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.
Highlights
Cymbidium ensifolium, is a diploid plant with an estimated haploid genome size of 4,000 Mb and 2n = 2x = 40 chromosomes [1,2]
C. ensifolium takes a bigger share of the orchid flower market than other Chinese Cymbidiums
We identified a large number of genic-SSRs and genic-SNPs, which will increase the number of molecular markers, facilitate gene mapping, and genetic diversity analysis for C. ensifolium
Summary
Researchers urgently need a collection of EST sequences for C. ensifolium to facilitate whole genome annotation, molecular marker development, and studies on C. The high cost of reagents hinders the use of Roche 454 for complex uncharacterized genomes Software such as MIRA [31], Velvet [32], Oases [33], ABySS [34], Trans-ABySS [35], SOAPdenovo6 [36], and Trinity [37] have been developed for RNA-Seq assembly using short sequence reads, and have been widely and successfully applied in various experiments [31,32,33,34,35,36,37]. We identified a large number of genic-SSRs and genic-SNPs, which will increase the number of molecular markers, facilitate gene mapping, and genetic diversity analysis for C. ensifolium
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