Abstract
As one of the largest families of angiosperms, the Orchidaceae family is diverse. Dendrobium represents the second largest genus of the Orchidaceae. However, an assembled high-quality genome of species in this genus is lacking. Here, we report a chromosome-scale reference genome of Dendrobium chrysotoxum, an important ornamental and medicinal orchid species. The assembled genome size of D. chrysotoxum was 1.37 Gb, with a contig N50 value of 1.54 Mb. Of the sequences, 95.75% were anchored to 19 pseudochromosomes. There were 30,044 genes predicted in the D. chrysotoxum genome. Two whole-genome polyploidization events occurred in D. chrysotoxum. In terms of the second event, whole-genome duplication (WGD) was also found to have occurred in other Orchidaceae members, which diverged mainly via gene loss immediately after the WGD event occurred; the first duplication was found to have occurred in most monocots (tau event). We identified sugar transporter (SWEET) gene family expansion, which might be related to the abundant medicinal compounds and fleshy stems of D. chrysotoxum. MADS-box genes were identified in D. chrysotoxum, as well as members of TPS and Hsp90 gene families, which are associated with resistance, which may contribute to the adaptive evolution of orchids. We also investigated the interplay among carotenoid, ABA, and ethylene biosynthesis in D. chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers. The reference D. chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.
Highlights
With more than 25,000 species, Orchidaceae is the largest angiosperm family[1] and comprises 8–10% of flowering plants
Genome sequencing and characteristics D. chrysotoxum has a karyotype of 2N = 2X = 38, with uniform chromosomes[31]
This study found that D. chrysotoxum experienced two polyploidization events: an early whole-genome duplication (WGD) event was shared among all extant orchid species, and a later event that was shared among most monocot species
Summary
With more than 25,000 species, Orchidaceae is the largest angiosperm family[1] and comprises 8–10% of flowering plants. Guchui Shihu (鼓槌石斛) Dendrobium chrysotoxum, a medicinal species, is listed in the Chinese Pharmacopoeia (2020, 2015, and 2010 edition) and contains an abundance of erianin, gigantol, polysaccharides, and fluorenones, among other compounds[11,12,13,14,15,16,17,18,19] (Fig. 1). Only two Dendrobium spp. genomes have been sequenced, and some candidate genes involved in polysaccharide metabolic pathways have been identified in those two species[24,29,30]. These studies were largely limited due to their low-quality genome assemblies. High-quality reference genomes and additional Dendrobium species need to be sequenced to better understand the molecular mechanisms underlying the production of medicinal compounds and enable the breeding of new varieties
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