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.

Fig. 1. High-quality assembly of the C. ensifolium genome.

I Chromosome numbers, II Gene density, III Repeat sequence density, IV GC content density, V Collinear regions. Each line connects a pair of homologous genes (from outside to inside)

Fig. 2. Evolution of gene families and whole-genome duplication (WGD) in C. ensifolium.

a Expansion and contraction of gene families and phylogenetic relationships and divergence times between C. ensifolium and other plant species. The green numbers represent the numbers of expanded gene families, and the red numbers represent the numbers of contracted gene families. Blue in the circle indicates the gene families with a constant copy number, while orange indicates the proportions of 11,968 gene families of most recent common ancestors (MRCAs) that expanded or contracted during late differentiation. b Ks distribution and WGD events in C. ensifolium. The Ks distribution of C. ensifolium showed two peaks, one at approximately 0.9 (WGD2), indicating that C. ensifolium experienced the last WGD event shared by all orchids, and another at approximately 1.7 (WGD1), which was likely the more ancient τ event shared by most monocots. The red stars represent the WGD events

Fig. 3. MADS-box model of C. ensifolium flowers.

AP3: CeAP3-1, CeAP3-2, CeAP3-3, and CeAP3-4. PI: CePI. SEP: CeSEP-1, CeSEP-2, CeSEP-3, and CeSEP-4. AGL6-1: CeAGL6-1. AGL6-2: CeAGL6-2. AG: CeAG-1, CeAG-2, and CeAG-3. See Gene ID in Supplementary Table 24

Fig. 4. Flower morphology and the expression patterns of regulatory genes of different mutants of C. ensifolium.

a Wild-type flowers and the expression patterns of regulatory genes. b Branched inflorescence with multitepal flowers and the expression patterns of regulatory genes. c Peloric flower mutant and the expression patterns of regulatory genes. d Column-like petal mutant and the expression patterns of regulatory genes. e Lip-like petal mutant and the expression patterns of regulatory genes. f Lip-like sepal mutant and the expression patterns of regulatory genes. Se, sepal; Pe, petal; Li, lip; Co, column. The rectangles of different colors (blue, red, green, yellow, pink, orange and gray) indicate that the genes were expressed in the floral organs, while a white rectangle indicates that the gene was not expressed or was expressed at a low level in that floral organ. See Gene ID in Supplementary Table 24

Fig. 5. Expression levels of genes encoding enzymes involved in jasmonate biosynthesis and terpene backbone biosynthesis.

a Jasmonate signal pathway. b Mevalonate pathway. c Methylerythritol phosphate pathway. The heat map was plotted based on FPKM values, and min-max normalization was performed. Red indicates high levels of expression, while blue indicates low levels of expression. The abbreviated names of the enzymes (full name see Supplementary Table 26) involved in each catalytic step are shown in bold. The intermediate compounds in the pathways are OPDA, 12-oxo-phytodienoic acid; HMG-CoA, S-3-hydroxy-3-methylglutaryl-CoA; MVP, mevalonate-5-phosphate; MVPP, mevalonate diphosphate; CDP-ME, 4-diphosphocytidyl-2-C-methylerythritol; CDP-MEP, 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate; DXP, 1-deoxy-D-xylulose 5-phosphate; G3P, glyceraldehyde-3-phosphate; HMBPP, 4-hydroxy-3-methyl-but-2-enyl pyrophosphate; and ME-cPP, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate