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Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). 2014
Masafumi Yagi, and
Shunichi Kosugi, and
Hideki Hirakawa, and
Akemi Ohmiya, and
Koji Tanase, and
Taro Harada, and
Kyutaro Kishimoto, and
Masayoshi Nakayama, and
Kazuo Ichimura, and
Takashi Onozaki, and
Hiroyasu Yamaguchi, and
Nobuhiro Sasaki, and
Taira Miyahara, and
Yuzo Nishizaki, and
Yoshihiro Ozeki, and
Noriko Nakamura, and
Takamasa Suzuki, and
Yoshikazu Tanaka, and
Shusei Sato, and
Kenta Shirasawa, and
Sachiko Isobe, and
Yoshinori Miyamura, and
Akiko Watanabe, and
Shinobu Nakayama, and
Yoshie Kishida, and
Mitsuyo Kohara, and
Satoshi Tabata
NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
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.
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