De novo transcriptome sequencing and comparative analysis to discover genes related to floral development in Cymbidium faberi Rolfe

Abstract

Cymbidium faberi is a traditional orchid flower in China that is highly appreciated for its fragrant aroma from its zygomorphic flowers. One bottleneck of the commercial production of C. faberi is the long vegetative growth phase of the orchid and the difficulty of the regulation of its flowering time. Moreover, its flower size, shape and color are often targeting traits for orchid breeders. Understanding the molecular mechanisms of floral development in C. faberi will ultimately benefit the genetic improvement of this orchid plant. The goal of this study is to identify potential genes and regulatory networks related to the floral development in C. faberi by using transcriptome sequencing, de novo assembly and computational analyses. The vegetative and flower buds of C. faberi were sampled for such comparisons. The RNA-seq yielded about 189,300 contigs that were assembled into 172,959 unigenes. Furthermore, a total of 13,484 differentially expressed unigenes (DEGs) were identified between the vegetative and flower buds. There were 7683 down-regulated and 5801 up-regulated DEGs in the flower buds compared to those in the vegetative buds, among which 3430 and 6556 DEGs were specifically enriched in the flower or vegetative buds, respectively. A total of 173 DEGs orthologous to known genes associated with the floral organ development, floral symmetry and flowering time were identified, including 12 TCP transcription factors, 34 MADS-box genes and 28 flowering time related genes. Furthermore, expression levels of ten genes potentially involved in floral development and flowering time were verified by quantitative real-time PCR. The identified DEGs will facilitate the functional genetic studies for further understanding the flower development of C. faberi.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-3089-1) contains supplementary material, which is available to authorized users.

Genome-Wide Identification and Expression Analysis of Terpene Synthase Genes in Cymbidium faberi

“…Orchids are among the largest angiosperm families in angiosperms and demonstrate a diversity of epiphytic and terrestrial growth forms ( Hsiao et al, 2011 ). Cymbidium faberi is one of the longest cultivated orchids planted in China and has high ornamental value due to its characteristic flower scent and beautiful flower shape ( Omata et al, 1990 ; Hsiao et al, 2011 ; Sun et al, 2016 ). Terpenoids play an essential role in floral scent and can attract pollinating insects and defend against environmental stresses ( Wagner and Elmadfa, 2003 ; Dudareva et al, 2006 ; Sun et al, 2016 ).…”

“…Cymbidium faberi is one of the longest cultivated orchids planted in China and has high ornamental value due to its characteristic flower scent and beautiful flower shape ( Omata et al, 1990 ; Hsiao et al, 2011 ; Sun et al, 2016 ). Terpenoids play an essential role in floral scent and can attract pollinating insects and defend against environmental stresses ( Wagner and Elmadfa, 2003 ; Dudareva et al, 2006 ; Sun et al, 2016 ). Plants have enzymes called TPSs, which encode the synthesis of monoterpene (C10), sesquiterpene (C15), or diterpenes (C20) from DMAPP, GPP, and GGPP, respectively ( Pichersky et al, 2006 ).…”

Morphological Characterization of Flower Buds Development and Related Gene Expression Profiling at Bud Break Stage in Heterodichogamous Cyclocarya paliurus (Batal.) lljinskaja

“…The process of flowering is a transition from vegetative growth to reproductive growth under the interaction and coordination of internal and external factors, forming a complex network system to regulate flower formation [13]. Currently, the comprehensive and mature studies on the flowering network of Arabidopsis thaliana include six pathways mainly.…”

Comparative transcriptomic analysis of normal and abnormal in vitro flowers in Cymbidium nanulum Y. S. Wu et S. C. Chen identifies differentially expressed genes and candidate genes involved in flower formation

“…Benzylaminopurine, a synthetic cytokinin, promotes blooming in Orchidaceae in vitro and in vivo ( Sakai and Ichihara, 2010 ; Teixeira da Silva et al., 2014 ). Evidence from transcriptome analysis also suggests that the cytokinin-responsive genes are dynamic in flower formation and development in a variety of orchids ( Sun et al., 2016 ; Yang et al., 2017 ; Shen et al., 2021 ). Among the selected key genes in our study, all A-ARR genes were upregulated, whereas most B-ARR genes were downregulated.…”