TheChrysanthemum lavandulifoliumgenome and the molecular mechanism underlying diverse capitulum types

Abstract

Cultivated chrysanthemum (Chrysanthemum × morifolium Ramat.) is a beloved ornamental crop due to the diverse capitula types among varieties, but the molecular mechanism of capitulum development remains unclear. Here, we report a 2.60 Gb chromosome-scale reference genome of C. lavandulifolium, a wild Chrysanthemum species found in China, Korea and Japan. The evolutionary analysis of the genome revealed that only recent tandem duplications occurred in the C. lavandulifolium genome after the shared whole genome triplication (WGT) in Asteraceae. Based on the transcriptomic profiling of six important developmental stages of the radiate capitulum in C. lavandulifolium, we found genes in the MADS-box, TCP, NAC and LOB gene families that were involved in disc and ray floret primordia differentiation. Notably, NAM and LOB30 homologs were specifically expressed in the radiate capitulum, suggesting their pivotal roles in the genetic network of disc and ray floret primordia differentiation in chrysanthemum. The present study not only provides a high-quality reference genome of chrysanthemum but also provides insight into the molecular mechanism underlying the diverse capitulum types in chrysanthemum.

A genome-wide association and fine-mapping study of white rust resistance in hexaploid chrysanthemum cultivars with a wild diploid reference genome

“…they were ultrafragmented. Such fragmentation was similarly observed in the de novo assemblies of diploid Chrysanthemum species genomes obtained at an early stage [ 20 , 44 ] because repetitive sequences occupied >68.6% of the whole genome in the genus Chrysanthemum [ 20 , 29 , 44 , 49 ]. In this study, the high ratio of repetitive sequences could be a major cause of the failure in assembling longer sequences in cultivated chrysanthemums.…”

From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes

“…We wished to include as many orders as possible in our study, ideally with access to at least six genomes with high quality, preferably chromosome-level, assemblies, distributed among at least three different families. At the time of data collection, we could obtain suitable data from three fabid orders, Fagales [20][21][22][23][24][25][26][27], Cucurbitales [28][29][30][31][32][33], Malpighiales [34][35][36][37][38][39]; three malvid orders, Myrtales [40][41][42][43][44], Malvales [45][46][47][48][49][50] and Sapindales [51][52][53][54][55][56][57][58][59][60][61]; one campanulid order, Asterales [62][63][64][65][66]…”

Co‐option of a carotenoid cleavage dioxygenase gene (CCD4a) into the floral symmetry gene regulatory network contributes to the polymorphic floral shape–color combinations in Chrysanthemum sensu lato

“…In our study, intact CCD4a sequences were detected in the genomes of all chrysanthemums with white/pink ray florets and some Ajania species, but were absent in most Ajania and yellow‐rayed chrysanthemums (Table 2). The absence of CCD4a in genomes of Chrysanthemum species with yellow marginal florets was supported by the whole‐genome sequence data of C. nankingensis (Song et al ., 2018), C. seticuspe (Hirakawa et al ., 2019) and C. lavandulifolium (Wen et al ., 2022). Our analyses revealed that CCD4a was specifically expressed in the white rays of radiate capitula, in which CYC2g was functional, but it was not expressed in the marginal florets of disciform capitula, in which CYC2g was dysfunctional (Figs 2, 3).…”