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

Abstract

Chrysanthemums 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.

Fig. 1

Morphological and color variation among chrysanthemum cultivars.

Fig. 2. Genome evolution of Chrysanthemum seticuspe.

a Phylogenetic tree of Asteraceae species. Grape and coffee plants were used as the outgroups. Arrows indicate ages of the whole-genome triplication (WGT-1) event common in Asteraceae; whole genome duplication (WGD-2) before diversification between M. micrantha and H. annuus; segmental duplications in M. micrantha (SD-3); before diversification between C. seticuspe and C. nankingense (SD-4); and in A. annua (GD-5). Mya, million years ago. b Distribution of synonymous substitutions per site (Ks). Pink and blue charts indicate plots of self-comparison and comparison with C. seticuspe, the peaks of which represent speciation time from C. seticuspe. c Distribution of the insertion time of intact long terminal repeat (LTR) retrotransposons in C. seticuspe.

Fig. 3. SHIBORIDAMA is the LEAFY ortholog in C. seticuspe.

a Capitula of wild-type (WT) C. seticuspe. b Organs corresponding to the capitula in the shiboridama (sbd) mutant. c Phylogenetic tree of LEAFY orthologs. CsFL is the LEAFY ortholog in C. seticuspe. Most LEAFY orthologs are single copies, with the exception of recently genome-duplicated species such as maize. d Structure of CsFL in sbd mutant. e Linkage analysis between the inflorescence phenotype and CsFL genotype. + and – indicate with and without insertion, respectively. Bars indicate 1 cm.

Fig. 4. Structure and distribution of shiboridama-retrotransposon.

a Structures of SbdRT in the C. seticuspe genome. SbdRT-nis-ori is the original SbdRT found in CsFL of the sbd mutant, which carries a noncoding insert instead of the long open reading frame (ORF) in SbdRT-orf. b Distribution of intact long terminal repeat-RTs in the pseudochromosomes of Gojo-0. Densities of predicted genes (high confidence), SbdRT copies of all types, and members of the Copia and Gypsy superfamilies are shown along with the nine linkage groups. c A phylogenetic tree of SbdRT copies in C. seticuspe and C. nankingense. Only the full-length SbdRT copies were subjected to analysis.

Fig. 5. Positional cloning of ALB1 in C. seticuspe.

a Phenotype of alb1. Left, two-week-old seedlings of selfed AEV02 progeny segregating wild-type (green) and alb1 mutant (white) phenotypes. Right, in vitro culture of alb1. Scale bar indicates 1 cm. b Structure of the ALB1 candidate region. Analysis of the F2 population revealed that ALB1 was located between SNP markers 257.216 and 255.277. c Structure of CsMurE in alb1. A single base pair deletion was observed in the third exon (heterozygous in AEV02) resulting in a frameshift and premature stop codon.