Severe Plastid Genome Size Reduction in a Mycoheterotrophic Orchid, Danxiaorchis singchiana, Reveals Heavy Gene Loss and Gene Relocations

Lee, Shiou Yih; Meng, Kaikai; Wang, Haowei; Zhou, Renchao; Liao, Wenbo; Chen, Fang; Zhang, Shouzhou; Fan, Qingxia

doi:10.3390/plants9040521

Cited by 6 publications

(6 citation statements)

References 53 publications

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“…Comparative analysis of plastomes showed that C. sinensis has one small inversion occurred in the LSC region. However, the larger inversions appear in D anxiaorchis singchiana ( Lee et al., 2020 ), C. maculata var. maculata ( Barrett et al., 2014 ) and C. maculata ( Kim et al., 2020 ), which had been reported.…”

Section: Discussionmentioning

confidence: 98%

Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China

et al. 2021

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Corallorhiza sinensis , a new species of mycoheterotrophic orchid from western Sichuan, China, is described and illustrated based on molecular and morphological evidence. It is morphologically similar to Corallorhiza trifida , but can be distinguished by bigger flowers, both sepals and petals with 3 veins, and longer lateral lobes of lip. To distinguish the new Corallorhiza species and explore its phylogenetic position within subtribe Calypsoinae, this study employed sequences of the nuclear ribosomal DNA (nrDNA) and whole plastome assembled from the genome skimming approach. The plastome is 148,124 bp in length, including a pair of inverted repeats (IRs) of 26,165 bp, a large single-copy region (LSC) of 82,207 bp, and a small single-copy region (SSC) of 13,587 bp. Further, phylogenetic analyses were performed using nrDNA sequence and 79 coding sequences (CDSs) from 26 complete plastomes of subtribe Calypsoinae. The phylogenetic tree based on nrDNA sequence suggested that Corallorhiza is a monophyletic group, and strongly support C. sinensis as sister to the rest species of Corallorhiza . The plastid tree showed that 10 Corallorhiza species grouped into two clades and C. sinensis is most closely related to the North American C . striata and C. bentleyi instead of Oreorchis foliosa and O . angustata in the same clade. The plastid tree and nrDNA tree indicate Oreorchis is a paraphyletic. Although the topological conflicts are displayed between plastome and nrDNA phylogenies of C. sinensis , it is still the most closely related to Corallorhiza . Comparative analysis showed that C. sinensis populations are characteristic of the intermediate morphological traits between Corallorhiza and Oreorchis . The finding of this new species from China shed new light on the phylogeny of Oreorchis and Corallorhiza .

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Section: Discussionmentioning

confidence: 98%

Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China

et al. 2021

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“…Flower gardening traditionally employs Phalaenopsis hybrid cultivars. Only one diploid cultivar has been documented, whereas over 80% of tetraploid cultivars have 76 chromosomes (Lee S. Y. et al, 2020). The domination of commercial tetraploid cultivars demonstrates the relevance of polyploidy in the development of better Phalaenopsis cultivars.…”

Section: Genome Size and Ploidy Analysis Of The Orchidmentioning

confidence: 99%

“…The comparative genomics of 12 tribe Neottieae orchids indicated that genes related to the NAD(P)H dehydrogenase complex, photosystems, and RNA polymerase were functionally lost many times (Feng et al, 2016). A phylogenetic analysis of 26 full plastome sequences from Epidendreae suggested that photosynthesis-related genes such as the atp complex had undergone severe gene loss (Lee S. Y. et al, 2020). Numerous investigation have identified evidence of fast plastome degradation in heterotrophic orchids based on the accumulation of pseudogenes and substantial deletions (Barrett and Kennedy, 2018;Barrett et al, 2019;Kim et al, 2019).…”

Section: Sequencing and Evolution Of The Chloroplast Genome In Orchidmentioning

confidence: 99%

In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing

et al. 2022

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High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies.

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confidence: 99%

“…Full mycoheterotrophy has evolved repeatedly across land plants with associated losses of photosynthesis. Over half of the origins are thought to have occurred in Orchidaceae (Merckx and Freudenstein, 2010;Merckx et al, 2013), but to date only a subset of the independent transitions to heterotrophy in this family have been characterized with fully sequenced plastid genomes (Delannoy et al, 2011;Logacheva et al, 2011;Barrett and Davis, 2012;Schelkunov et al, 2015;Feng et al, 2016;Huo et al, 2018;Barrett et al, 2019;Kim et al, 2019;Kim et al, 2020;Lee et al, 2020;Z.-H. Li et al, 2020). Sequenced plastid genomes of mycoheterotrophic plants can provide useful phylogenetic information and insights into patterns of genome evolution and changes in selection with the loss of photosynthesis (e.g., Barrett and Davis, 2012;Barrett et al, 2014;Wicke et al, 2016;Graham et al, 2017).…”

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confidence: 99%

Phylogenomics and plastome evolution of a Brazilian mycoheterotrophic orchid, Pogoniopsis schenckii

Klimpert

Mayer

Sarzi

et al. 2022

American J of Botany

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Premise Pogoniopsis likely represents an independent photosynthesis loss in orchids. We use phylogenomic data to better identify the phylogenetic placement of this fully mycoheterotrophic taxon, and investigate its molecular evolution. Methods We performed likelihood analysis of plastid and mitochondrial phylogenomic data to localize the position of Pogoniopsis schenckii in orchid phylogeny, and investigated the evolution of its plastid genome. Results All analyses place Pogoniopsis in subfamily Epidendroideae, with strongest support from mitochondrial data, which also place it near tribe Sobralieae with moderately strong support. Extreme rate elevation in Pogoniopsis plastid genes broadly depresses branch support; in contrast, mitochondrial genes are only mildly rate elevated and display very modest and localized reductions in bootstrap support. Despite considerable genome reduction, including loss of photosynthesis genes and multiple translation apparatus genes, gene order in Pogoniopsis plastomes is identical to related autotrophs, apart from moderately shifted inverted repeat (IR) boundaries. All cis‐spliced introns have been lost in retained genes. Two plastid genes (accD, rpl2) show significant strengthening of purifying selection. A retained plastid tRNA gene (trnE‐UUC) of Pogoniopsis lacks an anticodon; we predict that it no longer functions in translation but retains a secondary role in heme biosynthesis. Conclusions Slowly evolving mitochondrial genes clarify the placement of Pogoniopsis in orchid phylogeny, a strong contrast with analysis of rate‐elevated plastome data. We documented the effects of the novel loss of photosynthesis: for example, despite massive gene loss, its plastome is fully colinear with other orchids, and it displays only moderate shifts in selective pressure in retained genes.

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Severe Plastid Genome Size Reduction in a Mycoheterotrophic Orchid, Danxiaorchis singchiana, Reveals Heavy Gene Loss and Gene Relocations

Cited by 6 publications

References 53 publications

Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China

Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China

In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing

Phylogenomics and plastome evolution of a Brazilian mycoheterotrophic orchid, Pogoniopsis schenckii

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