Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology

Abstract

BackgroundCarnation (Dianthus caryophyllus L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST) database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology.ResultsWe constructed a normalized cDNA library and a 3’-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380) of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO) and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs) in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway.ConclusionsWe present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

Analysis of Scents Emitted from Flowers of Interspecific Hybrids between Carnation and Fragrant Wild Dianthus Species

“…As indicated in a study on roses (Spiller et al, 2010), QTL analysis using genetic markers seems a suitable technique to clarify the factors involved in a complex phenomenon. Now we are developing genetic markers of carnation (Tanase et al, 2012;Yagi et al, 2006) and will apply them to the analysis of scent traits.…”

Recent Progress in Genomic Analysis of Ornamental Plants, with a Focus on Carnation

“…Because ESTs only reflect genes that are expressed, their corresponding analyses are effective and relatively inexpensive. Only 669 carnation ESTs were available on the NCBI website as of early June 2012 (Tanase et al, 2012). Tanase et al (2012) sequenced the transcripts from various vegetative tissues, flowers at different developmental stages, and ethylenetreated flowers from 'Francesco' by 454 sequencing.…”

“…Only 669 carnation ESTs were available on the NCBI website as of early June 2012 (Tanase et al, 2012). Tanase et al (2012) sequenced the transcripts from various vegetative tissues, flowers at different developmental stages, and ethylenetreated flowers from 'Francesco' by 454 sequencing. Clustering and assembly of the generated sequences resulted in 300,740 unigenes consisting of 37,844 contigs and 262,896 singletons.…”

“…A subset of these primer pairs was used for linkage map construction . Ohmiya et al (2013) prepared a custom oligonucleotide array based on the carnation EST database generated by Tanase et al (2012) and compared carotenogenic gene expression levels in pale-green and white petals. Because plants in the order Caryophyllales, including carnation, do not accumulate carotenoids in petals, there are no carnation cultivars with deep-yellow flowers.…”

Transcriptional regulators of flavonoid biosynthesis and their application to flower color modification in Japanese gentians

“…This approach to creating desirable flower colors will also have a significant impact on plant biotechnology and may be used in breeding programs for most flowers. Recent nextgeneration sequencing technologies have been applied to several flower species including petunia (Zenoni et al 2011), rose (Kim et al 2012), carnation (Tanase et al 2012), and orchid (Chou et al 2013), yielding data that have provided a foundation for novel research. It is noteworthy that the whole genome sequence of carnation, one of the major cut-flowers sold worldwide, has recently been reported (Yagi et al 2013); the data will be useful for the discovery of novel genes and the elucidation of the complex metabolic networks of flavonoid biosynthesis in flowers.…”