Open Access Research article

Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development

Jianxia Zhang12, Kunlin Wu1, Songjun Zeng1, Jaime A Teixeira da Silva3, Xiaolan Zhao4, Chang-En Tian5, Haoqiang Xia6 and Jun Duan1*

Author Affiliations

1 Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China

2 Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China

3 Faculty of Agriculture and Graduate School of Agriculture, Kagawa University, Miki-cho, Kagawa, 761-0795, Japan

4 Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China

5 School of Life Sciences, Guangzhou University, Guangzhou, 510006, China

6 Guangzhou Genedenovo Biotechnology Co.,Ltd, Guangzhou, 510006, China

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BMC Genomics 2013, 14:279  doi:10.1186/1471-2164-14-279

Published: 24 April 2013



Cymbidium sinense belongs to the Orchidaceae, which is one of the most abundant angiosperm families. C. sinense, a high-grade traditional potted flower, is most prevalent in China and some Southeast Asian countries. The control of flowering time is a major bottleneck in the industrialized development of C. sinense. Little is known about the mechanisms responsible for floral development in this orchid. Moreover, genome references for entire transcriptome sequences do not currently exist for C. sinense. Thus, transcriptome and expression profiling data for this species are needed as an important resource to identify genes and to better understand the biological mechanisms of floral development in C. sinense.


In this study, de novo transcriptome assembly and gene expression analysis using Illumina sequencing technology were performed. Transcriptome analysis assembles gene-related information related to vegetative and reproductive growth of C. sinense. Illumina sequencing generated 54,248,006 high quality reads that were assembled into 83,580 unigenes with an average sequence length of 612 base pairs, including 13,315 clusters and 70,265 singletons. A total of 41,687 (49.88%) unique sequences were annotated, 23,092 of which were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with metabolic and cellular processes, cell and cell parts, catalytic activity and binding. Furthermore, 120 flowering-associated unigenes, 73 MADS-box unigenes and 28 CONSTANS-LIKE (COL) unigenes were identified from our collection. In addition, three digital gene expression (DGE) libraries were constructed for the vegetative phase (VP), floral differentiation phase (FDP) and reproductive phase (RP). The specific expression of many genes in the three development phases was also identified. 32 genes among three sub-libraries with high differential expression were selected as candidates connected with flower development.


RNA-seq and DGE profiling data provided comprehensive gene expression information at the transcriptional level that could facilitate our understanding of the molecular mechanisms of floral development at three development phases of C. sinense. This data could be used as an important resource for investigating the genetics of the flowering pathway and various biological mechanisms in this orchid.

Floral development; Flowering time; Digital gene expression; Transcriptome; Cymbidium sinense