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About Mum GARDEN

Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n=6x=54) and large genome size. The diploid chrysanthemum C. seticuspe is often used as a model of cultivated chrysanthemum, since the two species are closely related.

To expand our knowledge of the cultivated chrysanthemum, we here performed de novo whole-genome assembly in C. seticuspe using the Illumina sequencing platform. XMRS10, a C. seticuspe accession developed by five generations of self-crossing from a self-compatible strain, AEV2, was used for genome sequencing.

The 2.72 Gb of assembled sequences (CSE_r1.0), consisting of 354,212 scaffolds, covered 89.0% of the 3.06 Gb C. seticuspe genome estimated by k-mer analysis. The N50 length of scaffolds was 44,741 bp. For protein-encoding genes, 71,057 annotated genes were deduced (CSE_r1.1_cds). Next, based on the assembled genome sequences, we performed linkage map construction, gene discovery and comparative analyses for C. seticuspe and cultivated chrysanthemum. A total of 9605 SSR markers were also developed based on the transcript sequences of C. seticuspe.


De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis

DNA Research, dsy048,

Running title: Whole-genome assembly in Chrysanthemum seticuspe

Hideki Hirakawa, Katsuhiko Sumitomo, Tamotsu Hisamatsu, Soichiro Nagano, Kenta Shirasawa, Yohei Higuchi, Makoto Kusaba, Masaji Koshioka, Yoshihiro Nakano, Masafumi Yagi, Hiroyasu Yamaguchi, Kenji Taniguchi, Michiharu Nakano and Sachiko N Isobe