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Morphology of Neottia nidus-avis and Epipogium aphyllum. Top left: roots of N. nidus-avis. Bottom left: inflorescence of N. nidus-avis. Top right:
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Mycoheterotrophic plants have lost the ability to photosynthesize and they parasitize their associated fungus to get the mineral and organic nutrients they need. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy to mycoheterotrophy occurred independently in almost all major lineages...
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Mycoheterotrophic plants have lost the ability to photosynthesize and obtain essential mineral and organic nutrients from associated soil fungi. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy to mycoheterotrophy has occurred independently in many major lineages of land plants, mo...
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... We found that only 935 (64.9%) of the 1440 highly conserved orthologs are present as complete genes in the G. elata genome, indicating that 451 (31.3%) genes are missing from G. elata, which is consistent with results from the previous genome assembly (Yuan et al. 2018). The gene loss events are frequently observed in plastid genome of mycoheterotrophic orchids (Barrett and Davis 2012;Logacheva et al. 2014;Petersen et al. 2018;Kim et al. 2019), but only a few cases are reported in nuclear genome (Yuan et al. 2018;Jakalski et al. 2020). The extensive gene loss in nuclear genome could also be related to mycoheterotrophic lifestyle and may be associated with the large abundance of repetitive elements in G. elata. ...
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.
... It was hypothesised that chlorophyll may have some functions other than photosynthesis (Cummings & Welschmeyer, 1998;Barrett et al., 2014). Analyses of transcriptomes and genomes revealed that the pathways for synthesis and breakdown of chlorophyll are indeed probably retained in some non-photosynthetic species (Wickett et al., 2011;Schelkunov, Penin & Logacheva, 2018;Marcin et al., 2020); however, they are likely lost in some other species (Ng et al., 2018;Schelkunov, Penin & Logacheva, 2018;Chen et al., 2020b). In Rhopalocnemis phalloides and Balanophora fungosa, RBH analysis indicated the complete disappearance of chlorophyll synthesis and breakdown genes. ...
The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.
... It was hypothesised that the chlorophyll may have some functions other than photosynthesis (Cummings & Welschmeyer, 1998). Analyses of transcriptomes and genomes showed that the pathways for synthesis and breakdown of the chlorophyll are indeed probably retained in some non-photosynthetic species (Wickett et al., 2011;Schelkunov, Penin & Logacheva, 2018;Marcin et al., 2020), though likely lost in some others (Ng et al., 2018;Schelkunov, Penin & Logacheva, 2018;Chen et al., 2020b). In Rhopalocnemis phalloides and Balanophora fungosa the RBH analysis indicates complete disappearance of chlorophyll synthesis and breakdown genes. ...
The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have shown that plastid genomes of Balanophoraceae have a number of interesting features, one of the most prominent of those being a tremendous AT content close to 90%. Also, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is greater by an order of magnitude compared to photosynthetic relatives, without signs of relaxed selection. All these features have no definite explanations.
Given these unusual features, we supposed that it would be interesting to gain insight into the characteristics of nuclear genomes of Balanophoraceae. To do this, in the present study we analysed transcriptomes of two species from Balanophoraceae, namely Rhopalocnemis phalloides and Balanophora fungosa , and compared them with transcriptomes of their close photosynthetic relatives Daenikera sp., Dendropemon caribaeus, Malania oleifera .
The analysis showed that the AT content of nuclear genes of Balanophoraceae does not markedly differ from that of photosynthetic relatives. The nucleotide substitution rate in genes of Balanophoraceae is for an unknown reason several times larger than in genes of photosynthetic Santalales, though the negative selection in Balanophoraceae is likely stronger.
We observed an extensive loss of photosynthesis-related genes in Balanophoraceae. Also, for Balanophoraceae we did not see transcripts of several genes whose products participate in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.
