The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution

Abstract

Orchids make up about 10% of all seed plant species, have great economical value, and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes, and find evidence of a whole genome duplication shared with Phalaenopsis. We observed the expansion of many resistance-related genes, suggesting a powerful immune system responsible for adaptation to a wide range of ecological niches. We also discovered extensive duplication of genes involved in glucomannan synthase activities, likely related to the synthesis of medicinal polysaccharides. Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC(*), involved in the regulation of development and growth, suggests that these expansions are associated with the astonishing diversity of plant architecture in the genus Dendrobium. On the contrary, members of the type I MADS box gene family are missing, which might explain the loss of the endospermous seed. The findings reported here will be important for future studies into polysaccharide synthesis, adaptations to diverse environments and flower architecture of Orchidaceae.

Figure 1. Phylogenetic position and Ks distributions for D. catenatum.

(a) Phylogenetic tree showing the topology and divergence times for 12 plant species, including D. catenatum. Estimated divergence times are indicated by light blue boxes at internodes. Numbers at nodes indicate bootstrap values. The brown bar indicates the orchid-specific whole-genome duplication (WGD), while the green bar indicates a more ancient monocot-specific WGD (Thanks Li-Jun Chen for taking the images of species). (b) Distribution of synonymous substitutions per synonymous site (Ks) for the whole D. catenatum paranome. (c) Distribution of synonymous substitutions per synonymous site (Ks) for orthologous genes found in syntenic regions. Two consistent peaks highlighted by the dashed rectangles are considered to reflect the most recent and older WGD events.

Figure 2. Phylogeny of putative full-length TPSs from D. catenatum (green), P. equestris (purple), O. sativa (blue) and A. thaliana (cyan).

See text for details.

Figure 3. Proposed biosynthetic pathway of GM and GGM in Dendrobium stem.

The biosynthetic pathway was modified according to the pathways proposed in Amorphophallus konjac. GM or GGM biosynthesis is supposed to be generated from sucrose, mainly produced by photosynthesis in the leaf tissue (Supplementary Note 7). The enzymes indicated in red are highly expressed in the stem. Only abbreviations of gene names are shown: Csl, Cellulose synthase like gene; FRK, fructokinase; Fru, fructose; Fru-6-P, Fructose-6-phosphate; GGP, GDP-glucose-pyrophosphorylase; GMPP, GDP-mannose pyrophosphorylase; GT, glycosyltransferase; HXK, hexokinase; INV, invertase; MSR, mannan synthesis-related; PGI, phosphoglucose isomerase; PGM, phosphoglucomutase; PMI, phosphomannose isomerase; PMM, phosphomannomutase; RWA, Reduced Wall Acetylation proten; SuS, sucrose synthase; UGE, UDP-galactose epimerase; UGP, UDP-glucose pyrophosphorylase.