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Open Access Highly Accessed Research article

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

Koji Tanase1*, Chikako Nishitani2, Hideki Hirakawa3, Sachiko Isobe3, Satoshi Tabata3, Akemi Ohmiya1 and Takashi Onozaki1

Author Affiliations

1 National Institute of Floricultural Sciences, National Agriculture and Food Research Organization, Fujimoto 2-1, Tsukuba, Ibaraki, 305-8519, Japan

2 National Institute of Fruit Tree Science, National Agriculture and Food Research Organization, Fujimoto 2-1, Tsukuba, Ibaraki, 8605, Japan

3 Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan

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BMC Genomics 2012, 13:292  doi:10.1186/1471-2164-13-292

Published: 2 July 2012

Abstract

Background

Carnation (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.

Results

We 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.

Conclusions

We 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.

Keywords:
Carnation; Dianthus caryopyllus L.; Next-generation sequencing technology; SSR; Transcriptome