Carnation (Dianthus caryophyllus L.) is one of the most popular cut flowers, and hundreds of cultivars are grown around the world. Dianthus is a genus of about 300 species in the Caryophyllaceae family. Several species, including Dianthus caryophyllus
D. superbus, and their hybrids are widely used as horticultural cultivars . The many flower varieties of carnation are divided into three groups (standards, sprays, and pot carnations) based on plant form, flower size, and flower shape. Standards have a single large flower per stem, whereas sprays have a larger number of smaller flowers; both types are used for cut flowers . Pot carnation is a dwarf with many small flowers that is used as a potted plant. Most carnation cultivars are diploid (2n = 2x = 30), although some species of Dianthus are tetraploid or hexaploid [3–6]. According to the Plant C-values Database (http://data.kew.org/cvalues/), the total genome size (C-value) in carnation is 613 Mb (1.23 pg/2 C), which is four times that of the model plant Arabidopsis (0.30 pg/2 C) . The genome of carnation is very small compared with those of other ornamental flowers, such as Antirrhinum majus (1,568 Mb), Chrysanthemum morifolium (9,384 Mb), Ipomoea nil (Pharbitis nil) (1,127 Mb), Lilium longiflorum (34,496 Mb), Petunia hybrida (1,642 Mb), Rosa hybrida (1,127 Mb), and Tulipa gesneriana (26,093 Mb).
Carnation cultivars are developed to be highly heterozygous so as to avoid the effects of inbreeding depression . Most commercially important cultivars are hybrids that are propagated vegetatively. Carnation cultivars have been bred for attractive characteristics such as flower color, flower size, fragrance, and flower longevity. Carnation cultivars have a wide range of colors, including red, yellow, white, green, and brown. In addition, some flowers show marginal variegation, flecks, or sectors . Recently, transgenic carnations with blue or violet flowers have been developed by the introduction of a heterologous flavonoid 3’, 5’-hydroxylase gene [10–12].
The vase life of cut flowers is one of the most important ornamental traits, because it affects consumer satisfaction and repeat purchasing. Carnation is a typical ethylene-sensitive flower [13, 14], and its flower life is normally short (about 7 days) if preservatives are not used . In the ethylene biosynthesis pathway, the conversion of S-adenosylmethionine (AdoMet) to 1-aminocyclopropane-1-carboxylate (ACC) and of ACC to ethylene are catalyzed by ACC synthase (ACS) and ACC oxidase (ACO), respectively. Transgenic carnations containing an antisense ACO gene exhibited low ethylene production and delayed petal senescence . When the Arabidopsis etr1-1 gene, capable of conferring ethylene insensitivity, was introduced into carnation, the transgenic carnation plants had reduced ethylene sensitivity caused by suppression of ACO expression, which prolonged flower life . On the other hand, by repeated selection for lines with longer vase life, Onozaki et al.  produced two carnation cultivars (named ‘Miracle Rouge’ and ‘Miracle Symphony’) with improved vase life in which expression of three ethylene biosynthesis genes (DcACS1
DcACS2, and DcACO1) was suppressed in flowers of both cultivars, which resulted in extremely low levels of ethylene production [18, 19].
Expressed sequence tag (EST) sequencing is essential for functional genomics studies: it has been used to identify novel genes from a broad range of organisms and to provide an indication of gene expression levels in specific tissues. Currently, there are more than 69 million ESTs in the database (dbEST) at NCBI. Since the development of high-throughput DNA sequencing technologies, analyses using next-generation sequencers have been performed in cereals, legumes, and fruits, and large amounts of EST data have been submitted to various DNA databases. These studies have revealed that high-throughput DNA sequencing is a cost-effective approach to analyzing the ESTs of both model plants and non-model plants. Surprisingly, in Arabidopsis, at least 60 transcripts which did not exist in previous EST collections were identified by next-generation sequencing . Furthermore, large-scale EST collection facilitates the design of microarrays and the high-throughput identification of simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNPs).
To identify the genes related to flower quality and important agronomic traits such as disease resistance, extensive gene expression profiling would be extremely valuable, but only 669 carnation ESTs were available on the NCBI website (http://www.ncbi.nlm.nih.gov/) at the early June 2012. Other genomics resources, such as markers and genomic sequences have yet to be developed for carnation. To improve the DNA sequence information available for carnation, we performed large-scale transcriptome sequencing of carnation using a next-generation sequencer (a Roche 454 GS FLX) and obtained more than 300,000 transcripts. This work will make a significant contribution toward plant physiology, biotechnology, and molecular genetics studies in carnation.