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Wu H, Li DZ, Ma PF. Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales. BMC Biol 2024; 22:97. [PMID: 38679718 PMCID: PMC11057118 DOI: 10.1186/s12915-024-01890-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. RESULTS We acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern. Extensive variation including the largest one in monocots with 225,293 bp in size, heterogeneous GC content, and a wide variety of gene duplication and loss were revealed. Moreover, rare occurrences of three inverted repeat (IR) copies in angiosperms and one IR loss were observed, accompanied by short IR (sIR) and small direct repeat (DR). Widespread structural heteroplasmy, diversified inversions, and unusual genomic rearrangements all appeared in Poales, occasionally within a single species. Extensive repeats in the plastomes were found to be positively correlated with the observed inversions and rearrangements. The variation all showed a "small-large-moderate" trend along the evolution of Poales, as well as for the sequence substitution rate. Finally, we found some positively selected genes, mainly in C4 lineages, while the closely related lineages of those experiencing gene loss tended to have undergone more relaxed purifying selection. CONCLUSIONS The variation of plastomes in Poales may be related to its successful diversification into diverse habitats and multiple photosynthetic pathway transitions. Our order-scale analyses revealed unusual evolutionary scenarios for plastomes in the photoautotrophic order of Poales and provided new insights into the plastome evolution in angiosperms as a whole.
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Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Hartenstein M, Albert M, Krause K. The plant vampire diaries: a historic perspective on Cuscuta research. J Exp Bot 2023; 74:2944-2955. [PMID: 36882965 DOI: 10.1093/jxb/erad082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/01/2023] [Indexed: 05/21/2023]
Abstract
The angiosperm genus Cuscuta lives as an almost achlorophyllous root- and leafless holoparasite and has therefore occupied scientists for more than a century. The 'evolution' of Cuscuta research started with early studies that established the phylogenetic framework for this unusual genus. It continued to produce groundbreaking cytological, morphological, and physiological insight throughout the second half of the 20th century and culminated in the last two decades in exciting discoveries regarding the molecular basis of Cuscuta parasitism that were facilitated by the modern 'omics' tools and traceable fluorescent marker technologies of the 21st century. This review will show how present activities are inspired by those past breakthroughs. It will describe significant milestones and recurring themes of Cuscuta research and connect these to the remaining as well as newly evolving questions and future directions in this research field that is expected to sustain its strong growth in the future.
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Affiliation(s)
- Maleen Hartenstein
- Department of Biology, Molecular Plant Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Markus Albert
- Department of Biology, Molecular Plant Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Kirsten Krause
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
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Cai L. Rethinking convergence in plant parasitism through the lens of molecular and population genetic processes. Am J Bot 2023; 110:e16174. [PMID: 37154532 DOI: 10.1002/ajb2.16174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 05/10/2023]
Abstract
The autotrophic lifestyle of photosynthetic plants has profoundly shaped their body plan, physiology, and gene repertoire. Shifts to parasitism and heterotrophy have evolved at least 12 times in more than 4000 species, and this transition has consequently left major evolutionary footprints among these parasitic lineages. Features that are otherwise rare at the molecular level and beyond have evolved repetitively, including reduced vegetative bodies, carrion-mimicking during reproduction, and the incorporation of alien genetic material. Here, I propose an integrated conceptual model, referred to as the funnel model, to define the general evolutionary trajectory of parasitic plants and provide a mechanistic explanation for their convergent evolution. This model connects our empirical understanding of gene regulatory networks in flowering plants with classical theories of molecular and population genetics. It emphasizes that the cascading effects brought about by the loss of photosynthesis may be a major force constraining the physiological capacity of parasitic plants and shaping their genomic landscapes. Here I review recent studies on the anatomy, physiology, and genetics of parasitic plants that lend support to this photosynthesis-centered funnel model. Focusing on nonphotosynthetic holoparasites, I elucidate how they may inevitably reach an evolutionary terminal status (i.e., extinction) and highlight the utility of a general, explicitly described and falsifiable model for future studies of parasitic plants.
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Affiliation(s)
- Liming Cai
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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Banerjee A, Stefanović S. A comparative study across the parasitic plants of Cuscuta subgenus Grammica (Convolvulaceae) reveals a possible loss of the plastid genome in its section Subulatae. Planta 2023; 257:66. [PMID: 36826697 DOI: 10.1007/s00425-023-04099-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Most species in Cuscuta subgenus Grammica retain many photosynthesis-related plastid genes, generally under purifying selection. A group of holoparasitic species in section Subulatae may have lost their plastid genomes entirely. The c. 153 species of plants belonging to Cuscuta subgenus Grammica are all obligate stem parasites. However, some have completely lost the ability to conduct photosynthesis while others retain photosynthetic machinery and genes. The plastid genome that primarily encodes key photosynthesis genes functions as a bellwether for how reliant plants are on primary production. This research assembles and analyses 17 plastomes across Cuscuta subgenus Grammica with the aim of characterizing the state of the plastome in each of its sections. By comparing the structure and content of plastid genomes across the subgenus, as well as by quantifying the selection acting upon each gene, we reconstructed the patterns of plastome change within the phylogenetic context for this group. We found that species in 13 of the 15 sections that comprise Grammica retain the bulk of plastid photosynthesis genes and are thus hemiparasitic. The complete loss of photosynthesis can be traced to two clades: the entire section Subulatae and a complex of three species within section Ceratophorae. We were unable to recover any significant plastome sequences from section Subulatae, suggesting that plastomes in these species are either drastically reduced or lost entirely.
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Affiliation(s)
- Arjan Banerjee
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada.
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
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Anderson BM, Krause K, Petersen G. Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmF C genes. BMC Genomics 2021; 22:816. [PMID: 34772334 DOI: 10.1186/s12864-021-08105-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/19/2021] [Indexed: 01/30/2023] Open
Abstract
Background The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. Conclusions The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08105-z.
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García MA, Stefanović S, Weiner C, Olszewski M, Costea M. Cladogenesis and reticulation in Cuscuta sect. Denticulatae (Convolvulaceae). ORG DIVERS EVOL 2018; 18:383-398. [PMID: 30930685 PMCID: PMC6405177 DOI: 10.1007/s13127-018-0383-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 10/11/2018] [Indexed: 01/08/2023]
Abstract
As traditionally circumscribed, Cuscuta sect. Denticulatae is a group of three parasitic plant species native to the deserts of Western USA (Cuscuta denticulata, Cuscuta nevadensis) and the central region of Baja California, Mexico (Cuscuta veatchii). Molecular phylogenetic studies confirmed the monophyly of this group and suggested that the disjunct C. veatchii is a hybrid between the other two species. However, the limited sampling left the possibility of alternative biological and methodological explanations. We expanded our sampling to multiple individuals of all the species collected from across their entire geographical ranges. Sequence data from the nuclear and plastid regions were used to reconstruct the phylogeny and find out if the topological conflict was maintained. We obtained karyotype information from multiple individuals, investigated the morphological variation of the group thorough morphometric analyses, and compiled data on ecology, host range, and geographical distribution. Our results confirmed that C. veatchii is an allotetraploid. Furthermore, we found previously unknown autotetraploid population of C. denticulata, and we describe a new hybrid species, Cuscuta psorothamnensis. We suggest that this newly discovered natural hybrid is resulting from an independent (and probably more recent) hybridization event between the same diploid parental species as those of C. veatchii. All the polyploids showed host shift associated with hybridization and/or polyploidy and are found growing on hosts that are rarely or never frequented by their diploid progenitors. The great potential of this group as a model to study host shift in parasitic plants associated with recurrent allopolyploidy is discussed.
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Affiliation(s)
- Miguel A García
- 1Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6 Canada.,2Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE UK
| | - Saša Stefanović
- 1Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6 Canada
| | - Catherine Weiner
- 3Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L3C5 Canada
| | - Magdalena Olszewski
- 3Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L3C5 Canada
| | - Mihai Costea
- 3Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L3C5 Canada
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Lee H, Golicz AA, Bayer PE, Severn-Ellis AA, Chan CKK, Batley J, Kendrick GA, Edwards D. Genomic comparison of two independent seagrass lineages reveals habitat-driven convergent evolution. J Exp Bot 2018; 69:3689-3702. [PMID: 29912443 PMCID: PMC6022596 DOI: 10.1093/jxb/ery147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 04/12/2018] [Indexed: 05/06/2023]
Abstract
Seagrasses are marine angiosperms that live fully submerged in the sea. They evolved from land plant ancestors, with multiple species representing at least three independent return-to-the-sea events. This raises the question of whether these marine angiosperms followed the same adaptation pathway to allow them to live and reproduce under the hostile marine conditions. To compare the basis of marine adaptation between seagrass lineages, we generated genomic data for Halophila ovalis and compared this with recently published genomes for two members of Zosteraceae, as well as genomes of five non-marine plant species (Arabidopsis, Oryza sativa, Phoenix dactylifera, Musa acuminata, and Spirodela polyrhiza). Halophila and Zosteraceae represent two independent seagrass lineages separated by around 30 million years. Genes that were lost or conserved in both lineages were identified. All three species lost genes associated with ethylene and terpenoid biosynthesis, and retained genes related to salinity adaptation, such as those for osmoregulation. In contrast, the loss of the NADH dehydrogenase-like complex is unique to H. ovalis. Through comparison of two independent return-to-the-sea events, this study further describes marine adaptation characteristics common to seagrass families, identifies species-specific gene loss, and provides molecular evidence for convergent evolution in seagrass lineages.
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Affiliation(s)
- HueyTyng Lee
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
- School of Biological Sciences, University of Western Australia, WA, Australia
| | - Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, WA, Australia
| | | | | | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, WA, Australia
| | - Gary A Kendrick
- School of Biological Sciences, University of Western Australia, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, WA, Australia
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Sun SS, Fu PC, Zhou XJ, Cheng YW, Zhang FQ, Chen SL, Gao QB. The Complete Plastome Sequences of Seven Species in Gentiana sect. Kudoa (Gentianaceae): Insights Into Plastid Gene Loss and Molecular Evolution. Front Plant Sci 2018; 9:493. [PMID: 29765380 PMCID: PMC5938401 DOI: 10.3389/fpls.2018.00493] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 04/03/2018] [Indexed: 05/15/2023]
Abstract
The chloroplast (cp) genome is useful in the study of phylogenomics, molecular dating, and molecular evolution. Gentiana sect. Kudoa is a predominantly alpine flowering plant that is valued for its contributions to medicine, ecology, and horticulture. Previous evolutionary studies showed that the plastid gene loss pattern and intra-sectional phylogenetics in sect. Kudoa are still unclear. In this study, we compared 11 Gentiana plastomes, including 7 newly sequenced plastomes from sect. Kudoa, to represent its three serious: ser. Ornatae, ser. Verticillatae, and ser. Monanthae. The cp genome sizes of the seven species ranged from 137,278 to 147,156 bp. The plastome size variation mainly occurred in the small single-copy and long single-copy regions rather than the inverted repeat regions. Compared with sect. Cruciata, the plastomes in ser. Ornatae and ser. Verticillatae had lost approximately 11 kb of sequences containing 11 ndh genes. Conversely, far fewer losses were observed in ser. Monanthae. The phylogenetic tree revealed that sect. Kudoa was not monophyletic and that ser. Monanthae was more closely related to other sections rather than sect. Kudoa. The molecular dating analysis indicated that ser. Monanthae and sect. Kudoa diverged around 8.23 Ma. In ser. Ornatae and ser. Verticillatae, the divergence occurred at around 0.07-1.78 Ma. The nucleotide diversity analysis indicated that the intergenic regions trnH-psbA, trnK-trnQ, ycf3-trnS and rpl32-trnL constituted divergence hotspots in both sect. Kudoa and Gentiana, and would be useful for future phylogenetic and population genetic studies.
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Affiliation(s)
- Shan-Shan Sun
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Peng-Cheng Fu
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Xiao-Jun Zhou
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Yan-Wei Cheng
- College of Life Science, Luoyang Normal University, Luoyang, China
| | - Fa-Qi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
- *Correspondence: Qing-Bo Gao,
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Fu PC, Zhang YZ, Geng HM, Chen SL. The complete chloroplast genome sequence of Gentiana lawrencei var . farreri (Gentianaceae) and comparative analysis with its congeneric species. PeerJ 2016; 4:e2540. [PMID: 27703869 PMCID: PMC5047142 DOI: 10.7717/peerj.2540] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/07/2016] [Indexed: 01/06/2023] Open
Abstract
Background The chloroplast (cp) genome is useful in plant systematics, genetic diversity analysis, molecular identification and divergence dating. The genus Gentiana contains 362 species, but there are only two valuable complete cp genomes. The purpose of this study is to report the characterization of complete cp genome of G. lawrencei var. farreri, which is endemic to the Qinghai-Tibetan Plateau (QTP). Methods Using high throughput sequencing technology, we got the complete nucleotide sequence of the G. lawrencei var. farreri cp genome. The comparison analysis including genome difference and gene divergence was performed with its congeneric species G. straminea. The simple sequence repeats (SSRs) and phylogenetics were studied as well. Results The cp genome of G. lawrencei var. farreri is a circular molecule of 138,750 bp, containing a pair of 24,653 bp inverted repeats which are separated by small and large single-copy regions of 11,365 and 78,082 bp, respectively. The cp genome contains 130 known genes, including 85 protein coding genes (PCGs), eight ribosomal RNA genes and 37 tRNA genes. Comparative analyses indicated that G. lawrencei var. farreri is 10,241 bp shorter than its congeneric species G. straminea. Four large gaps were detected that are responsible for 85% of the total sequence loss. Further detailed analyses revealed that 10 PCGs were included in the four gaps that encode nine NADH dehydrogenase subunits. The cp gene content, order and orientation are similar to those of its congeneric species, but with some variation among the PCGs. Three genes, ndhB, ndhF and clpP, have high nonsynonymous to synonymous values. There are 34 SSRs in the G. lawrencei var. farreri cp genome, of which 25 are mononucleotide repeats: no dinucleotide repeats were detected. Comparison with the G. straminea cp genome indicated that five SSRs have length polymorphisms and 23 SSRs are species-specific. The phylogenetic analysis of 48 PCGs from 12 Gentianales taxa cp genomes clearly identified three clades, which indicated the potential of cp genomes in phylogenetics. Discussion The “missing” sequence of G. lawrencei var. farreri mainly consistent of ndh genes which could be dispensable under chilling-stressed conditions in the QTP. The complete cp genome sequence of G. lawrencei var. farreri provides intragenic information that will contribute to genetic and phylogenetic research in the Gentianaceae.
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Affiliation(s)
- Peng-Cheng Fu
- College of Life Science, Luoyang Normal University , Luoyang , China
| | - Yan-Zhao Zhang
- College of Life Science, Luoyang Normal University , Luoyang , China
| | - Hui-Min Geng
- College of Life Science, Luoyang Normal University , Luoyang , China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining , China
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Abstract
Oxygenic photosynthesis converts solar energy into chemical energy in the chloroplasts of plants and microalgae as well as in prokaryotic cyanobacteria using a complex machinery composed of two photosystems and both membrane-bound and soluble electron carriers. In addition to the major photosynthetic complexes photosystem II (PSII), cytochrome b6f, and photosystem I (PSI), chloroplasts also contain minor components, including a well-conserved type I NADH dehydrogenase (NDH-1) complex that functions in close relationship with photosynthesis and likewise originated from the endosymbiotic cyanobacterial ancestor. Some plants and many microalgal species have lost plastidial ndh genes and a functional NDH-1 complex during evolution, and studies have suggested that a plastidial type II NADH dehydrogenase (NDH-2) complex substitutes for the electron transport activity of NDH-1. However, although NDH-1 was initially thought to use NAD(P)H as an electron donor, recent research has demonstrated that both chloroplast and cyanobacterial NDH-1s oxidize reduced ferredoxin. We discuss more recent findings related to the biochemical composition and activity of NDH-1 and NDH-2 in relation to the physiology and regulation of photosynthesis, particularly focusing on their roles in cyclic electron flow around PSI, chlororespiration, and acclimation to changing environments.
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Affiliation(s)
- Gilles Peltier
- Institute of Environmental Biology and Biotechnology, CEA, CNRS, Aix-Marseille University, CEA Cadarache, 13018 Saint-Paul-lès-Durance, France;
| | - Eva-Mari Aro
- Department of Biochemistry, University of Turku, 20014 Turku, Finland;
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Ross TG, Barrett CF, Soto Gomez M, Lam VK, Henriquez CL, Les DH, Davis JI, Cuenca A, Petersen G, Seberg O, Thadeo M, Givnish TJ, Conran J, Stevenson DW, Graham SW. Plastid phylogenomics and molecular evolution of Alismatales. Cladistics 2015; 32:160-178. [DOI: 10.1111/cla.12133] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2015] [Indexed: 11/27/2022] Open
Affiliation(s)
- T. Gregory Ross
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Craig F. Barrett
- Department of Biological Sciences 5151 State University Dr. California State University Los Angeles CA 90032‐8201 USA
| | - Marybel Soto Gomez
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Vivienne K.Y. Lam
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Claudia L. Henriquez
- Evolution, Ecology & Population Biology Division of Biology Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Donald H. Les
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT 06269‐3043 USA
| | - Jerrold I. Davis
- L. H. Bailey Hortorium and Section of Plant Biology Cornell University Ithaca NY 14853 USA
| | - Argelia Cuenca
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | - Gitte Petersen
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | - Ole Seberg
- Natural History Museum of Denmark University of Copenhagen Sølvgade 83 Opg. S DK‐1307 Copenhagen Denmark
| | | | | | - John Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre School of Biological Sciences Benham Bldg DX 650 312 The University of Adelaide Adelaide SA 5005 Australia
| | | | - Sean W. Graham
- Department of Botany 6270 University Boulevard University of British Columbia Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research 6804 Marine Drive SW University of British Columbia Vancouver BC V6T 1Z4 Canada
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12
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Švubová R, Ovečka M, Pavlovič A, Slováková Ľ, Blehová A. Cuscuta europaea plastid apparatus in various developmental stages: localization of THF1 protein. Plant Signal Behav 2013; 8:e24037. [PMID: 23438585 PMCID: PMC3907459 DOI: 10.4161/psb.24037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 02/18/2013] [Indexed: 05/05/2023]
Abstract
It was generally accepted that Cuscuta europaea is mostly adapted to a parasitic lifestyle with no detectable levels of chlorophylls. We found out relatively high level of chlorophylls (Chls a+b) in young developmental stages of dodder. Significant lowering of Chls (a+b) content and increase of carotenoid concentration was typical only for ontogenetically more developed stages. Lower content of photosynthesis-related proteins involved in Chls biosynthesis and in photosystem formation as well as low photochemical activity of PSII indicate that photosynthesis is not the main activity of C. europaea plastids. Previously, it has been shown in other species that the Thylakoid Formation Protein 1 (THF1) is involved in thylakoid membrane differentiation, plant-fungal and plant-bacterial interactions and in sugar signaling with its preferential localization to plastids. Our immunofluorescence localization studies and analyses of haustorial plasma membrane fractions revealed that in addition to plastids, the THF1 protein localizes also to the plasma membrane and plasmodesmata in developing C. europaea haustorium, most abundantly in the digitate cells of the endophyte primordium. These results are supported by western blot analysis, documenting the highest levels of the THF1 protein in "get together" tissues of dodder and tobacco. Based on the fact that photosynthesis is not a typical process in the C. europaea haustorium and on the extra-plastidial localization pattern of the THF1, our data support rather other functions of this protein in the complex relationship between C. europaea and its host.
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Affiliation(s)
- Renáta Švubová
- Department of Plant Physiology; Faculty of Natural Sciences; Comenius University in Bratislava; Bratislava, Slovak Republic
| | - Miroslav Ovečka
- Institute of Botany; Slovak Academy of Sciences; Bratislava, Slovak Republic
- Centre of the Region Hana for Biotechnological and Agricultural Researc; Faculty of Science; Palacky University in Olomouc; Olomouc, Czech Republic
| | - Andrej Pavlovič
- Department of Plant Physiology; Faculty of Natural Sciences; Comenius University in Bratislava; Bratislava, Slovak Republic
| | - Ľudmila Slováková
- Department of Plant Physiology; Faculty of Natural Sciences; Comenius University in Bratislava; Bratislava, Slovak Republic
| | - Alžbeta Blehová
- Department of Plant Physiology; Faculty of Natural Sciences; Comenius University in Bratislava; Bratislava, Slovak Republic
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Braukmann T, Kuzmina M, Stefanovic S. Plastid genome evolution across the genus Cuscuta (Convolvulaceae): two clades within subgenus Grammica exhibit extensive gene loss. J Exp Bot 2013; 64:977-89. [PMID: 23349139 PMCID: PMC3580819 DOI: 10.1093/jxb/ers391] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The genus Cuscuta (Convolvulaceae, the morning glory family) is one of the most intensely studied lineages of parasitic plants. Whole plastome sequencing of four Cuscuta species has demonstrated changes to both plastid gene content and structure. The presence of photosynthetic genes under purifying selection indicates that Cuscuta is cryptically photosynthetic. However, the tempo and mode of plastid genome evolution across the diversity of this group (~200 species) remain largely unknown. A comparative investigation of plastid genome content, grounded within a phylogenetic framework, was conducted using a slot-blot Southern hybridization approach. Cuscuta was extensively sampled (~56% of species), including groups previously suggested to possess more altered plastomes compared with other members of this genus. A total of 56 probes derived from all categories of protein-coding genes, typically found within the plastomes of flowering plants, were used. The results indicate that two clades within subgenus Grammica (clades 'O' and 'K') exhibit substantially more plastid gene loss relative to other members of Cuscuta. All surveyed members of the 'O' clade show extensive losses of plastid genes from every category of genes typically found in the plastome, including otherwise highly conserved small and large ribosomal subunits. The extent of plastid gene losses within this clade is similar in magnitude to that observed previously in some non-asterid holoparasites, in which the very presence of a plastome has been questioned. The 'K' clade also exhibits considerable loss of plastid genes. Unlike in the 'O' clade, in which all species seem to be affected, the losses in clade 'K' progress phylogenetically, following a pattern consistent with the Evolutionary Transition Series hypothesis. This clade presents an ideal opportunity to study the reduction of the plastome of parasites 'in action'. The widespread plastid gene loss in these two clades is hypothesized to be a consequence of the complete loss of photosynthesis. Additionally, taxa that would be the best candidates for entire plastome sequencing are identified in order to investigate further the loss of photosynthesis and reduction of the plastome within Cuscuta.
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Affiliation(s)
- Thomas Braukmann
- Department of Biology, University of Toronto-Mississauga, 3359 Mississauga Rd. N, Mississauga, Ontario, Canada.
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Davis JI, Soreng RJ. Migration of endpoints of two genes relative to boundaries between regions of the plastid genome in the grass family (Poaceae). Am J Bot 2010; 97:874-92. [PMID: 21622452 DOI: 10.3732/ajb.0900228] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Overlapping genes occur widely in microorganisms and in some plastid genomes, but unique properties are observed when such genes span the boundaries between single-copy and repeat regions. The termini of ndhH and ndhF, situated near opposite ends of the small single-copy region (SSC) in the plastid genomes of grasses (Poaceae), have migrated repeatedly into and out of the adjacent inverted-repeat regions (IR). The two genes are transcribed in the same direction, and the 5' terminus of ndhH extends into the IR in some species, while the 3' terminus of ndhF extends into the IR in others. When both genes extend into the IR, portions of the genes overlap and are encoded by the same nucleotide positions. Fine-scale mapping of the SSC-IR junctions across a sample of 92 grasses and outgroups, integrated into a phylogenetic analysis, indicates that the earliest grasses resembled the related taxa Joinvillea (Joinvilleaceae) and Ecdeiocolea (Ecdeiocoleaceae), with ca. 180 nucleotides of ndhH extending into the IR, and with ndhF confined to the SSC. This structure is maintained in early-diverging grass lineages and in most species of the BEP clade. In the PACMAD clade, ndhH lies completely or nearly completely within the SSC, and ca. 20 nucleotides of ndhF extend into the IR. The nucleotide substitution rate has increased in the PACMAD clade in the portion of ndhH that has migrated into the SSC.
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Affiliation(s)
- Jerrold I Davis
- L.H. Bailey Hortorium and Department of Plant Biology, Cornell University, 412 Mann Library, Ithaca, New York 14853-4301 USA
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Braukmann TWA, Kuzmina M, Stefanović S. Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny. Curr Genet 2009; 55:323-37. [DOI: 10.1007/s00294-009-0249-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 04/22/2009] [Accepted: 04/27/2009] [Indexed: 10/20/2022]
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HEADS MICHAEL. Globally basal centres of endemism: the Tasman-Coral Sea region (south-west Pacific), Latin America and Madagascar/South Africa. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01118.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Krause K. From chloroplasts to “cryptic” plastids: evolution of plastid genomes in parasitic plants. Curr Genet 2008; 54:111-21. [DOI: 10.1007/s00294-008-0208-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 07/21/2008] [Accepted: 07/22/2008] [Indexed: 10/21/2022]
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McNeal JR, Arumugunathan K, Kuehl JV, Boore JL, Depamphilis CW. Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). BMC Biol 2007; 5:55. [PMID: 18078516 PMCID: PMC2242782 DOI: 10.1186/1741-7007-5-55] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 12/13/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Cuscuta L. (Convolvulaceae), commonly known as dodders, are epiphytic vines that invade the stems of their host with haustorial feeding structures at the points of contact. Although they lack expanded leaves, some species are noticeably chlorophyllous, especially as seedlings and in maturing fruits. Some species are reported as crop pests of worldwide distribution, whereas others are extremely rare and have local distributions and apparent niche specificity. A strong phylogenetic framework for this large genus is essential to understand the interesting ecological, morphological and molecular phenomena that occur within these parasites in an evolutionary context. RESULTS Here we present a well-supported phylogeny of Cuscuta using sequences of the nuclear ribosomal internal transcribed spacer and plastid rps2, rbcL and matK from representatives across most of the taxonomic diversity of the genus. We use the phylogeny to interpret morphological and plastid genome evolution within the genus. At least three currently recognized taxonomic sections are not monophyletic and subgenus Cuscuta is unequivocally paraphyletic. Plastid genes are extremely variable with regards to evolutionary constraint, with rbcL exhibiting even higher levels of purifying selection in Cuscuta than photosynthetic relatives. Nuclear genome size is highly variable within Cuscuta, particularly within subgenus Grammica, and in some cases may indicate the existence of cryptic species in this large clade of morphologically similar species. CONCLUSION Some morphological characters traditionally used to define major taxonomic splits within Cuscuta are homoplastic and are of limited use in defining true evolutionary groups. Chloroplast genome evolution seems to have evolved in a punctuated fashion, with episodes of loss involving suites of genes or tRNAs followed by stabilization of gene content in major clades. Nearly all species of Cuscuta retain some photosynthetic ability, most likely for nutrient apportionment to their seeds, while complete loss of photosynthesis and possible loss of the entire chloroplast genome is limited to a single small clade of outcrossing species found primarily in western South America.
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Affiliation(s)
- Joel R McNeal
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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Hansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl JV, Boore JL, Jansen RK. Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Mol Phylogenet Evol 2007; 45:547-63. [PMID: 17644003 DOI: 10.1016/j.ympev.2007.06.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 06/05/2007] [Accepted: 06/11/2007] [Indexed: 10/23/2022]
Abstract
We have determined the complete chloroplast genome sequences of four early-diverging lineages of angiosperms, Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae), to examine the organization and evolution of plastid genomes and to estimate phylogenetic relationships among angiosperms. For the most part, the organization of these plastid genomes is quite similar to the ancestral angiosperm plastid genome with a few notable exceptions. Dioscorea has lost one protein-coding gene, rps16; this gene loss has also happened independently in four other land plant lineages, liverworts, conifers, Populus, and legumes. There has also been a small expansion of the inverted repeat (IR) in Dioscorea that has duplicated trnH-GUG. This event has also occurred multiple times in angiosperms, including in monocots, and in the two basal angiosperms Nuphar and Drimys. The Illicium chloroplast genome is unusual by having a 10 kb contraction of the IR. The four taxa sequenced represent key groups in resolving phylogenetic relationships among angiosperms. Illicium is one of the basal angiosperms in the Austrobaileyales, Chloranthus (Chloranthales) remains unplaced in angiosperm classifications, and Buxus and Dioscorea are early-diverging eudicots and monocots, respectively. We have used sequences for 61 shared protein-coding genes from these four genomes and combined them with sequences from 35 other genomes to estimate phylogenetic relationships using parsimony, likelihood, and Bayesian methods. There is strong congruence among the trees generated by the three methods, and most nodes have high levels of support. The results indicate that Amborella alone is sister to the remaining angiosperms; the Nymphaeales represent the next-diverging clade followed by Illicium; Chloranthus is sister to the magnoliids and together this group is sister to a large clade that includes eudicots and monocots; and Dioscorea represents an early-diverging lineage of monocots just internal to Acorus.
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Affiliation(s)
- Debra R Hansen
- Section of Integrative Biology and Institute of Cellular and Molecular Biology, Biological Laboratories 404, University of Texas, Austin, TX 78712, USA
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Legen J, Wanner G, Herrmann RG, Small I, Schmitz-Linneweber C. Plastid tRNA genes trnC-GCA and trnN-GUU are essential for plant cell development. Plant J 2007; 51:751-62. [PMID: 17573798 DOI: 10.1111/j.1365-313x.2007.03177.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Higher plant chloroplast genomes code for a conserved set of 30 tRNAs. This set is believed to be sufficient to support translation, although import of cytosolic tRNA has been proposed to provide additional tRNA species to the chloroplast. Previous knock-outs of tRNA genes, or the pronounced reduction of the level of selected tRNAs, has not led to severe phenotypes. We deleted the two tRNA genes trnN-GUU and trnC-GCA independently from the plastid chromosome of tobacco. No homoplastomic tissue of either DeltatrnN or DeltatrnC plants could be isolated. Both mutants exhibit occasional loss of leaf sectors, and mutant plastid chromosomes are rapidly lost upon relief of selective pressure. This suggests that the knock-out of both trn genes is lethal, and that both tRNA species are required for cell survival. Surprisingly, the impact on chloroplast and cell development differs pronouncedly between the two mutants. Heteroplastomic DeltatrnC and DeltatrnN tissue exhibit different aberrations of the internal membrane systems and, more importantly, heteroplastomic DeltatrnN plants are variegated. Accumulation of tRNA-N and plastid-encoded proteins is reduced in white sectors of DeltatrnN plants, and differentiation of palisade cells is abolished. Our data demonstrate that plastid tRNAs are essential, i.e. not complemented by cytosolic tRNA, and have a differential impact on chloroplast and plant cell development.
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Affiliation(s)
- Julia Legen
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany
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Funk HT, Berg S, Krupinska K, Maier UG, Krause K. Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii. BMC Plant Biol 2007; 7:45. [PMID: 17714582 PMCID: PMC2089061 DOI: 10.1186/1471-2229-7-45] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 08/22/2007] [Indexed: 05/06/2023]
Abstract
BACKGROUND The holoparasitic plant genus Cuscuta comprises species with photosynthetic capacity and functional chloroplasts as well as achlorophyllous and intermediate forms with restricted photosynthetic activity and degenerated chloroplasts. Previous data indicated significant differences with respect to the plastid genome coding capacity in different Cuscuta species that could correlate with their photosynthetic activity. In order to shed light on the molecular changes accompanying the parasitic lifestyle, we sequenced the plastid chromosomes of the two species Cuscuta reflexa and Cuscuta gronovii. Both species are capable of performing photosynthesis, albeit with varying efficiencies. Together with the plastid genome of Epifagus virginiana, an achlorophyllous parasitic plant whose plastid genome has been sequenced, these species represent a series of progression towards total dependency on the host plant, ranging from reduced levels of photosynthesis in C. reflexa to a restricted photosynthetic activity and degenerated chloroplasts in C. gronovii to an achlorophyllous state in E. virginiana. RESULTS The newly sequenced plastid genomes of C. reflexa and C. gronovii reveal that the chromosome structures are generally very similar to that of non-parasitic plants, although a number of species-specific insertions, deletions (indels) and sequence inversions were identified. However, we observed a gradual adaptation of the plastid genome to the different degrees of parasitism. The changes are particularly evident in C. gronovii and include (a) the parallel losses of genes for the subunits of the plastid-encoded RNA polymerase and the corresponding promoters from the plastid genome, (b) the first documented loss of the gene for a putative splicing factor, MatK, from the plastid genome and (c) a significant reduction of RNA editing. CONCLUSION Overall, the comparative genomic analysis of plastid DNA from parasitic plants indicates a bias towards a simplification of the plastid gene expression machinery as a consequence of an increasing dependency on the host plant. A tentative assignment of the successive events in the adaptation of the plastid genomes to parasitism can be inferred from the current data set. This includes (1) a loss of non-coding regions in photosynthetic Cuscuta species that has resulted in a condensation of the plastid genome, (2) the simplification of plastid gene expression in species with largely impaired photosynthetic capacity and (3) the deletion of a significant part of the genetic information, including the information for the photosynthetic apparatus, in non-photosynthetic parasitic plants.
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Affiliation(s)
- Helena T Funk
- Department of Cell Biology, Philipps-University Marburg, Karl-von-Frisch-Str., D-35032 Marburg, Germany
| | - Sabine Berg
- Botanisches Institut, Christian-Albrechts-Universität Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Karin Krupinska
- Botanisches Institut, Christian-Albrechts-Universität Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Uwe G Maier
- Department of Cell Biology, Philipps-University Marburg, Karl-von-Frisch-Str., D-35032 Marburg, Germany
| | - Kirsten Krause
- Botanisches Institut, Christian-Albrechts-Universität Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
- Institutt for Biologi, Universitetet i Tromsø, 9037 Tromsø, Norway
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