Abstract
BackgroundCymbidium 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.ResultsIn 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.ConclusionRNA-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.
Highlights
Cymbidium sinense belongs to the Orchidaceae, which is one of the most abundant angiosperm families
Illumina sequencing and sequence assembly To obtain an overview of the C. sinense transcriptome, a cDNA library was generated from an equal mixture of RNA isolated from all organs, and pair end sequenced using the Illumina HiseqTM2000 platform
Annotation of predicted proteins After searching the reference sequences using BLASTX against nr, SwissPort, COG and Kyoto Encyclopedia of Genes and Genomes (KEGG), we found a total of 41687 (49.88% of all unigenes) unigenes providing a significant BLAST result (Table 2)
Summary
Cymbidium sinense belongs to the Orchidaceae, which is one of the most abundant angiosperm families. Cymbidium sinense is a perennial terrestrial species native to China and has more than a thousand years of cultural history. It holds a strong position in traditional flower markets in China, Japan, Korea, and Southeast Asia. It is of great horticultural value as an ornamental plant because of its elegance, its upright leaves, and beautiful and fragrant flowers. Flowering regulation technology for C. sinense is currently scarce on the market, which seriously hinders the development of the orchid industry and reduces the economic value of C. sinense
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