title: Sequence analysis of the genome of carnation (Dianthus caryophyllus L.).
abstract: The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. 'Francesco' was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568,887,315 bp, consisting of 45,088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16,644 bp and 60,737 bp, respectively, and the longest scaffold was 1,287,144 bp. The average GC content of the contig sequences was 36%. A total of 1050, 13, 92 and 143 genes for tRNAs, rRNAs, snoRNA and miRNA, respectively, were identified in the assembled genomic sequences. For protein-encoding genes, 43 266 complete and partial gene structures excluding those in transposable elements were deduced. Gene coverage was ∼ 98%, as deduced from the coverage of the core eukaryotic genes. Intensive characterization of the assigned carnation genes and comparison with those of other plant species revealed characteristic features of the carnation genome. The results of this study will serve as a valuable resource for fundamental and applied research of carnation, especially for breeding new carnation varieties. Further information on the genomic sequences is available at http://carnation.kazusa.or.jp.
authors.affiliation: NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
authors.forename: Masafumi
authors.initials: M
authors.lastname: Yagi
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Shunichi
authors.initials: S
authors.lastname: Kosugi
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Hirakawa
authors.affiliation: NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
authors.forename: Akemi
authors.initials: A
authors.lastname: Ohmiya
authors.affiliation: NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Tanase
authors.affiliation: NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
authors.forename: Taro
authors.initials: T
authors.lastname: Harada
authors.affiliation: NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
authors.forename: Kyutaro
authors.initials: K
authors.lastname: Kishimoto
authors.affiliation: NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
authors.forename: Masayoshi
authors.initials: M
authors.lastname: Nakayama
authors.affiliation: NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Ichimura
authors.affiliation: NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Onozaki
authors.affiliation: NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
authors.forename: Hiroyasu
authors.initials: H
authors.lastname: Yamaguchi
authors.affiliation: Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Sasaki
authors.affiliation: Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
authors.forename: Taira
authors.initials: T
authors.lastname: Miyahara
authors.affiliation: Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
authors.forename: Yuzo
authors.initials: Y
authors.lastname: Nishizaki
authors.affiliation: Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Ozeki
authors.affiliation: Research Institute, Suntory Global Innovation Center, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan.
authors.forename: Noriko
authors.initials: N
authors.lastname: Nakamura
authors.affiliation: JST, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan.
authors.forename: Takamasa
authors.initials: T
authors.lastname: Suzuki
authors.affiliation: Research Institute, Suntory Global Innovation Center, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan.
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Tanaka
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Shusei
authors.initials: S
authors.lastname: Sato
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Kenta
authors.initials: K
authors.lastname: Shirasawa
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Sachiko
authors.initials: S
authors.lastname: Isobe
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Miyamura
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Akiko
authors.initials: A
authors.lastname: Watanabe
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Shinobu
authors.initials: S
authors.lastname: Nakayama
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Yoshie
authors.initials: Y
authors.lastname: Kishida
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
authors.forename: Mitsuyo
authors.initials: M
authors.lastname: Kohara
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan tabata@kazusa.or.jp.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
mesh_terms: D001483:Base Sequence; D018744:DNA, Plant / Q000235:genetics; D030541:Databases, Genetic; D029749:Dianthus / Q000235:genetics*; D017343:Genes, Plant; D008040:Genetic Linkage; D018745:Genome, Plant; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: Dianthus caryophyllus L.; carnation; gene prediction; genome sequencing