Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)

Unruh, Sarah A.; McKain, Michael R.; Lee, Yung‐I; Yukawa, Tomohisa; McCormick, Melissa; Shefferson, Richard P.; Smithson, Ann; Leebens‐Mack, James H.; Pires, J. Chris

doi:10.1002/ajb2.1047

Cited by 36 publications

(36 citation statements)

References 84 publications

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“…(the dataset lacked representatives of the genera Selenipedium and Mexipedium ). For purposes of comparison, we also found mycorrhizal information for four species of the subfamily Apostasioideae, which we used as an outgroup (Li et al, ; Unruh et al, ).…”

Section: Methodsmentioning

confidence: 99%

“…Although species in the Cypripedioideae are represented in the Open Tree of Life, species were not resolved within genera at the time of writing. Instead, we used the general phylogeny of the Orchidaceae and of genera in the Cypripedioideae presented in Unruh et al () as a backbone. Onto this we added the phylogeny of genus Cypripedium developed in Li et al (), and phylogenies that we developed of sampled Paphiopedilum species and Apostasioideae species.…”

Section: Methodsmentioning

confidence: 99%

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Does evolutionary history determine specificity in broad ecological interactions?

et al. 2019

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Most species engage in broad interactions, in which they interact with multiple partner species. The evolutionary processes that generate such generalized interactions remain unknown, partly due to the difficulty in comparing their breadth. We argue that the interaction specificity of species involved in broad interactions evolves in three ways: (a) assemblage specialization, in which a species specializes on particular host species that contribute unique resources, yielding specialization on the entire host assemblage; (b) apparent generalism, in which a species specializes on one or few host species that contribute unique resources, but also associates with other host species that contribute functionally redundant resources; and (c) true generalism, in which a species associates with multiple hosts that overlap functionally, and that are geographically interchangeable based on opportunity for encounter, leading to frequent host switching. We performed a phylogenetically controlled analysis of data on mycorrhizal fungal associations for approximately 25% of the orchid subfamily Cypripedioideae to determine whether these plants have specialized on their mycorrhizal fungal communities, or whether they are true generalists. We also assessed the impact of environmental factors on these associations. Our results suggested strong support for apparent generalism, suggesting strong specialization on particular, dominant fungi and weak specialization on others. Large orchid clades associated with dominant fungal species, notably Tulasnella cystidiophora for genus Cypripedium, and T. cystidiophora and T. calospora for genus Paphiopedilum. Significant phylogenetic signal in fungal species richness per plant species, but not in the fungal phylogenetic diversity per plant species nor in the composition of fungal assemblages across orchid species suggested that plant phylogeny is an important determinant of fungal association. Mixed linear models showed that environment influenced specificity across plant species, and that observed differences were strongly driven by differences in sampling effort. Synthesis. We found evidence of specialization of plant species on dominant fungal species, and to a lesser extent on their close relatives. The strong dominance of particular fungal species in these associations suggests important ecological roles for them, while environmental gradients in specificity suggest strong environmental filtering of these interactions.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Does evolutionary history determine specificity in broad ecological interactions?

et al. 2019

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“…The evolutionary direction of the life forms of orchids can be roughly outlined from terrestrial to epiphytic, while saprophytic species independently evolved several times ( Sosa et al, 2016 ). Recent plastome analysis of orchid species has focused on comparisons with partially and fully mycoheterotrophic species ( Feng et al, 2016 ; Barrett & Kennedy, 2018 ; Unruh et al, 2018 ; Yuan et al, 2018 ). The molecular information on these species is of interest not only for the study of phylogenetics but also for evolutionary studies and species conservation.…”

Section: Introductionmentioning

confidence: 99%

Plastome structure and adaptive evolution ofCalanthes.l. species

Chen

Zhong

Zhu

et al. 2020

PeerJ

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Calanthe s.l. is the most diverse group in the tribe Collabieae (Orchidaceae), which are pantropical in distribution. Illumina sequencing followed by de novo assembly was used in this study, and the plastid genetic information of Calanthe s.l. was used to investigate the adaptive evolution of this taxon. Herein, the complete plastome of five Calanthe s.l. species (Calanthe davidii, Styloglossum lyroglossa, Preptanthe rubens, Cephalantheropsis obcordata, and Phaius tankervilliae) were determined, and the two other published plastome sequences of Calanthe s.l. were added for comparative analyses to examine the evolutionary pattern of the plastome in the alliance. The seven plastomes ranged from 150,181 bp (C. delavayi) to 159,014 bp (C. davidii) in length and were all mapped as circular structures. Except for the three ndh genes (ndhC, ndhF, and ndhK) lost in C. delavayi, the remaining six species contain identical gene orders and numbers (115 gene). Nucleotide diversity was detected across the plastomes, and we screened 14 mutational hotspot regions, including 12 non-coding regions and two gene regions. For the adaptive evolution investigation, three species showed positive selected genes compared with others, C. obcordata (cemA), S. lyroglossa (infA, ycf1 and ycf2) and C. delavayi (nad6 and ndhB). Six genes were under site-specific positive selection in Calanthe s.l., namely, accD, ndhB, ndhD, rpoC2, ycf1, and ycf2, most of which are involved in photosynthesis. These results, including the new plastomes, provide resources for the comparative plastome, breeding, and plastid genetic engineering of orchids and flowering plants.

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“…RNA-seq can be used to identify exon-exon splice junctions and different splicing patterns from different samples (Wilks et al 2018). In the slipper orchids (Cypripedioideae), results derived from RNA-seq data analysis showed the identification of mechanisms associated with genome evolution and transcriptomic data that were used to identify low-copy orthologous genes demonstrated that 775 single-copy nuclear genes should be valuable in future investigations of orchid evolution (Unruh et al 2018).…”

Section: Slipper Orchidsmentioning

confidence: 99%

Biological significance of RNA-seq and single-cell genomic research in woody plants

Tang

2019

J. For. Res.

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RNA-seq and single-cell genomic research emerge as an important research area in the recent years due to its ability to examine genetic information of any number of single cells in all living organisms. The knowledge gained from RNA-seq and single-cell genomic research will have a great impact in many aspects of plant biology. In this review, we summary and discuss the biological significance of RNA-seq and single-cell genomic research in plants including the single-cell DNA-sequencing, RNA-seq and single-cell RNA sequencing in woody plants, methods of RNA-seq and single-cell RNA-sequencing, single-cell RNA-sequencing for studying plant development, and single-cell RNA-sequencing for elucidating cell type composition. We will focus on RNA-seq and single-cell RNA sequencing in woody plants, understanding of plant development through single-cell RNAsequencing, and elucidation of cell type composition via single-cell RNA-sequencing. Information presented in this review will be helpful to increase our understanding of plant genomic research in a way with the power of plant single-cell RNA-sequencing analysis.

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Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)

Cited by 36 publications

References 84 publications

Does evolutionary history determine specificity in broad ecological interactions?

Does evolutionary history determine specificity in broad ecological interactions?

Plastome structure and adaptive evolution ofCalanthes.l. species

Biological significance of RNA-seq and single-cell genomic research in woody plants

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