The Gastrodia elata genome provides insights into plant adaptation to heterotrophy

Abstract

We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.

Mitochondrial genome of non-photosynthetic mycoheterotrophic plant Hypopitys monotropa,its structure, gene expression and RNA editing

“…However this expansion is unlikely to be associated with the heterotrophy. Large mitogenomes are known for heterotrophic plants, in particular for the mycoheterotrophic orchid Gastrodia elata (~ 1.3 Mbp) (Yuan et al, 2018), and the parasitic Cynomorium (1 Mbp) (Bellot et al, 2016) and Lophophytum mirabile (Balanophoraceae) (~820 Kbp) (in two latter cases the size is shaped by the fragments horizontally transferred from its host – see below). On the other extreme are highly miniaturized mitogenomes of V. scurruloideum (Skippington et al, 2015).…”

“…In contrast, there are no traces of HGT in H. monotropa mitogenome. Nuclear and mitochondrial genomes of a mycoheterotrophic orchid Gastrodia elata were recently characterized (Yuan et al, 2018) and there were also no observations of HGT. Despite that mycoheterotrophic plants are usually regarded alongside the parasitic plants that fed on other plants, the interactions between plant and its host are very different in these two cases.…”

“…The sampling is obviously insufficient even for parasitic plants; regarding mycoheterotrophs the data are almost completely lacking. The only mitochondrial genome of a mycoheterotrophic plant characterized by date is that of orchid Gastrodia elata (Yuan et al, 2018). Taking this into account, we set the following objectives: 1) to characterize the structure and gene content of the mitochondrial genome of H. monotropa 2) to estimate if horizontal gene transfer (HGT) from fungi took place 3) to study the mitochondrial gene expression and RNA editing.…”

New Insights into the Symbiotic Relationship between Orchids and Fungi

“…In the past decade, the next-generation sequencing (NGS) tools were widely applied in whole genome sequencing and RNA sequencing (RNA-seq). The first whole genome sequence of the orchid Phalaenopsis equestris was published in 2015 [51] and the number of orchid genomes has continuously increased [52][53][54][55][56]. The whole genome sequencing of Orchidaceae provides a gateway into orchid research, including flower morphology, sexual deception, environmental stress responses and symbiosis.…”

Transcriptome analysis reveals underlying immune response mechanism of fungal (Penicillium oxalicum) disease in Gastrodia elata Bl. f. glauca S. Chow (Orchidaceae)

“…is an heterotrophic plant with highly degraded leaves and bracts. More than 80% of its life cycle exists underground in the form of tuber, depending almost entirely on fungi to provide nutrient [30]. It is closely related to at least two types of fungi: Mycena to promote seed germination and Armillaria Mellea to ensure reproductive growth.…”