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
NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.
DNA Res. 2014 Jun;21(3):231-41. doi: 10.1093/dnares/dst053. Epub 2013 Dec 17.
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.
利用不同新一代多重测序平台的组合，测定了康乃馨（石竹）品种‘弗朗切斯科’的全基因组序列。非冗余序列的总长度为568,887,315碱基对，由45,088个支架组成，覆盖了通过k-mer分析估计的622兆碱基康乃馨基因组的91%。重叠群和支架的N50值分别为16,644碱基对和60,737碱基对，最长的支架为1,287,144碱基对。重叠群序列的平均GC含量为36%。在组装的基因组序列中分别鉴定出1050个、13个、92个和143个tRNA、rRNA、snoRNA和miRNA基因。对于蛋白质编码基因，推断出43266个完整和部分基因结构，不包括转座元件中的基因结构。从核心真核基因的覆盖范围推断，基因覆盖率约为98%。对已确定的康乃馨基因进行深入表征并与其他植物物种的基因进行比较，揭示了康乃馨基因组的特征。本研究结果将为康乃馨的基础研究和应用研究，特别是培育新的康乃馨品种提供宝贵资源。有关基因组序列的更多信息可在http://carnation.kazusa.or.jp上获取。
