The Cymbidium genome reveals the evolution of unique morphological traits

Abstract

The marvelously diverse Orchidaceae constitutes the largest family of angiosperms. The genus Cymbidium in Orchidaceae is well known for its unique vegetation, floral morphology, and flower scent traits. Here, a chromosome-scale assembly of the genome of Cymbidium ensifolium (Jianlan) is presented. Comparative genomic analysis showed that C. ensifolium has experienced two whole-genome duplication (WGD) events, the most recent of which was shared by all orchids, while the older event was the τ event shared by most monocots. The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation, and flower shape mutations in C. ensifolium were shown to be associated with the abnormal expression of MADS-box genes. The most abundant floral scent components identified included methyl jasmonate, acacia alcohol and linalool, and the genes involved in the floral scent component network of C. ensifolium were determined. Furthermore, the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves, while the increased expression of MADS-box genes in leaves led to perianth-like leaves. Our results provide fundamental insights into orchid evolution and diversification.

Haplotype‐resolved genome assembly of Bletilla striata (Thunb.) Reichb.f. to elucidate medicinal value

“…The divergence time between the most closely related orchid plants B. striata and G. elata was estimated to be 55.1 Mya. Bletilla striata has experienced two WGD events, and the recent WGD was similar to that found in other orchid genomes (Ai et al., 2021; Chung et al., 2021; Niu et al., 2021; Yang, Gao, et al., 2021b; Zhang et al., 2017; Zhang et al., 2021), suggesting that this WGD was shared by all extant orchid genomes. There is sufficient evidence to confirm that WGD events have been frequent in the evolutionary history of flowering plant genomes, and they usually shape the evolutionary trajectory of genes and genomes, especially the genes related to plant‐specialized phenotypes and/or agronomic traits(Clark & Donoghue, 2017; Guo et al., 2013; Soltis & Soltis, 2016).…”

Genome-Wide Identification of the MYB Gene Family in Cymbidiumensifolium and Its Expression Analysis in Different Flower Colors

“…Gene duplication plays an important role in plant evolution and is a main mechanism of gene family expansion. Three whole-genome duplication (WGD) events have occurred in A. thaliana [32], and C. ensifolium has experienced two WGD events [33]. The result showed that segmental and tandem duplication events occured unevenly on chromosomes.…”

Genome-Wide Identification and Expression Pattern Analysis of KNOX Gene Family in Orchidaceae

“…Given the conserved nature of gene structure within the same clade, we found that orchid KNOXs have a similar exon–intron structure compared to A. thaliana and O. sativa , except that most orchids exhibited longer intron length ( Figure 3C ). Long intron has been reported in almost all sequenced orchid species ( Cai et al, 2014 ; Zhang et al, 2016 , 2017 ; Yuan et al, 2018 ; Ai et al, 2021 ), which might be a unique feature of Orchidaceae. Longer introns are favored in the course of gene evolution because they promote the efficiency of natural selection by increasing the recombination between two adjacent exons ( Jo and Choi, 2015 ), which may account for the marvelous richness of orchids.…”