De novo whole-genome assembly of Chrysanthemum makinoi, a key wild ancestor to hexaploid Chrysanthemum

Chrysanthemum is among the top ten cut, potted and perennial garden flowers in the world. Despite this, to date, only the genomes of two wild diploid chrysanthemums have been sequenced and assembled. Here we present the most complete and contiguous chrysanthemum de novo assembly published so far, as well as a corresponding ab initio annotation. The wild diploid Chrysanthemum makinoi is thought to be one of the ancestors of the cultivated hexaploid varieties which are currently grown all around the world. Using a combination of Oxford Nanopore long reads, Pacific Biosciences long reads, Illumina short reads, Dovetail sequences and a genetic map, we assembled 3.1 Gb of its sequence into 9 pseudochromosomes, with an N50 of 330 Mb and BUSCO complete score of 92.1%. Our ab initio annotation pipeline predicted 95 074 genes and marked 80.0% of the genome as repetitive. This genome assembly of C. makinoi provides an important step forward in understanding the chrysanthemum genome, evolution and history.