A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum

• DOI: 10.1038/s42003-021-02704-y
• Publication Date: 2021-10-07T10:25:59Z
• Authors: Michiharu Nakano; Hideki Hirakawa; Eigo Fukai; Atsushi Toyoda; Rei Kajitani; Yohei Minakuchi; Takehiko Itoh; Yohei Higuchi; Toshiaki Kozuka; Hidemasa Bono; Kenta Shirasawa; Ippei Shiraiwa; Katsuhiko Sumitomo; Tamotsu Hisamatsu; Michio Shibata; Sachiko Isobe; Kenji Taniguchi; Makoto Kusaba
• Keywords: Polyploidy; 0303 health sciences; 03 medical and health sciences; QH301-705.5; Chrysanthemum; Biology (General); Article; Chromosomes, Plant; Genome, Plant

AbstractChrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspersed repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to arelatively large genome size. Furthermore, we identified a retrotransposon family, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.