Sequence analysis of the genome of carnation (Dianthus caryophyllus L.)

Masafumi Yagi, Shunichi Kosugi, Hideki Hirakawa, Akemi Ohmiya, Koji Tanase, Taro Harada, Kyutaro Kishimoto, Masayoshi Nakayama, Kazuo Ichimura, Takashi Onozaki, Hiroyasu Yamaguchi, Nobuhiro Sasaki, Taira Miyahara, Yuzo Nishizaki, Yoshihiro Ozeki, Noriko Nakamura, Takamasa Suzuki, Yoshikazu Tanaka, Shusei Sato, Kenta Shirasawa & 7 others Sachiko Isobe, Yoshinori Miyamura, Akiko Watanabe, Shinobu Nakayama, Yoshie Kishida, Mitsuyo Kohara, Satoshi Tabata

Research output: Contribution to journalArticle

40 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)231-241
Number of pages11
JournalDNA Research
Volume21
Issue number3
DOIs
Publication statusPublished - 2014
Externally publishedYes

Fingerprint

Dianthus
Sequence Analysis
Genome
Genes
Small Nucleolar RNA
DNA Transposable Elements
Base Composition
Transfer RNA
MicroRNAs
rRNA Genes
Breeding

Keywords

  • carnation
  • Dianthus caryophyllus L.
  • gene prediction
  • genome sequencing

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Medicine(all)

Cite this

Yagi, M., Kosugi, S., Hirakawa, H., Ohmiya, A., Tanase, K., Harada, T., ... Tabata, S. (2014). Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). DNA Research, 21(3), 231-241. https://doi.org/10.1093/dnares/dst053

Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). / Yagi, Masafumi; Kosugi, Shunichi; Hirakawa, Hideki; Ohmiya, Akemi; Tanase, Koji; Harada, Taro; Kishimoto, Kyutaro; Nakayama, Masayoshi; Ichimura, Kazuo; Onozaki, Takashi; Yamaguchi, Hiroyasu; Sasaki, Nobuhiro; Miyahara, Taira; Nishizaki, Yuzo; Ozeki, Yoshihiro; Nakamura, Noriko; Suzuki, Takamasa; Tanaka, Yoshikazu; Sato, Shusei; Shirasawa, Kenta; Isobe, Sachiko; Miyamura, Yoshinori; Watanabe, Akiko; Nakayama, Shinobu; Kishida, Yoshie; Kohara, Mitsuyo; Tabata, Satoshi.

In: DNA Research, Vol. 21, No. 3, 2014, p. 231-241.

Research output: Contribution to journalArticle

Yagi, M, Kosugi, S, Hirakawa, H, Ohmiya, A, Tanase, K, Harada, T, Kishimoto, K, Nakayama, M, Ichimura, K, Onozaki, T, Yamaguchi, H, Sasaki, N, Miyahara, T, Nishizaki, Y, Ozeki, Y, Nakamura, N, Suzuki, T, Tanaka, Y, Sato, S, Shirasawa, K, Isobe, S, Miyamura, Y, Watanabe, A, Nakayama, S, Kishida, Y, Kohara, M & Tabata, S 2014, 'Sequence analysis of the genome of carnation (Dianthus caryophyllus L.)', DNA Research, vol. 21, no. 3, pp. 231-241. https://doi.org/10.1093/dnares/dst053
Yagi, Masafumi ; Kosugi, Shunichi ; Hirakawa, Hideki ; Ohmiya, Akemi ; Tanase, Koji ; Harada, Taro ; Kishimoto, Kyutaro ; Nakayama, Masayoshi ; Ichimura, Kazuo ; Onozaki, Takashi ; Yamaguchi, Hiroyasu ; Sasaki, Nobuhiro ; Miyahara, Taira ; Nishizaki, Yuzo ; Ozeki, Yoshihiro ; Nakamura, Noriko ; Suzuki, Takamasa ; Tanaka, Yoshikazu ; Sato, Shusei ; Shirasawa, Kenta ; Isobe, Sachiko ; Miyamura, Yoshinori ; Watanabe, Akiko ; Nakayama, Shinobu ; Kishida, Yoshie ; Kohara, Mitsuyo ; Tabata, Satoshi. / Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). In: DNA Research. 2014 ; Vol. 21, No. 3. pp. 231-241.
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AU - Harada, Taro

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AU - Yamaguchi, Hiroyasu

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