Chromosome-level genome assembly of the fully mycoheterotrophic orchid Gastrodia elata

Abstract

Gastrodia elata, an obligate mycoheterotrophic orchid, requires complete carbon and mineral nutrient supplementation from mycorrhizal fungi during its entire life cycle. Although full mycoheterotrophy occurs most often in the Orchidaceae family, no chromosome-level reference genome from this group has been assembled to date. Here, we report a high-quality chromosome-level genome assembly of G. elata, using Illumina and PacBio sequencing methods with Hi-C technique. The assembled genome size was found to be 1,045 Mb, with an N50 of 50.6 Mb and 488 scaffolds. A total of 935 complete (64.9%) matches to the 1,440 embryophyte Benchmarking Universal Single-Copy Orthologs were identified in this genome assembly. Hi-C scaffolding of the assembled genome resulted in 18 pseudochromosomes, 1,008 Mb in size and containing 96.5% of the scaffolds. A total of 18,844 protein-coding sequences (CDSs) were predicted in the G. elata genome, of which 15,619 CDSs (82.89%) were functionally annotated. In addition, 74.92% of the assembled genome was found to be composed of transposable elements. Phylogenetic analysis indicated a significant contraction of genes involved in various biosynthetic processes and cellular components and an expansion of genes for novel metabolic processes and mycorrhizal association. This result suggests an evolutionary adaptation of G. elata to a mycoheterotrophic lifestyle. In summary, the genomic resources generated in this work will provide a valuable reference genome for investigating the molecular mechanisms of G. elata biological functions. Further, the complete G. elata genome will greatly improve our understanding of the genetics of Orchidaceae and its mycoheterotrophic evolution.

The role of symbiotic fungi in the life cycle of Gastrodia elata Blume (Orchidaceae): a comprehensive review

“…The genome of G. elata has been continuously reported in recent years, offering insights into how G. elata adapted to heterotrophy in Mycena and Armillaria . In G. elata , genes important in the control of flowering time, the circadian clock, nutrient absorption, immunity, growth of the roots and leaves, and photosynthesis were all severely lost ( Yuan et al., 2018 ; Park et al., 2020 ; Xu et al., 2021 ; Bae et al., 2022 ).…”

“…The expansion of many gene families in G. elata is additional evidence for adaptation to the mycoheterotrophic lifestyle of fungi. Phylogenetic analysis showed that the number of genes of G. elata concerned with mycorrhizal association was significantly expanded ( Bae et al., 2022 ; Jiang et al., 2022 ). These phenomena represent evolutionary events and may be the result of G. elata adapting to a heterotrophic lifestyle in the presence of Armillaria ( Yuan et al., 2018 ; Bae et al., 2022 ).…”

Decrease in beneficial bacteria and increase in harmful bacteria in Gastrodia seedlings and their surrounding soil are mainly responsible for degradation of Gastrodia asexual propagation

“…Gastrodia elata Bl. f. glauca S. chow (GeB) is a non-toxic perennial herbaceous heterotrophic plant with a sweet flavor, smooth texture, and various benefits ( Hong et al., 2018 ; Liu et al., 2018 ; Gong et al., 2021 ; Shan et al., 2021 ; Shan et al., 2021 ; Bae et al., 2022 ). GeB has no roots and no green leaves, so it cannot directly absorb water and inorganic salts from the soil for the growth of its plants, nor it can photosynthesize to produce organic nutrients for itself.…”

Whole genome sequencing and analysis of Armillaria gallica Jzi34 symbiotic with Gastrodia elata

“…The symbiotic mechanism between G. elata and Armillaria has rarely been revealed from the perspective of Armillaria , and most studies have focused on G. elata . Previous G. elata genomic analyses indicated an expansion of genes for novel metabolic processes and mycorrhizal association [ 9 , 10 ]. Yuan et al [ 9 ] found that strigolactone could stimulate the hyphal branching and development of A. mellea .…”