource for C. ensifolium and the most comprehensive transcriptomic resource for genus Cymbidium. These sequences provide valuable information for understanding the molecular mechanisms of floral development and flowering. Sequences predicted to be unique to C. ensifolium would provide more insights into C. ensifolium gene diversity. The numerous SNPs and SSRs identified in the present study will contribute to marker development for C. ensifolium.
authors.affiliation: Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People's Republic of China.
authors.forename: Xiaobai
authors.initials: X
authors.lastname: Li
authors.affiliation: Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People's Republic of China.
authors.forename: Jie
authors.initials: J
authors.lastname: Luo
authors.affiliation: Department of Gastroenterology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China.
authors.forename: Tianlian
authors.initials: T
authors.lastname: Yan
authors.affiliation: Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People's Republic of China.
authors.forename: Lin
authors.initials: L
authors.lastname: Xiang
authors.affiliation: College of Life Sciences, Hubei University, Wuhan, People's Republic of China.
authors.forename: Feng
authors.initials: F
authors.lastname: Jin
authors.affiliation: Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People's Republic of China.
authors.forename: Dehui
authors.initials: D
authors.lastname: Qin
authors.affiliation: Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People's Republic of China.
authors.forename: Chongbo
authors.initials: C
authors.lastname: Sun
authors.affiliation: Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People's Republic of China.
authors.forename: Ming
authors.initials: M
authors.lastname: Xie
mesh_terms: D035264:Flowers / Q000235:genetics*; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats / Q000235:genetics; D058977:Molecular Sequence Annotation; D029595:Orchidaceae / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers