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Samigullin TH, Logacheva MD, Averyanov LV, Zeng SJ, Fu LF, Nuraliev MS. Phylogenetic position and plastid genome structure of Vietorchis, a mycoheterotrophic genus of Orchidaceae (subtribe Orchidinae) endemic to Vietnam. FRONTIERS IN PLANT SCIENCE 2024; 15:1393225. [PMID: 38855461 PMCID: PMC11157612 DOI: 10.3389/fpls.2024.1393225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/12/2024] [Indexed: 06/11/2024]
Abstract
The orchid genus Vietorchis comprises three species, all discovered in the 21 century. Each of these species is achlorophyllous, mycoheterotrophic and is known to be endemic to Vietnam. The type species of the genus, V. aurea, occurs in a single location in northern Vietnam within a lowland limestone karstic area. Vietorchis furcata and V. proboscidea, in contrast, are confined to mountains of southern Vietnam, far away from any limestone formations. Taxonomic placement of Vietorchis remained uncertain for the reason of inconclusive morphological affinities. At the same time, the genus has never been included into molecular phylogenetic studies. We investigate the phylogenetic relationships of two species of Vietorchis (V. aurea and V. furcata) based on three DNA datasets: (1) a dataset comprising two nuclear regions, (2) a dataset comprising two plastid regions, and (3) a dataset employing data on the entire plastid genomes. Our phylogenetic reconstructions support the placement of Vietorchis into the subtribe Orchidinae (tribe Orchideae, subfamily Orchidoideae). This leads to a conclusion that the previously highlighted similarities in the rhizome morphology between Vietorchis and certain mycoheterotrophic genera of the subfamilies Epidendroideae and Vanilloideae are examples of a convergence. Vietorchis is deeply nested within Orchidinae, and therefore the subtribe Vietorchidinae is to be treated as a synonym of Orchidinae. In the obtained phylogenetic reconstructions, Vietorchis is sister to the photosynthetic genus Sirindhornia. Sirindhornia is restricted to limestone mountains, which allows to speculate that association with limestone karst is plesiomorphic for Vietorchis. Flower morphology is concordant with the molecular data in placing Vietorchis into Orchidinae and strongly supports the assignment of the genus to one of the two major clades within this subtribe. Within this clade, however, Vietorchis shows no close structural similarity with any of its genera; in particular, the proximity between Vietorchis and Sirindhornia has never been proposed. Finally, we assembled the plastid genome of V. furcata, which is 65969 bp long and contains 45 unique genes, being one of the most reduced plastomes in the subfamily Orchidoideae. The plastome of Vietorchis lacks any rearrangements in comparison with the closest studied autotrophic species, and possesses substantially contracted inverted repeats. No signs of positive selection acting on the protein-coding plastid sequences were detected.
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Affiliation(s)
- Tahir H. Samigullin
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Maria D. Logacheva
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Leonid V. Averyanov
- Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Si-Jin Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops / Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China and South China National Botanical Garden, Guangzhou, China
| | - Long-Fei Fu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Maxim S. Nuraliev
- Department of Higher Plants, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Joint Russian-Vietnamese Tropical Scientific and Technological Center, Hanoi, Vietnam
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Sanchez-Puerta MV, Ceriotti LF, Gatica-Soria LM, Roulet ME, Garcia LE, Sato HA. Invited Review Beyond parasitic convergence: unravelling the evolution of the organellar genomes in holoparasites. ANNALS OF BOTANY 2023; 132:909-928. [PMID: 37503831 PMCID: PMC10808021 DOI: 10.1093/aob/mcad108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/27/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND The molecular evolution of organellar genomes in angiosperms has been studied extensively, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and is found in ~10 % of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments. SCOPE This review summarizes current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles. CONCLUSIONS Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.
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Affiliation(s)
- M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Luis F Ceriotti
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Leonardo M Gatica-Soria
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - M Emilia Roulet
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
| | - Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA, Mendoza, Argentina
| | - Hector A Sato
- Facultad de Ciencias Agrarias, Cátedra de Botánica General–Herbario JUA, Alberdi 47, Universidad Nacional de Jujuy, 4600 Jujuy, Argentina
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Kim W, Lautenschläger T, Bolin JF, Rees M, Nzuzi A, Zhou R, Wanke S, Jost M. Extreme plastomes in holoparasitic Balanophoraceae are not the norm. BMC Genomics 2023; 24:330. [PMID: 37322447 DOI: 10.1186/s12864-023-09422-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Balanophoraceae plastomes are known for their highly condensed and re-arranged nature alongside the most extreme nucleotide compositional bias known to date, culminating in two independent reconfigurations of their genetic code. Currently, a large portion of the Balanophoraceae diversity remains unexplored, hindering, among others, evolutionary pattern recognition. Here, we explored newly sequenced plastomes of Sarcophyte sanguinea and Thonningia sanguinea. The reconstructed plastomes were analyzed using various methods of comparative genomics based on a representative taxon sampling. RESULTS Sarcophyte, recovered sister to the other sampled Balanophoraceae s. str., has plastomes up to 50% larger than those currently published. Its gene set contains five genes lost in any other species, including matK. Five cis-spliced introns are maintained. In contrast, the Thonningia plastome is similarly reduced to published Balanophoraceae and retains only a single cis-spliced intron. Its protein-coding genes show a more biased codon usage compared to Sarcophyte, with an accumulation of in-frame TAG stop codons. Structural plastome comparison revealed multiple, previously unknown, structural rearrangements within Balanophoraceae. CONCLUSIONS For the "minimal plastomes" of Thonningia, we propose a genetic code change identical to sister genus Balanophora. Sarcophyte however differs drastically from our current understanding on Balanophoraceae plastomes. With a less-extreme nucleotide composition, there is no evidence for an altered genetic code. Using comparative genomics, we identified a hotspot for plastome reconfiguration in Balanophoraceae. Based on previously published and newly identified structural reconfigurations, we propose an updated model of evolutionary plastome trajectories for Balanophoraceae, illustrating a much greater plastome diversity than previously known.
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Affiliation(s)
- Woorin Kim
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Thea Lautenschläger
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Botanischer Garten Hamburg, Universität Hamburg, Hamburg, Germany
| | - Jay F Bolin
- Department of Biology, Catawba College, Salisbury, USA
| | - Mathew Rees
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden, Edinburgh, UK
| | - Albertina Nzuzi
- Instituto Nacional da Biodiversidade e Conservação, Luanda, Angola
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, China
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany.
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Garrett N, Viruel J, Klimpert N, Soto Gomez M, Lam VKY, Merckx VSFT, Graham SW. Plastid phylogenomics and molecular evolution of Thismiaceae (Dioscoreales). AMERICAN JOURNAL OF BOTANY 2023; 110:e16141. [PMID: 36779918 DOI: 10.1002/ajb2.16141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Species in Thismiaceae can no longer photosynthesize and instead obtain carbon from soil fungi. Here we infer Thismiaceae phylogeny using plastid genome data and characterize the molecular evolution of this genome. METHODS We assembled five Thismiaceae plastid genomes from genome skimming data, adding to previously published data for phylogenomic inference. We investigated plastid-genome structural changes, considering locally colinear blocks (LCBs). We also characterized possible shifts in selection pressure in retained genes by considering changes in the ratio of nonsynonymous to synonymous changes (ω). RESULTS Thismiaceae experienced two major pulses of gene loss around the early diversification of the family, with subsequent scattered gene losses across descendent lineages. In addition to massive size reduction, Thismiaceae plastid genomes experienced occasional inversions, and there were likely two independent losses of the plastid inverted repeat (IR) region. Retained plastid genes remain under generally strong purifying selection (ω << 1), with significant and sporadic weakening or strengthening in several instances. The bifunctional trnE-UUC gene of Thismia huangii may retain a secondary role in heme biosynthesis, despite a probable loss of functionality in protein translation. Several cis-spliced group IIA introns have been retained, despite the loss of the plastid intron maturase, matK. CONCLUSIONS We infer that most gene losses in Thismiaceae occurred early and rapidly, following the initial loss of photosynthesis in its stem lineage. As a species-rich, fully mycoheterotrophic lineage, Thismiaceae provide a model system for uncovering the unique and divergent ways in which plastid genomes evolve in heterotrophic plants.
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Affiliation(s)
- Natalie Garrett
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - Nathaniel Klimpert
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | | | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Sciencepark 904, 1098, XH, Amsterdam, The Netherlands
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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Ceriotti LF, Gatica-Soria L, Sanchez-Puerta MV. Cytonuclear coevolution in a holoparasitic plant with highly disparate organellar genomes. PLANT MOLECULAR BIOLOGY 2022; 109:673-688. [PMID: 35359176 DOI: 10.1007/s11103-022-01266-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Contrasting substitution rates in the organellar genomes of Lophophytum agree with the DNA repair, replication, and recombination gene content. Plastid and nuclear genes whose products form multisubunit complexes co-evolve. The organellar genomes of the holoparasitic plant Lophophytum (Balanophoraceae) show disparate evolution. In the plastid, the genome has been severely reduced and presents a > 85% AT content, while in the mitochondria most protein-coding genes have been replaced by homologs acquired by horizontal gene transfer (HGT) from their hosts (Fabaceae). Both genomes carry genes whose products form multisubunit complexes with those of nuclear genes, creating a possible hotspot of cytonuclear coevolution. In this study, we assessed the evolutionary rates of plastid, mitochondrial and nuclear genes, and their impact on cytonuclear evolution of genes involved in multisubunit complexes related to lipid biosynthesis and proteolysis in the plastid and those in charge of the oxidative phosphorylation in the mitochondria. Genes from the plastid and the mitochondria (both native and foreign) of Lophophytum showed extremely high and ordinary substitution rates, respectively. These results agree with the biased loss of plastid-targeted proteins involved in angiosperm organellar repair, replication, and recombination machinery. Consistent with the high rate of evolution of plastid genes, nuclear-encoded subunits of plastid complexes showed disproportionate increases in non-synonymous substitution rates, while those of the mitochondrial complexes did not show different rates than the control (i.e. non-organellar nuclear genes). Moreover, the increases in the nuclear-encoded subunits of plastid complexes were positively correlated with the level of physical interaction they possess with the plastid-encoded ones. Overall, these results suggest that a structurally-mediated compensatory factor may be driving plastid-nuclear coevolution in Lophophytum, and that mito-nuclear coevolution was not altered by HGT.
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Affiliation(s)
- Luis F Ceriotti
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - Leonardo Gatica-Soria
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina.
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Gene Losses and Plastome Degradation in the Hemiparasitic Species Plicosepalus acaciae and Plicosepalus curviflorus: Comparative Analyses and Phylogenetic Relationships among Santalales Members. PLANTS 2022; 11:plants11141869. [PMID: 35890506 PMCID: PMC9317152 DOI: 10.3390/plants11141869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/18/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
The Plicosepalus genus includes hemiparasitic mistletoe and belongs to the Loranthaceae family, and it has several medicinal uses. In the present study, we sequenced the complete plastomes of two species, Plicosepalus acaciae and Plicosepalus curviflorus, and compared them with the plastomes of photosynthetic species (hemiparasites) and nonphotosynthetic species (holoparasites) in the order Santalales. The complete chloroplast genomes of P. acaciae and P. curviflorus are circular molecules with lengths of 120,181 bp and 121,086 bp, respectively, containing 106 and 108 genes and 63 protein-coding genes, including 25 tRNA and 4 rRNA genes for each species. We observed a reduction in the genome size of P. acaciae and P. curviflorus and the loss of certain genes, although this reduction was less than that in the hemiparasite and holoparasitic cp genomes of the Santalales order. Phylogenetic analysis supported the taxonomic state of P. acaciae and P. curviflorus as members of the family Loranthaceae and tribe Lorantheae; however, the taxonomic status of certain tribes of Loranthaceae must be reconsidered and the species that belong to it must be verified. Furthermore, available chloroplast genome data of parasitic plants could help to strengthen efforts in weed management and encourage biotechnology research to improve host resistance.
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Gatica-Soria LM, Ceriotti LF, Garcia LE, Virginia Sanchez-Puerta M. Native and foreign mitochondrial and nuclear encoded proteins conform the OXPHOS complexes of a holoparasitic plant. Gene 2022; 817:146176. [PMID: 35031426 DOI: 10.1016/j.gene.2021.146176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 12/31/2022]
Abstract
The intimate contact between the holoparasitic plant Lophophytum mirabile (Balanophoraceae) and its host plant (Fabaceae) facilitates the exchange of genetic information, increasing the frequency of horizontal gene transfer (HGT). Lophophytum stands out because it acquired a large number of mitochondrial genes (greater than 20) from its legume host that replaced the majority of the native homologs. These foreign genes code for proteins that form multisubunit enzyme complexes, such as those in the oxidative phosphorylation system (OXPHOS) and cytochrome c maturation (ccm) system, together with dozens of nuclear-encoded subunits. However, the existence and the origin of the nuclear subunits that form the major part of the OXPHOS and ccm system in Lophophytum remain unknown. It was proposed that nuclear-encoding genes whose products interact with foreign mitochondrial proteins are also foreign, minimizing the incompatibilities that could arise in the assembly and functioning of these multiprotein complexes. We identified a nearly complete set of OXPHOS and ccm system subunits evolving under selective constraints in the transcriptome of Lophophytum, indicating that OXPHOS is functional and resembles that of free-living angiosperms. Maximum Likelihood phylogenetic analyses revealed a single case of HGT in the nuclear genes, which results in mosaic OXPHOS and ccm system in Lophophytum. These observations raise new questions about the evolution and physiology of this parasitic plant. A putative case of cooperation between two foreign (one mitochondrial and one nuclear) genes is presented.
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Affiliation(s)
- Leonardo M Gatica-Soria
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB Mendoza, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina
| | - Luis F Ceriotti
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB Mendoza, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina
| | - Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB Mendoza, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB Mendoza, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina.
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Smith DR. Genome evolution: Minicircular mtDNA and unusual heteroplasmy in a parasitic plant. Curr Biol 2022; 32:R86-R89. [DOI: 10.1016/j.cub.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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The minicircular and extremely heteroplasmic mitogenome of the holoparasitic plant Rhopalocnemis phalloides. Curr Biol 2021; 32:470-479.e5. [PMID: 34906352 DOI: 10.1016/j.cub.2021.11.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/25/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022]
Abstract
The plastid and nuclear genomes of parasitic plants exhibit deeply altered architectures,1-13 whereas the few examined mitogenomes range from deeply altered to conventional.14-20 To provide further insight on mitogenome evolution in parasitic plants, we report the highly modified mitogenome of Rhopalocnemis phalloides, a holoparasite in Balanophoraceae. Its mitogenome is uniquely arranged in 21 minicircular chromosomes that vary in size from 4,949 to 7,861 bp, with a total length of only 130,713 bp. All chromosomes share an identical 896 bp conserved region, with a large stem-loop that acts as the origin of replication, flanked on each side by hypervariable and semi-conserved regions. Similar minicircular structures with shared and unique regions have been observed in parasitic animals and free-living protists,21-24 suggesting convergent structural evolution. Southern blots confirm both the minicircular structure and the replication origin of the mitochondrial chromosomes. PacBio reads provide evidence for chromosome recombination and rolling-circle replication for the R. phalloides mitogenome. Despite its small size, the mitogenome harbors a typical set of genes and introns within the unique regions of each chromosome, yet introns are the smallest among seed plants and ferns. The mitogenome also exhibits extreme heteroplasmy, predominantly involving short indels and more complex variants, many of which cause potential loss-of-function mutations for some gene copies. All heteroplasmic variants are transcribed, and functional and nonfunctional protein-coding variants are spliced and RNA edited. Our findings offer a unique perspective into how mitogenomes of parasitic plants can be deeply altered and shed light on plant mitogenome replication.
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Schelkunov MI, Nuraliev MS, Logacheva MD. Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives. PeerJ 2021; 9:e12106. [PMID: 34540375 PMCID: PMC8415285 DOI: 10.7717/peerj.12106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 08/11/2021] [Indexed: 12/02/2022] Open
Abstract
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.
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Affiliation(s)
- Mikhail I Schelkunov
- Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute for Information Transmission Problems, Moscow, Russia
| | - Maxim S Nuraliev
- Faculty of Biology, Moscow State University, Moscow, Russia.,Joint Russian-Vietnamese Tropical Scientific and Technological Center, Hanoi, Vietnam
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Lyko P, Wicke S. Genomic reconfiguration in parasitic plants involves considerable gene losses alongside global genome size inflation and gene births. PLANT PHYSIOLOGY 2021; 186:1412-1423. [PMID: 33909907 PMCID: PMC8260112 DOI: 10.1093/plphys/kiab192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/13/2021] [Indexed: 05/02/2023]
Abstract
Parasitic plant genomes and transcriptomes reveal numerous genetic innovations, the functional-evolutionary relevance and roles of which open unprecedented research avenues.
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Affiliation(s)
- Peter Lyko
- Institute for Biology, Humboldt-University of Berlin, Germany
| | - Susann Wicke
- Institute for Biology, Humboldt-University of Berlin, Germany
- Author for communication:
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Ceriotti LF, Roulet ME, Sanchez-Puerta MV. Plastomes in the holoparasitic family Balanophoraceae: Extremely high AT content, severe gene content reduction, and two independent genetic code changes. Mol Phylogenet Evol 2021; 162:107208. [PMID: 34029719 DOI: 10.1016/j.ympev.2021.107208] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 12/29/2022]
Abstract
The transition to a heterotrophic lifestyle in angiosperms is characterized by convergent evolutionary changes. Plastid genome remodeling includes dramatic functional and physical reductions with the highest degrees observed in fully heterotrophic plants. Genes related to photosynthesis are generally absent or pseudogenized, while a few genes related to other metabolic processes that take place within the plastid are almost invariably maintained. The family Balanophoraceae consists of root holoparasites that present reduced plastid genomes with an extraordinarily elevated AT content and the single genetic code change ever documented in land plant plastomes (the stop codon TAG now codes for tryptophan). Here, we studied the plastomes of Lophophytum leandri and Ombrophytum subterraneum (Balanophoraceae) that showed the remarkable absence of the gene trnE, a highly biased nucleotide composition, and an independent genetic code change (the standard stop codon TGA codes for tryptophan). This is the second genetic code change identified in land plant plastomes. Analysis of the transcriptome of Lophophytum indicated that the entire C5 pathway typical of plants is conserved despite the lack of trnE in its plastome. A hypothetical model of plastome evolution in the Balanophoraceae is presented.
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Affiliation(s)
- Luis Federico Ceriotti
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB Chacras de Coria, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina
| | - M Emilia Roulet
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB Chacras de Coria, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB Chacras de Coria, Argentina; Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, M5502JMA Mendoza, Argentina.
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13
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Yudina SV, Schelkunov MI, Nauheimer L, Crayn D, Chantanaorrapint S, Hroneš M, Sochor M, Dančák M, Mar SS, Luu HT, Nuraliev MS, Logacheva MD. Comparative Analysis of Plastid Genomes in the Non-photosynthetic Genus Thismia Reveals Ongoing Gene Set Reduction. FRONTIERS IN PLANT SCIENCE 2021; 12:602598. [PMID: 33796122 PMCID: PMC8009136 DOI: 10.3389/fpls.2021.602598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/22/2021] [Indexed: 05/14/2023]
Abstract
Heterotrophic plants provide intriguing examples of reductive evolution. This is especially evident in the reduction of their plastid genomes, which can potentially proceed toward complete genome loss. Several milestones at the beginning of this path of degradation have been described; however, little is known about the latest stages of plastome reduction. Here we analyze a diversity of plastid genomes in a set of closely related non-photosynthetic plants. We demonstrate how a gradual loss of genes shapes the miniaturized plastomes of these plants. The subject of our study, the genus Thismia, represents the mycoheterotrophic monocot family Thismiaceae, a group that may have experienced a very ancient (60-80 mya) transition to heterotrophy. In all 18 species examined, the plastome is reduced to 14-18 kb and is highly AT-biased. The most complete observed gene set includes accD, seven ribosomal protein genes, three rRNA, and two tRNA genes. Different clades of Thismia have undergone further gene loss (complete absence or pseudogenization) compared to this set: in particular, we report two independent losses of rps2 and rps18.
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Affiliation(s)
- Sophia V. Yudina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems, Moscow, Russia
- Joint Russian-Vietnamese Tropical Scientific and Technological Center, Hanoi, Vietnam
| | - Mikhail I. Schelkunov
- Institute for Information Transmission Problems, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Sahut Chantanaorrapint
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
| | - Michal Hroneš
- Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Michal Sochor
- Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Olomouc, Czechia
| | - Martin Dančák
- Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | | | - Hong Truong Luu
- Southern Institute of Ecology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Maxim S. Nuraliev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Joint Russian-Vietnamese Tropical Scientific and Technological Center, Hanoi, Vietnam
| | - Maria D. Logacheva
- Institute for Information Transmission Problems, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
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14
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Roulet ME, Garcia LE, Gandini CL, Sato H, Ponce G, Sanchez-Puerta MV. Multichromosomal structure and foreign tracts in the Ombrophytum subterraneum (Balanophoraceae) mitochondrial genome. PLANT MOLECULAR BIOLOGY 2020; 103:623-638. [PMID: 32440763 DOI: 10.1007/s11103-020-01014-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Horizontal gene transfer (HGT) is frequent in parasitic plant mitochondria as a result of vascular connections established in host-parasite relationships. Recent studies of the holoparasitic plant Lophophytum mirabile (Balanophoraceae) revealed the unprecedented acquisition of a large amount of mitochondrial sequences from its legume host. We focused on a close relative, the generalist holoparasite Ombrophytum subterraneum, to examine the incidence of HGT events in the mitochondrial genome (mtDNA). The mtDNA of O. subterraneum assembles into 54 circular chromosomes, only 34 of which contain the 51 full-length coding regions. Numerous foreign tracts (totaling almost 100 kb, ~ 14% of the mtDNA), including 12 intact genes, were acquired by HGT from the Asteraceae hosts. Nine chromosomes concentrate most of those regions and eight are almost entirely foreign. Native homologs of each foreign gene coexist in the mtDNA and are potentially functional. A large proportion of shorter regions were related to the Fabaceae (a total of ~ 110 kb, 15.4%), some of which were shared with L. mirabile. We also found evidence of foreign sequences donated by angiosperm lineages not reported as hosts (Apocynaceae, Euphorbiaceae, Lamiaceae, and Malvales). We propose an evolutionary hypothesis that involves ancient transfers from legume hosts in the common ancestor of Ombrophytum and Lophophytum followed by more recent transfer events in L. mirabile. Besides, the O. subterraneum mtDNA was also subjected to additional HGT events from diverse angiosperm lineages, including large and recent transfers from the Asteraceae, and also from Lamiaceae.
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Affiliation(s)
- M Emilia Roulet
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Laura E Garcia
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - Carolina L Gandini
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
| | - Hector Sato
- Facultad de Ciencias Agrarias, Universidad Nacional de Jujuy, Cátedra de Botánica General-Herbario JUA, Alberdi 47, 4600, San Salvador de Jujuy, Jujuy, Argentina
| | - Gabriela Ponce
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina.
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15
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Chen X, Fang D, Wu C, Liu B, Liu Y, Sahu SK, Song B, Yang S, Yang T, Wei J, Wang X, Zhang W, Xu Q, Wang H, Yuan L, Liao X, Chen L, Chen Z, Yuan F, Chang Y, Lu L, Yang H, Wang J, Xu X, Liu X, Wicke S, Liu H. Comparative Plastome Analysis of Root- and Stem-Feeding Parasites of Santalales Untangle the Footprints of Feeding Mode and Lifestyle Transitions. Genome Biol Evol 2020; 12:3663-3676. [PMID: 31845987 PMCID: PMC6953812 DOI: 10.1093/gbe/evz271] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2019] [Indexed: 12/17/2022] Open
Abstract
In plants, parasitism triggers the reductive evolution of plastid genomes (plastomes). To disentangle the molecular evolutionary associations between feeding on other plants below- or aboveground and general transitions from facultative to obligate parasitism, we analyzed 34 complete plastomes of autotrophic, root- and stem-feeding hemiparasitic, and holoparasitic Santalales. We observed inexplicable losses of housekeeping genes and tRNAs in hemiparasites and dramatic genomic reconfiguration in holoparasitic Balanophoraceae, whose plastomes have exceptionally low GC contents. Genomic changes are related primarily to the evolution of hemi- or holoparasitism, whereas the transition from a root- to a stem-feeding mode plays no major role. In contrast, the rate of molecular evolution accelerates in a stepwise manner from autotrophs to root- and then stem-feeding parasites. Already the ancestral transition to root-parasitism coincides with a relaxation of selection in plastomes. Another significant selectional shift in plastid genes occurs as stem-feeders evolve, suggesting that this derived form coincides with trophic specialization despite the retention of photosynthetic capacity. Parasitic Santalales fill a gap in our understanding of parasitism-associated plastome degeneration. We reveal that lifestyle-genome associations unfold interdependently over trophic specialization and feeding mode transitions, where holoparasitic Balanophoraceae provide a system for exploring the functional realms of plastomes.
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Affiliation(s)
- Xiaoli Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Dongming Fang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Chenyu Wu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- BGI-Shenzhen, Shenzhen, China.,Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, China
| | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Bo Song
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Shuai Yang
- BGI-Shenzhen, Shenzhen, China.,School of Basic Medical, Qingdao University, China
| | - Tuo Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jinpu Wei
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xuebing Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Wen Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Qiwu Xu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Huafeng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Langxing Yuan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xuezhu Liao
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lipeng Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ziqiang Chen
- College of Chinese Medicine Materials, Jilin Agricultural University, China
| | - Fu Yuan
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yue Chang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lihua Lu
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Germany†These authors contributed equally to this work
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
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16
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Kim YK, Jo S, Cheon SH, Joo MJ, Hong JR, Kwak M, Kim KJ. Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences. FRONTIERS IN PLANT SCIENCE 2020; 11:22. [PMID: 32153600 PMCID: PMC7047749 DOI: 10.3389/fpls.2020.00022] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/10/2020] [Indexed: 05/08/2023]
Abstract
In order to understand the evolution of the orchid plastome, we annotated and compared 124 complete plastomes of Orchidaceae representing all the major lineages in their structures, gene contents, gene rearrangements, and IR contractions/expansions. Forty-two of these plastomes were generated from the corresponding author's laboratory, and 24 plastomes-including nine genera (Amitostigma, Bulbophyllum, Dactylorhiza, Dipodium, Galearis, Gymnadenia, Hetaeria, Oreorchis, and Sedirea)-are new in this study. All orchid plastomes, except Aphyllorchis montana, Epipogium aphyllum, and Gastrodia elata, have a quadripartite structure consisting of a large single copy (LSC), two inverted repeats (IRs), and a small single copy (SSC) region. The IR region was completely lost in the A. montana and G. elata plastomes. The SSC is lost in the E. aphyllum plastome. The smallest plastome size was 19,047 bp, in E. roseum, and the largest plastome size was 178,131 bp, in Cypripedium formosanum. The small plastome sizes are primarily the result of gene losses associated with mycoheterotrophic habitats, while the large plastome sizes are due to the expansion of noncoding regions. The minimal number of common genes among orchid plastomes to maintain minimal plastome activity was 15, including the three subunits of rpl (14, 16, and 36), seven subunits of rps (2, 3, 4, 7, 8, 11, and 14), three subunits of rrn (5, 16, and 23), trnC-GCA, and clpP genes. Three stages of gene loss were observed among the orchid plastomes. The first was ndh gene loss, which is widespread in Apostasioideae, Vanilloideae, Cypripedioideae, and Epidendroideae, but rare in the Orchidoideae. The second stage was the loss of photosynthetic genes (atp, pet, psa, and psb) and rpo gene subunits, which are restricted to Aphyllorchis, Hetaeria, Hexalectris, and some species of Corallorhiza and Neottia. The third stage was gene loss related to prokaryotic gene expression (rpl, rps, trn, and others), which was observed in Epipogium, Gastrodia, Lecanorchis, and Rhizanthella. In addition, an intermediate stage between the second and third stage was observed in Cyrtosia (Vanilloideae). The majority of intron losses are associated with the loss of their corresponding genes. In some orchid taxa, however, introns have been lost in rpl16, rps16, and clpP(2) without their corresponding gene being lost. A total of 104 gene rearrangements were counted when comparing 116 orchid plastomes. Among them, many were concentrated near the IRa/b-SSC junction area. The plastome phylogeny of 124 orchid species confirmed the relationship of {Apostasioideae [Vanilloideae (Cypripedioideae (Orchidoideae, Epidendroideae))]} at the subfamily level and the phylogenetic relationships of 17 tribes were also established. Molecular clock analysis based on the whole plastome sequences suggested that Orchidaceae diverged from its sister family 99.2 mya, and the estimated divergence times of five subfamilies are as follows: Apostasioideae (79.91 mya), Vanilloideae (69.84 mya), Cypripedioideae (64.97 mya), Orchidoideae (59.16 mya), and Epidendroideae (59.16 mya). We also released the first nuclear ribosomal (nr) DNA unit (18S-ITS1-5.8S-ITS2-28S-NTS-ETS) sequences for the 42 species of Orchidaceae. Finally, the phylogenetic tree based on the nrDNA unit sequences is compared to the tree based on the 42 identical plastome sequences, and the differences between the two datasets are discussed in this paper.
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Affiliation(s)
- Young-Kee Kim
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Sangjin Jo
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Se-Hwan Cheon
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Min-Jung Joo
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Ja-Ram Hong
- Division of Life Sciences, Korea University, Seoul, South Korea
| | - Myounghai Kwak
- Department of Plant Resources, National Institute of Biological Resources, Incheon, South Korea
| | - Ki-Joong Kim
- Division of Life Sciences, Korea University, Seoul, South Korea
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17
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Nie L, Cui Y, Wu L, Zhou J, Xu Z, Li Y, Li X, Wang Y, Yao H. Gene Losses and Variations in Chloroplast Genome of Parasitic Plant Macrosolen and Phylogenetic Relationships within Santalales. Int J Mol Sci 2019; 20:E5812. [PMID: 31752332 PMCID: PMC6888684 DOI: 10.3390/ijms20225812] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/15/2019] [Accepted: 11/17/2019] [Indexed: 11/16/2022] Open
Abstract
Macrosolen plants are parasitic shrubs, several of which are important medicinal plants, that are used as folk medicine in some provinces of China. However, reports on Macrosolen are limited. In this study, the complete chloroplast genome sequences of Macrosolen cochinchinensis, Macrosolen tricolor and Macrosolen bibracteolatus are reported. The chloroplast genomes were sequenced by Illumina HiSeq X. The length of the chloroplast genomes ranged from 129,570 bp (M. cochinchinensis) to 126,621 bp (M. tricolor), with a total of 113 genes, including 35 tRNA, eight rRNA, 68 protein-coding genes, and two pseudogenes (ycf1 and rpl2). The simple sequence repeats are mainly comprised of A/T mononucleotide repeats. Comparative genome analyses of the three species detected the most divergent regions in the non-coding spacers. Phylogenetic analyses using maximum parsimony and maximum likelihood strongly supported the idea that Loranthaceae and Viscaceae are monophyletic clades. The data obtained in this study are beneficial for further investigations of Macrosolen in respect to evolution and molecular identification.
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Affiliation(s)
- Liping Nie
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Yingxian Cui
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Liwei Wu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Jianguo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Yonghua Li
- College of Pharmacy, Guangxi University of Traditional Chinese Medicine, Nanning 530200, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
| | - Yu Wang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; (L.N.); (Y.C.); (L.W.); (J.Z.); (Z.X.); (Y.W.)
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing 100193, China
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