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Alenazi AS, Pereira L, Christin PA, Osborne CP, Dunning LT. Identifying genomic regions associated with C 4 photosynthetic activity and leaf anatomy in Alloteropsis semialata. THE NEW PHYTOLOGIST 2024; 243:1698-1710. [PMID: 38953386 DOI: 10.1111/nph.19933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024]
Abstract
C4 photosynthesis is a complex trait requiring multiple developmental and metabolic alterations. Despite this complexity, it has independently evolved over 60 times. However, our understanding of the transition to C4 is complicated by the fact that variation in photosynthetic type is usually segregated between species that diverged a long time ago. Here, we perform a genome-wide association study (GWAS) using the grass Alloteropsis semialata, the only known species to have C3, intermediate, and C4 accessions that recently diverged. We aimed to identify genomic regions associated with the strength of the C4 cycle (measured using δ13C), and the development of C4 leaf anatomy. Genomic regions correlated with δ13C include regulators of C4 decarboxylation enzymes (RIPK), nonphotochemical quenching (SOQ1), and the development of Kranz anatomy (SCARECROW-LIKE). Regions associated with the development of C4 leaf anatomy in the intermediate individuals contain additional leaf anatomy regulators, including those responsible for vein patterning (GSL8) and meristem determinacy (GIF1). The parallel recruitment of paralogous leaf anatomy regulators between A. semialata and other C4 lineages implies the co-option of these genes is context-dependent, which likely has implications for the engineering of the C4 trait into C3 species.
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Affiliation(s)
- Ahmed S Alenazi
- Department of Biological Sciences, College of Science, Northern Border University, Arar, 91431, Saudi Arabia
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Colin P Osborne
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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2
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Heckman RW, Pereira CG, Aspinwall MJ, Juenger TE. Physiological Responses of C 4 Perennial Bioenergy Grasses to Climate Change: Causes, Consequences, and Constraints. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:737-769. [PMID: 38424068 DOI: 10.1146/annurev-arplant-070623-093952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
C4 perennial bioenergy grasses are an economically and ecologically important group whose responses to climate change will be important to the future bioeconomy. These grasses are highly productive and frequently possess large geographic ranges and broad environmental tolerances, which may contribute to the evolution of ecotypes that differ in physiological acclimation capacity and the evolution of distinct functional strategies. C4 perennial bioenergy grasses are predicted to thrive under climate change-C4 photosynthesis likely evolved to enhance photosynthetic efficiency under stressful conditions of low [CO2], high temperature, and drought-although few studies have examined how these species will respond to combined stresses or to extremes of temperature and precipitation. Important targets for C4 perennial bioenergy production in a changing world, such as sustainability and resilience, can benefit from combining knowledge of C4 physiology with recent advances in crop improvement, especially genomic selection.
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Affiliation(s)
- Robert W Heckman
- Rocky Mountain Research Station, US Department of Agriculture Forest Service, Cedar City, Utah, USA;
| | - Caio Guilherme Pereira
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA;
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA;
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Bellasio C, Lundgren MR. The operation of PEPCK increases light harvesting plasticity in C 4 NAD-ME and NADP-ME photosynthetic subtypes: A theoretical study. PLANT, CELL & ENVIRONMENT 2024; 47:2288-2309. [PMID: 38494958 DOI: 10.1111/pce.14869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 03/19/2024]
Abstract
The repeated emergence of NADP-malic enzyme (ME), NAD-ME and phosphoenolpyruvate carboxykinase (PEPCK) subtypes of C4 photosynthesis are iconic examples of convergent evolution, which suggests that these biochemistries do not randomly assemble, but are instead specific adaptations resulting from unknown evolutionary drivers. Theoretical studies that are based on the classic biochemical understanding have repeatedly proposed light-use efficiency as a possible benefit of the PEPCK subtype. However, quantum yield measurements do not support this idea. We explore this inconsistency here via an analytical model that features explicit descriptions across a seamless gradient between C4 biochemistries to analyse light harvesting and dark photosynthetic metabolism. Our simulations show that the NADP-ME subtype, operated by the most productive crops, is the most efficient. The NAD-ME subtype has lower efficiency, but has greater light harvesting plasticity (the capacity to assimilate CO2 in the broadest combination of light intensity and spectral qualities). In both NADP-ME and NAD-ME backgrounds, increasing PEPCK activity corresponds to greater light harvesting plasticity but likely imposed a reduction in photosynthetic efficiency. We draw the first mechanistic links between light harvesting and C4 subtypes, providing the theoretical basis for future investigation.
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Affiliation(s)
- Chandra Bellasio
- Laboratory of Theoretical and Applied Crop Ecophysiology, School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Department of Chemistry, Biology ond Biotechnology, Università Degli Studi Di Perugia, Perugia, Italy
- Department of Biology, University of the Balearic Islands, Palma, Illes Balears, Spain
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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Sotelo G, Gamboa S, Dunning LT, Christin PA, Varela S. C 4 photosynthesis provided an immediate demographic advantage to populations of the grass Alloteropsis semialata. THE NEW PHYTOLOGIST 2024; 242:774-785. [PMID: 38389217 DOI: 10.1111/nph.19606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
C4 photosynthesis is a key innovation in land plant evolution, but its immediate effects on population demography are unclear. We explore the early impact of the C4 trait on the trajectories of C4 and non-C4 populations of the grass Alloteropsis semialata. We combine niche models projected into paleoclimate layers for the last 5 million years with demographic models based on genomic data. The initial split between C4 and non-C4 populations was followed by a larger expansion of the ancestral C4 population, and further diversification led to the unparalleled expansion of descendant C4 populations. Overall, C4 populations spread over three continents and achieved the highest population growth, in agreement with a broader climatic niche that rendered a large potential range over time. The C4 populations that remained in the region of origin, however, experienced lower population growth, rather consistent with local geographic constraints. Moreover, the posterior transfer of some C4-related characters to non-C4 counterparts might have facilitated the recent expansion of non-C4 populations in the region of origin. Altogether, our findings support that C4 photosynthesis provided an immediate demographic advantage to A. semialata populations, but its effect might be masked by geographic contingencies.
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Affiliation(s)
- Graciela Sotelo
- Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
| | - Sara Gamboa
- Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
- Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, S10 2TN, Sheffield, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, S10 2TN, Sheffield, UK
| | - Sara Varela
- Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain
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Sage RF, Gilman IS, Smith JAC, Silvera K, Edwards EJ. Atmospheric CO2 decline and the timing of CAM plant evolution. ANNALS OF BOTANY 2023; 132:753-770. [PMID: 37642245 PMCID: PMC10799994 DOI: 10.1093/aob/mcad122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/19/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND AND AIMS CAM photosynthesis is hypothesized to have evolved in atmospheres of low CO2 concentration in recent geological time because of its ability to concentrate CO2 around Rubisco and boost water use efficiency relative to C3 photosynthesis. We assess this hypothesis by compiling estimates of when CAM clades arose using phylogenetic chronograms for 73 CAM clades. We further consider evidence of how atmospheric CO2 affects CAM relative to C3 photosynthesis. RESULTS Where CAM origins can be inferred, strong CAM is estimated to have appeared in the past 30 million years in 46 of 48 examined clades, after atmospheric CO2 had declined from high (near 800 ppm) to lower (<450 ppm) values. In turn, 21 of 25 clades containing CAM species (but where CAM origins are less certain) also arose in the past 30 million years. In these clades, CAM is probably younger than the clade origin. We found evidence for repeated weak CAM evolution during the higher CO2 conditions before 30 million years ago, and possible strong CAM origins in the Crassulaceae during the Cretaceous period prior to atmospheric CO2 decline. Most CAM-specific clades arose in the past 15 million years, in a similar pattern observed for origins of C4 clades. CONCLUSIONS The evidence indicates strong CAM repeatedly evolved in reduced CO2 conditions of the past 30 million years. Weaker CAM can pre-date low CO2 and, in the Crassulaceae, strong CAM may also have arisen in water-limited microsites under relatively high CO2. Experimental evidence from extant CAM species demonstrates that elevated CO2 reduces the importance of nocturnal CO2 fixation by increasing the contribution of C3 photosynthesis to daily carbon gain. Thus, the advantage of strong CAM would be reduced in high CO2, such that its evolution appears less likely and restricted to more extreme environments than possible in low CO2.
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Affiliation(s)
- Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Ian S Gilman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - J Andrew C Smith
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Katia Silvera
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
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6
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Pereira L, Bianconi ME, Osborne CP, Christin PA, Dunning LT. Alloteropsis semialata as a study system for C4 evolution in grasses. ANNALS OF BOTANY 2023; 132:365-382. [PMID: 37422712 PMCID: PMC10667010 DOI: 10.1093/aob/mcad078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/07/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND Numerous groups of plants have adapted to CO2 limitations by independently evolving C4 photosynthesis. This trait relies on concerted changes in anatomy and biochemistry to concentrate CO2 within the leaf and thereby boost productivity in tropical conditions. The ecological and economic importance of C4 photosynthesis has motivated intense research, often relying on comparisons between distantly related C4 and non-C4 plants. The photosynthetic type is fixed in most species, with the notable exception of the grass Alloteropsis semialata. This species includes populations exhibiting the ancestral C3 state in southern Africa, intermediate populations in the Zambezian region and C4 populations spread around the palaeotropics. SCOPE We compile here the knowledge on the distribution and evolutionary history of the Alloteropsis genus as a whole and discuss how this has furthered our understanding of C4 evolution. We then present a chromosome-level reference genome for a C3 individual and compare the genomic architecture with that of a C4 accession of A. semialata. CONCLUSIONS Alloteropsis semialata is one of the best systems in which to investigate the evolution of C4 photosynthesis because the genetic and phenotypic variation provides a fertile ground for comparative and population-level studies. Preliminary comparative genomic investigations show that the C3 and C4 genomes are highly syntenic and have undergone a modest amount of gene duplication and translocation since the different photosynthetic groups diverged. The background knowledge and publicly available genomic resources make A. semialata a great model for further comparative analyses of photosynthetic diversification.
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Affiliation(s)
- Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN,UK
| | - Matheus E Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN,UK
| | - Colin P Osborne
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN,UK
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN,UK
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7
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Berasategui JA, Žerdoner Čalasan A, Zizka A, Kadereit G. Global distribution, climatic preferences and photosynthesis-related traits of C 4 eudicots and how they differ from those of C 4 grasses. Ecol Evol 2023; 13:e10720. [PMID: 37964791 PMCID: PMC10641307 DOI: 10.1002/ece3.10720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023] Open
Abstract
C₄ is one of three known photosynthetic processes of carbon fixation in flowering plants. It evolved independently more than 61 times in multiple angiosperm lineages and consists of a series of anatomical and biochemical modifications to the ancestral C3 pathway increasing plant productivity under warm and light-rich conditions. The C4 lineages of eudicots belong to seven orders and 15 families, are phylogenetically less constrained than those of monocots and entail an enormous structural and ecological diversity. Eudicot C4 lineages likely evolved the C4 syndrome along different evolutionary paths. Therefore, a better understanding of this diversity is key to understanding the evolution of this complex trait as a whole. By compiling 1207 recognised C4 eudicots species described in the literature and presenting trait data among these species, we identify global centres of species richness and of high phylogenetic diversity. Furthermore, we discuss climatic preferences in the context of plant functional traits. We identify two hotspots of C4 eudicot diversity: arid regions of Mexico/Southern United States and Australia, which show a similarly high number of different C4 eudicot genera but differ in the number of C4 lineages that evolved in situ. Further eudicot C4 hotspots with many different families and genera are in South Africa, West Africa, Patagonia, Central Asia and the Mediterranean. In general, C4 eudicots are diverse in deserts and xeric shrublands, tropical and subtropical grasslands, savannas and shrublands. We found C4 eudicots to occur in areas with less annual precipitation than C4 grasses which can be explained by frequently associated adaptations to drought stress such as among others succulence and salt tolerance. The data indicate that C4 eudicot lineages utilising the NAD-ME decarboxylating enzyme grow in drier areas than those using the NADP-ME decarboxylating enzyme indicating biochemical restrictions of the later system in higher temperatures. We conclude that in most eudicot lineages, C4 evolved in ancestrally already drought-adapted clades and enabled these to further spread in these habitats and colonise even drier areas.
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Affiliation(s)
- Jessica A. Berasategui
- Prinzessin Therese von Bayern Lehrstuhl für Systematik, Biodiversität & Evolution der PflanzenLudwig‐Maximilians Universität MünchenMünchenGermany
- Institute for Molecular PhysiologyJohannes Gutenberg‐University MainzMainzGermany
| | - Anže Žerdoner Čalasan
- Prinzessin Therese von Bayern Lehrstuhl für Systematik, Biodiversität & Evolution der PflanzenLudwig‐Maximilians Universität MünchenMünchenGermany
| | - Alexander Zizka
- Department of BiologyPhilipps‐University MarburgMarburgGermany
| | - Gudrun Kadereit
- Prinzessin Therese von Bayern Lehrstuhl für Systematik, Biodiversität & Evolution der PflanzenLudwig‐Maximilians Universität MünchenMünchenGermany
- Botanischer Garten München‐Nymphenburg und Botanische Staatssammlung MünchenStaatliche Naturwissenschaftliche Sammlungen BayernsMünchenGermany
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8
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Arce Cubas L, Rodrigues Gabriel Sales C, Vath RL, Bernardo EL, Burnett AC, Kromdijk J. Lessons from relatives: C4 photosynthesis enhances CO2 assimilation during the low-light phase of fluctuations. PLANT PHYSIOLOGY 2023; 193:1073-1090. [PMID: 37335935 PMCID: PMC10517189 DOI: 10.1093/plphys/kiad355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/19/2023] [Accepted: 06/03/2023] [Indexed: 06/21/2023]
Abstract
Despite the global importance of species with C4 photosynthesis, there is a lack of consensus regarding C4 performance under fluctuating light. Contrasting hypotheses and experimental evidence suggest that C4 photosynthesis is either less or more efficient in fixing carbon under fluctuating light than the ancestral C3 form. Two main issues have been identified that may underly the lack of consensus: neglect of evolutionary distance between selected C3 and C4 species and use of contrasting fluctuating light treatments. To circumvent these issues, we measured photosynthetic responses to fluctuating light across 3 independent phylogenetically controlled comparisons between C3 and C4 species from Alloteropsis, Flaveria, and Cleome genera under 21% and 2% O2. Leaves were subjected to repetitive stepwise changes in light intensity (800 and 100 µmol m-2 s-1 photon flux density) with 3 contrasting durations: 6, 30, and 300 s. These experiments reconciled the opposing results found across previous studies and showed that (i) stimulation of CO2 assimilation in C4 species during the low-light phase was both stronger and more sustained than in C3 species; (ii) CO2 assimilation patterns during the high-light phase could be attributable to species or C4 subtype differences rather than photosynthetic pathway; and (iii) the duration of each light step in the fluctuation regime can strongly influence experimental outcomes.
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Affiliation(s)
- Lucίa Arce Cubas
- Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA Cambridge, UK
| | | | - Richard L Vath
- Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA Cambridge, UK
| | - Emmanuel L Bernardo
- Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA Cambridge, UK
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna 4031, Philippines
| | - Angela C Burnett
- Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA Cambridge, UK
| | - Johannes Kromdijk
- Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA Cambridge, UK
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Alenazi AS, Bianconi ME, Middlemiss E, Milenkovic V, Curran EV, Sotelo G, Lundgren MR, Nyirenda F, Pereira L, Christin PA, Dunning LT, Osborne CP. Leaf anatomy explains the strength of C 4 activity within the grass species Alloteropsis semialata. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37184423 DOI: 10.1111/pce.14607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/23/2023] [Accepted: 05/01/2023] [Indexed: 05/16/2023]
Abstract
C4 photosynthesis results from anatomical and biochemical characteristics that together concentrate CO2 around ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), increasing productivity in warm conditions. This complex trait evolved through the gradual accumulation of components, and particular species possess only some of these, resulting in weak C4 activity. The consequences of adding C4 components have been modelled and investigated through comparative approaches, but the intraspecific dynamics responsible for strengthening the C4 pathway remain largely unexplored. Here, we evaluate the link between anatomical variation and C4 activity, focusing on populations of the photosynthetically diverse grass Alloteropsis semialata that fix various proportions of carbon via the C4 cycle. The carbon isotope ratios in these populations range from values typical of C3 to those typical of C4 plants. This variation is statistically explained by a combination of leaf anatomical traits linked to the preponderance of bundle sheath tissue. We hypothesize that increased investment in bundle sheath boosts the strength of the intercellular C4 pump and shifts the balance of carbon acquisition towards the C4 cycle. Carbon isotope ratios indicating a stronger C4 pathway are associated with warmer, drier environments, suggesting that incremental anatomical alterations can lead to the emergence of C4 physiology during local adaptation within metapopulations.
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Affiliation(s)
- Ahmed S Alenazi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Department of Biological Sciences, Northern Border University, Arar, Saudi Arabia
| | - Matheus E Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Ella Middlemiss
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Vanja Milenkovic
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Emma V Curran
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Marjorie R Lundgren
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Colin P Osborne
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
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10
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Arce Cubas L, Vath RL, Bernardo EL, Sales CRG, Burnett AC, Kromdijk J. Activation of CO 2 assimilation during photosynthetic induction is slower in C 4 than in C 3 photosynthesis in three phylogenetically controlled experiments. FRONTIERS IN PLANT SCIENCE 2023; 13:1091115. [PMID: 36684779 PMCID: PMC9848656 DOI: 10.3389/fpls.2022.1091115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/05/2022] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Despite their importance for the global carbon cycle and crop production, species with C4 photosynthesis are still somewhat understudied relative to C3 species. Although the benefits of the C4 carbon concentrating mechanism are readily observable under optimal steady state conditions, it is less clear how the presence of C4 affects activation of CO2 assimilation during photosynthetic induction. METHODS In this study we aimed to characterise differences between C4 and C3 photosynthetic induction responses by analysing steady state photosynthesis and photosynthetic induction in three phylogenetically linked pairs of C3 and C4 species from Alloteropsis, Flaveria, and Cleome genera. Experiments were conducted both at 21% and 2% O2 to evaluate the role of photorespiration during photosynthetic induction. RESULTS Our results confirm C4 species have slower activation of CO2 assimilation during photosynthetic induction than C3 species, but the apparent mechanism behind these differences varied between genera. Incomplete suppression of photorespiration was found to impact photosynthetic induction significantly in C4 Flaveria bidentis, whereas in the Cleome and Alloteropsis C4 species, delayed activation of the C3 cycle appeared to limit induction and a potentially supporting role for photorespiration was also identified. DISCUSSION The sheer variation in photosynthetic induction responses observed in our limited sample of species highlights the importance of controlling for evolutionary distance when comparing C3 and C4 photosynthetic pathways.
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Affiliation(s)
- Lucía Arce Cubas
- The University of Cambridge, Department of Plant Sciences, Cambridge, United Kingdom
| | - Richard L. Vath
- The University of Cambridge, Department of Plant Sciences, Cambridge, United Kingdom
| | - Emmanuel L. Bernardo
- The University of Cambridge, Department of Plant Sciences, Cambridge, United Kingdom
- University of the Philippines Los Baños, Institute of Crop Science, College of Agriculture and Food Science, College, Laguna, Philippines
| | | | - Angela C. Burnett
- The University of Cambridge, Department of Plant Sciences, Cambridge, United Kingdom
| | - Johannes Kromdijk
- The University of Cambridge, Department of Plant Sciences, Cambridge, United Kingdom
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11
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Young SNR, Dunning LT, Liu H, Stevens CJ, Lundgren MR. C4 trees have a broader niche than their close C3 relatives. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3189-3204. [PMID: 35293994 PMCID: PMC9126736 DOI: 10.1093/jxb/erac113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Previous studies have demonstrated the ecological sorting of herbaceous C3 and C4 species along gradients of precipitation and temperature: C4 herbaceous species typically occupy drier and warmer environments than their C3 relatives. However, it is unclear if this pattern holds true for C4 tree species, which are unique to Euphorbiaceae and found only on the Hawaiian Islands. Here, we combine occurrence data with local environmental and soil datasets to, for the first time, distinguish the ecological factors associated with photosynthetic diversification in the tree life form. These data are presented within a phylogenetic framework. We show that C3 and C4 trees inhabit similar environments, but that C4 photosynthesis expands the ecological niche in trees relative to that of C3 tree species. In particular, when compared with C3 trees, C4 trees moved into higher elevation habitats with characteristically sparse vegetation (and thus greater sunlight) and cooler temperatures, a pattern which contrasts with that of herbaceous species. Understanding the relationship between C4 photosynthesis and ecological niche in tree species has implications for establishing how C4 photosynthesis has, in this rare instance, evolved in trees, and whether this unique combination of traits could be exploited from an engineering perspective.
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Affiliation(s)
- Sophie N R Young
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Hui Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Guangzhou 510650, China
| | - Carly J Stevens
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
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12
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Mercado MA, Studer AJ. Meeting in the Middle: Lessons and Opportunities from Studying C 3-C 4 Intermediates. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:43-65. [PMID: 35231181 DOI: 10.1146/annurev-arplant-102720-114201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The discovery of C3-C4 intermediate species nearly 50 years ago opened up a new avenue for studying the evolution of photosynthetic pathways. Intermediate species exhibit anatomical, biochemical, and physiological traits that range from C3 to C4. A key feature of C3-C4 intermediates that utilize C2 photosynthesis is the improvement in photosynthetic efficiency compared with C3 species. Although the recruitment of some core enzymes is shared across lineages, there is significant variability in gene expression patterns, consistent with models that suggest numerous evolutionary paths from C3 to C4 photosynthesis. Despite the many evolutionary trajectories, the recruitment of glycine decarboxylase for C2 photosynthesis is likely required. As technologies enable high-throughput genotyping and phenotyping, the discovery of new C3-C4 intermediates species will enrich comparisons between evolutionary lineages. The investigation of C3-C4 intermediate species will enhance our understanding of photosynthetic mechanisms and evolutionary processes and will potentially aid in crop improvement.
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Affiliation(s)
| | - Anthony J Studer
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA; ,
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13
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Bianconi ME, Sotelo G, Curran EV, Milenkovic V, Samaritani E, Dunning LT, Bertolino LT, Osborne CP, Christin PA. Upregulation of C 4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass. PLANT, CELL & ENVIRONMENT 2022. [PMID: 35201618 DOI: 10.1101/2021.08.10.455822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
C4 photosynthesis is thought to have evolved via intermediate stages, with changes towards the C4 phenotype gradually enhancing photosynthetic performance. This hypothesis is widely supported by modelling studies, but experimental tests are missing. Mixing of C4 components to generate artificial intermediates can be achieved via crossing, and the grass Alloteropsis semialata represents an outstanding study system since it includes C4 and non-C4 populations. Here, we analyse F1 hybrids between C3 and C4 , and C3 +C4 and C4 genotypes to determine whether the acquisition of C4 characteristics increases photosynthetic performance. The hybrids have leaf anatomical characters and C4 gene expression profiles that are largely intermediate between those of their parents. Carbon isotope ratios are similarly intermediate, which suggests that a partial C4 cycle coexists with C3 carbon fixation in the hybrids. This partial C4 phenotype is associated with C4 -like photosynthetic efficiency in C3 +C4 × C4 , but not in C3 × C4 hybrids, which are overall less efficient than both parents. Our results support the hypothesis that the photosynthetic gains from the upregulation of C4 characteristics depend on coordinated changes in anatomy and biochemistry. The order of acquisition of C4 components is thus constrained, with C3 +C4 species providing an essential step for C4 evolution.
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Affiliation(s)
- Matheus E Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Emma V Curran
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Vanja Milenkovic
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Emanuela Samaritani
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Lígia T Bertolino
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Colin P Osborne
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK
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14
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Bianconi ME, Sotelo G, Curran EV, Milenkovic V, Samaritani E, Dunning LT, Bertolino LT, Osborne CP, Christin P. Upregulation of C 4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass. PLANT, CELL & ENVIRONMENT 2022; 45:1398-1411. [PMID: 35201618 PMCID: PMC9314825 DOI: 10.1111/pce.14301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/20/2021] [Accepted: 11/21/2021] [Indexed: 06/14/2023]
Abstract
C4 photosynthesis is thought to have evolved via intermediate stages, with changes towards the C4 phenotype gradually enhancing photosynthetic performance. This hypothesis is widely supported by modelling studies, but experimental tests are missing. Mixing of C4 components to generate artificial intermediates can be achieved via crossing, and the grass Alloteropsis semialata represents an outstanding study system since it includes C4 and non-C4 populations. Here, we analyse F1 hybrids between C3 and C4 , and C3 +C4 and C4 genotypes to determine whether the acquisition of C4 characteristics increases photosynthetic performance. The hybrids have leaf anatomical characters and C4 gene expression profiles that are largely intermediate between those of their parents. Carbon isotope ratios are similarly intermediate, which suggests that a partial C4 cycle coexists with C3 carbon fixation in the hybrids. This partial C4 phenotype is associated with C4 -like photosynthetic efficiency in C3 +C4 × C4 , but not in C3 × C4 hybrids, which are overall less efficient than both parents. Our results support the hypothesis that the photosynthetic gains from the upregulation of C4 characteristics depend on coordinated changes in anatomy and biochemistry. The order of acquisition of C4 components is thus constrained, with C3 +C4 species providing an essential step for C4 evolution.
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Affiliation(s)
- Matheus E. Bianconi
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Emma V. Curran
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Vanja Milenkovic
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Emanuela Samaritani
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Luke T. Dunning
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Lígia T. Bertolino
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Colin P. Osborne
- Plants, Photosynthesis and Soil, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
| | - Pascal‐Antoine Christin
- Ecology and Evolutionary Biology, School of BiosciencesUniversity of SheffieldWestern BankSheffieldUK
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15
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Curran EV, Scott MS, Olofsson JK, Nyirenda F, Sotelo G, Bianconi ME, Manzi S, Besnard G, Pereira L, Christin PA. Hybridization boosts dispersal of two contrasted ecotypes in a grass species. Proc Biol Sci 2022; 289:20212491. [PMID: 35078363 PMCID: PMC8790336 DOI: 10.1098/rspb.2021.2491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/23/2021] [Indexed: 11/12/2022] Open
Abstract
Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes and influence rates of hybridization. How these dynamics affect the emergence and spread of novel phenotypes remains only partially understood. Here, we use phylogenomics and population genomics to retrace the origin and spread of two geographically overlapping ecotypes of the African grass Alloteropsis angusta. In addition to an ecotype inhabiting wetlands, we report the existence of a previously undescribed ecotype inhabiting Miombo woodlands and grasslands. The two ecotypes are consistently associated with different nuclear groups, which represent an advanced stage of divergence with secondary low-level gene flow. However, the seed-transported chloroplast genomes are consistently shared by distinct ecotypes inhabiting the same region. These patterns suggest that the nuclear genome of one ecotype can enter the seeds of the other via occasional pollen movements with sorting of nuclear groups in subsequent generations. The contrasting ecotypes of A. angusta can thus use each other as a gateway to new locations across a large part of Africa, showing that hybridization can facilitate the geographical dispersal of distinct ecotypes of the same grass species.
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Affiliation(s)
- Emma V. Curran
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Matilda S. Scott
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jill K. Olofsson
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Matheus E. Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Sophie Manzi
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III – Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Guillaume Besnard
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III – Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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16
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Cui H. Challenges and Approaches to Crop Improvement Through C3-to-C4 Engineering. FRONTIERS IN PLANT SCIENCE 2021; 12:715391. [PMID: 34594351 PMCID: PMC8476962 DOI: 10.3389/fpls.2021.715391] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/06/2021] [Indexed: 05/24/2023]
Abstract
With a rapidly growing world population and dwindling natural resources, we are now facing the enormous challenge of increasing crop yields while simultaneously improving the efficiency of resource utilization. Introduction of C4 photosynthesis into C3 crops is widely accepted as a key strategy to meet this challenge because C4 plants are more efficient than C3 plants in photosynthesis and resource usage, particularly in hot climates, where the potential for productivity is high. Lending support to the feasibility of this C3-to-C4 engineering, evidence indicates that C4 photosynthesis has evolved from C3 photosynthesis in multiple lineages. Nevertheless, C3-to-C4 engineering is not an easy task, as several features essential to C4 photosynthesis must be introduced into C3 plants. One such feature is the spatial separation of the two phases of photosynthesis (CO2 fixation and carbohydrate synthesis) into the mesophyll and bundle sheath cells, respectively. Another feature is the Kranz anatomy, characterized by a close association between the mesophyll and bundle sheath (BS) cells (1:1 ratio). These anatomical features, along with a C4-specific carbon fixation enzyme (PEPC), form a CO2-concentration mechanism that ensures a high photosynthetic efficiency. Much effort has been taken in the past to introduce the C4 mechanism into C3 plants, but none of these attempts has met with success, which is in my opinion due to a lack of system-level understanding and manipulation of the C3 and C4 pathways. As a prerequisite for the C3-to-C4 engineering, I propose that not only the mechanisms that control the Kranz anatomy and cell-type-specific expression in C3 and C4 plants must be elucidated, but also a good understanding of the gene regulatory network underlying C3 and C4 photosynthesis must be achieved. In this review, I first describe the past and current efforts to increase photosynthetic efficiency in C3 plants and their limitations; I then discuss a systems approach to tackling down this challenge, some practical issues, and recent technical innovations that would help us to solve these problems.
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Affiliation(s)
- Hongchang Cui
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
- College of Life Science, Northwest Science University of Agriculture and Forestry, Yangling, China
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17
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Phansopa C, Dunning LT, Reid JD, Christin PA. Lateral Gene Transfer Acts As an Evolutionary Shortcut to Efficient C4 Biochemistry. Mol Biol Evol 2021; 37:3094-3104. [PMID: 32521019 PMCID: PMC7751175 DOI: 10.1093/molbev/msaa143] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The adaptation of proteins for novel functions often requires changes in their kinetics via amino acid replacement. This process can require multiple mutations, and therefore extended periods of selection. The transfer of genes among distinct species might speed up the process, by providing proteins already adapted for the novel function. However, this hypothesis remains untested in multicellular eukaryotes. The grass Alloteropsis is an ideal system to test this hypothesis due to its diversity of genes encoding phosphoenolpyruvate carboxylase, an enzyme that catalyzes one of the key reactions in the C4 pathway. Different accessions of Alloteropsis either use native isoforms relatively recently co-opted from other functions or isoforms that were laterally acquired from distantly related species that evolved the C4 trait much earlier. By comparing the enzyme kinetics, we show that native isoforms with few amino acid replacements have substrate KM values similar to the non-C4 ancestral form, but exhibit marked increases in catalytic efficiency. The co-option of native isoforms was therefore followed by rapid catalytic improvements, which appear to rely on standing genetic variation observed within one species. Native C4 isoforms with more amino acid replacements exhibit additional changes in affinities, suggesting that the initial catalytic improvements are followed by gradual modifications. Finally, laterally acquired genes show both strong increases in catalytic efficiency and important changes in substrate handling. We conclude that the transfer of genes among distant species sharing the same physiological novelty creates an evolutionary shortcut toward more efficient enzymes, effectively accelerating evolution.
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Affiliation(s)
- Chatchawal Phansopa
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - James D Reid
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
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18
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Olofsson JK, Curran EV, Nyirenda F, Bianconi ME, Dunning LT, Milenkovic V, Sotelo G, Hidalgo O, Powell RF, Lundgren MR, Leitch IJ, Nosil P, Osborne CP, Christin PA. Low dispersal and ploidy differences in a grass maintain photosynthetic diversity despite gene flow and habitat overlap. Mol Ecol 2021; 30:2116-2130. [PMID: 33682242 DOI: 10.1111/mec.15871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022]
Abstract
Geographical isolation facilitates the emergence of distinct phenotypes within a single species, but reproductive barriers or selection are needed to maintain the polymorphism after secondary contact. Here, we explore the processes that maintain intraspecific variation of C4 photosynthesis, a complex trait that results from the combined action of multiple genes. The grass Alloteropsis semialata includes C4 and non-C4 populations, which have coexisted as a polyploid series for more than 1 million years in the miombo woodlands of Africa. Using population genomics, we show that there is genome-wide divergence for the photosynthetic types, but the current geographical distribution does not reflect a simple habitat displacement scenario as the genetic clusters overlap, being occasionally mixed within a given habitat. Despite evidence of recurrent introgression between non-C4 and C4 groups, in both diploids and polyploids, the distinct genetic lineages retain their identity, potentially because of selection against hybrids. Coupled with strong isolation by distance within each genetic group, this selection created a geographical mosaic of photosynthetic types. Diploid C4 and non-C4 types never grew together, and the C4 type from mixed populations constantly belonged to the hexaploid lineage. By limiting reproductive interactions between photosynthetic types, the ploidy difference probably allows their co-occurrence, reinforcing the functional diversity within this species. Together, these factors enabled the persistence of divergent physiological traits of ecological importance within a single species despite gene flow and habitat overlap.
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Affiliation(s)
- Jill K Olofsson
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Emma V Curran
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Matheus E Bianconi
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Luke T Dunning
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Vanja Milenkovic
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Graciela Sotelo
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | | | | | - Marjorie R Lundgren
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | | | - Patrik Nosil
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Colin P Osborne
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
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19
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Russ Monson and the evolution of C 4 photosynthesis. Oecologia 2021; 197:823-840. [PMID: 33661402 DOI: 10.1007/s00442-021-04883-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/12/2021] [Indexed: 10/22/2022]
Abstract
Early in his career, Russ Monson produced a series of influential eco-physiological papers that helped lay the foundation for the study of C4 plant evolution. Among the most important was a 1984 paper with Maurice Ku and Gerry Edwards that outlined the pathway for the evolutionary bridge from C3 to C4 photosynthesis. This model proposed C4 photosynthesis arose out of a shuttle that imported photorespiratory metabolites into bundle sheath (BS) cells, where glycine decarboxylase cleaved off CO2, allowing it to accumulate and be efficiently refixed by BS Rubisco. By the mid-1990's, Monson's research focus had shifted away from C4 plants, save for one 2003 paper on C3 versus C4 stomatal control with Travis Huxman, and a series of critical reviews on C4 evolution. These reviews heavily influenced the modern synthesis of C4 evolutionary studies, which incorporates phylogenomic understanding with physiological, molecular, and structural characterizations of trait shifts in multiple evolutionary lineages. Subsequent research supported the Monson et al. model from 1984, by showing a glycine shuttle occurs in nearly all C3-C4 intermediate species identified. Monson also examined the physiological controls over the ecological distribution of C3, C3-C4 intermediate, and C4 photosynthesis, building our understanding of the fitness value of the intermediate and C4 pathway in relevant microenvironments. By establishing the foundation for discoveries that followed, Russ Monson can rightly be considered a leading pioneer contributing to the evolutionary biology of C4 photosynthesis.
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20
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Bianconi ME, Hackel J, Vorontsova MS, Alberti A, Arthan W, Burke SV, Duvall MR, Kellogg EA, Lavergne S, McKain MR, Meunier A, Osborne CP, Traiperm P, Christin PA, Besnard G. Continued Adaptation of C4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses. Syst Biol 2020; 69:445-461. [PMID: 31589325 PMCID: PMC7672695 DOI: 10.1093/sysbio/syz066] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/18/2019] [Accepted: 09/26/2019] [Indexed: 11/29/2022] Open
Abstract
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}{}$_{4}$\end{document} photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} lineages is Andropogoneae, a group of \documentclass[12pt]{minimal}
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}{}$\sim $\end{document}1200 grass species that includes some of the world’s most important crops and species dominating tropical and some temperate grasslands. Previous efforts to understand C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} evolution in the group have compared a few model C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} plants to distantly related C\documentclass[12pt]{minimal}
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}{}$_{3}$\end{document} species so that changes directly responsible for the transition to C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} could not be distinguished from those that preceded or followed it. In this study, we analyze the genomes of 66 grass species, capturing the earliest diversification within Andropogoneae as well as their C\documentclass[12pt]{minimal}
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}{}$_{3}$\end{document} relatives. Phylogenomics combined with molecular dating and analyses of protein evolution show that many changes linked to the evolution of C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} photosynthesis in Andropogoneae happened in the Early Miocene, between 21 and 18 Ma, after the split from its C\documentclass[12pt]{minimal}
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}{}$_{3}$\end{document} sister lineage, and before the diversification of the group. This initial burst of changes was followed by an extended period of modifications to leaf anatomy and biochemistry during the diversification of Andropogoneae, so that a single C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} origin gave birth to a diversity of C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} phenotypes during 18 million years of speciation events and migration across geographic and ecological spaces. Our comprehensive approach and broad sampling of the diversity in the group reveals that one key transition can lead to a plethora of phenotypes following sustained adaptation of the ancestral state. [Adaptive evolution; complex traits; herbarium genomics; Jansenelleae; leaf anatomy; Poaceae; phylogenomics.]
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Affiliation(s)
- Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Jan Hackel
- Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Adriana Alberti
- CEA - Institut de Biologie Francois-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Watchara Arthan
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
- School of Biological Sciences, University of Reading, Reading RG6 6AH, UK
| | - Sean V Burke
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Melvin R Duvall
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MI 63132, USA
| | - Sébastien Lavergne
- Laboratoire d’Ecologie Alpine, CNRS – Université Grenoble Alpes, UMR 5553, Grenoble, France
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, 500 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Alexandre Meunier
- Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Paweena Traiperm
- Department of Plant Science, Faculty of Science, Mahidol University, King Rama VI Road, Bangkok 10400, Thailand
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Guillaume Besnard
- Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France
- Correspondence to be sent to: Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France; E-mail:
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21
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Bianconi ME, Dunning LT, Curran EV, Hidalgo O, Powell RF, Mian S, Leitch IJ, Lundgren MR, Manzi S, Vorontsova MS, Besnard G, Osborne CP, Olofsson JK, Christin PA. Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species. Proc Biol Sci 2020; 287:20201960. [PMID: 33171085 PMCID: PMC7735283 DOI: 10.1098/rspb.2020.1960] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C4 physiology away from its region of origin.
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Affiliation(s)
- Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Emma V Curran
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Oriane Hidalgo
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Robyn F Powell
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Sahr Mian
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Ilia J Leitch
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Sophie Manzi
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III - Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Guillaume Besnard
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III - Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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22
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Young SNR, Sack L, Sporck-Koehler MJ, Lundgren MR. Why is C4 photosynthesis so rare in trees? JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4629-4638. [PMID: 32409834 PMCID: PMC7410182 DOI: 10.1093/jxb/eraa234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/12/2020] [Indexed: 05/08/2023]
Abstract
Since C4 photosynthesis was first discovered >50 years ago, researchers have sought to understand how this complex trait evolved from the ancestral C3 photosynthetic machinery on >60 occasions. Despite its repeated emergence across the plant kingdom, C4 photosynthesis is notably rare in trees, with true C4 trees only existing in Euphorbia. Here we consider aspects of the C4 trait that could limit but not preclude the evolution of a C4 tree, including reduced quantum yield, increased energetic demand, reduced adaptive plasticity, evolutionary constraints, and a new theory that the passive symplastic phloem loading mechanism observed in trees, combined with difficulties in maintaining sugar and water transport over a long pathlength, could make C4 photosynthesis largely incompatible with the tree lifeform. We conclude that the transition to a tree habit within C4 lineages as well as the emergence of C4 photosynthesis within pre-existing trees would both face a series of challenges that together explain the global rarity of C4 photosynthesis in trees. The C4 trees in Euphorbia are therefore exceptional in how they have circumvented every potential barrier to the rare C4 tree lifeform.
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Affiliation(s)
- Sophie N R Young
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Lawren Sack
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Marjorie R Lundgren
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
- Correspondence:
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23
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Veromann-Jürgenson LL, Brodribb TJ, Niinemets Ü, Tosens T. Variability in the chloroplast area lining the intercellular airspace and cell walls drives mesophyll conductance in gymnosperms. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4958-4971. [PMID: 32392579 DOI: 10.1093/jxb/eraa231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
The photosynthetic efficiency of plants in different environments is controlled by stomata, hydraulics, biochemistry, and mesophyll conductance (gm). Recently, gm was demonstrated to be the key limitation of photosynthesis in gymnosperms. Values of gm across gymnosperms varied over 20-fold, but this variation was poorly explained by robust structure-bound integrated traits such as leaf dry mass per area. Understanding how the component structural traits control gm is central for identifying the determinants of variability in gm across plant functional and phylogenetic groups. Here, we investigated the structural traits responsible for gm in 65 diverse gymnosperms. Although the integrated morphological traits, shape, and anatomical characteristics varied widely across species, the distinguishing features of all gymnosperms were thick mesophyll cell walls and low chloroplast area exposed to intercellular airspace (Sc/S) compared with angiosperms. Sc/S and cell wall thickness were the fundamental traits driving variations in gm across gymnosperm species. Chloroplast thickness was the strongest limitation of gm among liquid-phase components. The variation in leaf dry mass per area was not correlated with the key ultrastructural traits determining gm. Thus, given the absence of correlating integrated easy-to-measure traits, detailed knowledge of underlying component traits controlling gm across plant taxa is necessary to understand the photosynthetic limitations across ecosystems.
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Affiliation(s)
| | - Timothy J Brodribb
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Tiina Tosens
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
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24
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Wood D, Besnard G, Beerling DJ, Osborne CP, Christin PA. Phylogenomics indicates the "living fossil" Isoetes diversified in the Cenozoic. PLoS One 2020; 15:e0227525. [PMID: 32555586 PMCID: PMC7302493 DOI: 10.1371/journal.pone.0227525] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 05/14/2020] [Indexed: 11/19/2022] Open
Abstract
The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.
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Affiliation(s)
- Daniel Wood
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Guillaume Besnard
- CNRS, Université de Toulouse, IRD, UMR 5174, EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | - David J. Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Colin P. Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
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25
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Pollination Ecology of the Species Mollugo cerviana (L.) Ser. (Molluginaceae). TRANSYLVANIAN REVIEW OF SYSTEMATICAL AND ECOLOGICAL RESEARCH 2020. [DOI: 10.2478/trser-2019-0009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Mollugo cerviana is an annual herb which usually grows throughout the year in open dry sandy and sandy-loamy soils, but also occurs in moist habitats, especially in cultivated lands. Haplothrips uses the flowers for breeding and feeding; the feeding activity affects pollination. The flowers have specialized floral structural and functional behaviours for self-induced and spontaneous autogamy while keeping the options open for insect pollination after anthesis; it is facultative autogamous which is reflected in pollen-ovule ratio and natural fruit and seed set rates. Seed dispersal modes include anemochory, ombrohydrochory and hydrochory.
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26
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Olofsson JK, Dunning LT, Lundgren MR, Barton HJ, Thompson J, Cuff N, Ariyarathne M, Yakandawala D, Sotelo G, Zeng K, Osborne CP, Nosil P, Christin PA. Population-Specific Selection on Standing Variation Generated by Lateral Gene Transfers in a Grass. Curr Biol 2019; 29:3921-3927.e5. [DOI: 10.1016/j.cub.2019.09.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 12/26/2022]
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27
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Dunning LT, Moreno-Villena JJ, Lundgren MR, Dionora J, Salazar P, Adams C, Nyirenda F, Olofsson JK, Mapaura A, Grundy IM, Kayombo CJ, Dunning LA, Kentatchime F, Ariyarathne M, Yakandawala D, Besnard G, Quick WP, Bräutigam A, Osborne CP, Christin PA. Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3255-3268. [PMID: 30949663 PMCID: PMC6598098 DOI: 10.1093/jxb/erz149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/19/2019] [Indexed: 05/23/2023]
Abstract
C4 photosynthesis is a complex trait that boosts productivity in tropical conditions. Compared with C3 species, the C4 state seems to require numerous novelties, but species comparisons can be confounded by long divergence times. Here, we exploit the photosynthetic diversity that exists within a single species, the grass Alloteropsis semialata, to detect changes in gene expression associated with different photosynthetic phenotypes. Phylogenetically informed comparative transcriptomics show that intermediates with a weak C4 cycle are separated from the C3 phenotype by increases in the expression of 58 genes (0.22% of genes expressed in the leaves), including those encoding just three core C4 enzymes: aspartate aminotransferase, phosphoenolpyruvate carboxykinase, and phosphoenolpyruvate carboxylase. The subsequent transition to full C4 physiology was accompanied by increases in another 15 genes (0.06%), including only the core C4 enzyme pyruvate orthophosphate dikinase. These changes probably created a rudimentary C4 physiology, and isolated populations subsequently improved this emerging C4 physiology, resulting in a patchwork of expression for some C4 accessory genes. Our work shows how C4 assembly in A. semialata happened in incremental steps, each requiring few alterations over the previous step. These create short bridges across adaptive landscapes that probably facilitated the recurrent origins of C4 photosynthesis through a gradual process of evolution.
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Affiliation(s)
- Luke T Dunning
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | | | - Marjorie R Lundgren
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | | | - Paolo Salazar
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Claire Adams
- Botany Department, Rhodes University, Grahamstown, South Africa
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Jill K Olofsson
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | | | - Isla M Grundy
- Institute of Environmental Studies, University of Zimbabwe, Harare, Zimbabwe
| | | | - Lucy A Dunning
- Department of Social Sciences, University of Sheffield, Sheffield, UK
| | | | - Menaka Ariyarathne
- Department of Botany, Faculty of Science, University of Peradeniya, Peradeiya, Sri Lanka
| | - Deepthi Yakandawala
- Department of Botany, Faculty of Science, University of Peradeniya, Peradeiya, Sri Lanka
| | - Guillaume Besnard
- Laboratoire Évolution et Diversité Biologique (EDB UMR5174), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - W Paul Quick
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | | | - Colin P Osborne
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
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28
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Olofsson JK, Cantera I, Van de Paer C, Hong-Wa C, Zedane L, Dunning LT, Alberti A, Christin PA, Besnard G. Phylogenomics using low-depth whole genome sequencing: A case study with the olive tribe. Mol Ecol Resour 2019; 19:877-892. [PMID: 30934146 DOI: 10.1111/1755-0998.13016] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 12/20/2022]
Abstract
Species trees have traditionally been inferred from a few selected markers, and genome-wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historical species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these data sets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Here we evaluate different reference-based methods to infer phylogenies of large taxonomic groups from such data sets. Using the example of the Oleeae tribe, a worldwide-distributed group, we build phylogenies based on single nucleotide polymorphisms (SNPs) obtained using two reference genomes (the olive and ash trees). The inferred phylogenies are overall congruent, yet present differences that might reflect the effect of distance to the reference on the amount of missing data. To limit this issue, genome complexity was reduced by using pairs of orthologous coding sequences as the reference, thus allowing us to combine SNPs obtained using two distinct references. Concatenated and coalescence trees based on these combined SNPs suggest events of incomplete lineage sorting and/or hybridization during the diversification of this large phylogenetic group. Our results show that genome-wide phylogenetic trees can be inferred from low-depth sequence data sets for eukaryote groups with complex genomes, and histories of reticulate evolution. This opens new avenues for large-scale phylogenomics and biogeographical analyses covering both the extant and the historical diversity stored in museum collections.
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Affiliation(s)
- Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Isabel Cantera
- Laboratoire Évolution and Diversité Biologique (EDB, UMR5174), CNRS, UPS, IRD, Université de Toulouse, Toulouse, France
| | - Céline Van de Paer
- Laboratoire Évolution and Diversité Biologique (EDB, UMR5174), CNRS, UPS, IRD, Université de Toulouse, Toulouse, France
| | - Cynthia Hong-Wa
- Claude E. Phillips Herbarium, Delaware State University, Dover, Delaware
| | - Loubab Zedane
- Laboratoire Évolution and Diversité Biologique (EDB, UMR5174), CNRS, UPS, IRD, Université de Toulouse, Toulouse, France
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Adriana Alberti
- Genoscope, CEA - Institut de biologie François-Jacob, Evry Cedex, France
| | | | - Guillaume Besnard
- Laboratoire Évolution and Diversité Biologique (EDB, UMR5174), CNRS, UPS, IRD, Université de Toulouse, Toulouse, France
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29
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Moreno-Villena JJ, Dunning LT, Osborne CP, Christin PA. Highly Expressed Genes Are Preferentially Co-Opted for C4 Photosynthesis. Mol Biol Evol 2019; 35:94-106. [PMID: 29040657 PMCID: PMC5850498 DOI: 10.1093/molbev/msx269] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Novel adaptations are generally assembled by co-opting pre-existing genetic components, but the factors dictating the suitability of genes for new functions remain poorly known. In this work, we used comparative transcriptomics to determine the attributes that increased the likelihood of some genes being co-opted for C4 photosynthesis, a convergent complex trait that boosts productivity in tropical conditions. We show that independent lineages of grasses repeatedly co-opted the gene lineages that were the most highly expressed in non-C4 ancestors to produce their C4 pathway. Although ancestral abundance in leaves explains which genes were used for the emergence of a C4 pathway, the tissue specificity has surprisingly no effect. Our results suggest that levels of key genes were elevated during the early diversification of grasses and subsequently repeatedly used to trigger a weak C4 cycle via relatively few mutations. The abundance of C4-suitable transcripts therefore facilitated physiological innovation, but the transition to a strong C4 pathway still involved consequent changes in expression levels, leaf specificity, and coding sequences. The direction and amount of changes required for the strong C4 pathway depended on the identity of the genes co-opted, so that ancestral gene expression both facilitates adaptive transitions and constrains subsequent evolutionary trajectories.
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Affiliation(s)
| | - Luke T Dunning
- Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Colin P Osborne
- Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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30
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Abstract
A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism's adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its mutation rate. Lateral gene transfer (LGT) theoretically provides a mechanism to bypass many of these limitations, but the evolutionary importance and frequency of this process in multicellular eukaryotes, such as plants, remains debated. We address this issue by assembling a chromosome-level genome for the grass Alloteropsis semialata, a species surmised to exhibit two LGTs, and screen it for other grass-to-grass LGTs using genomic data from 146 other grass species. Through stringent phylogenomic analyses, we discovered 57 additional LGTs in the A. semialata nuclear genome, involving at least nine different donor species. The LGTs are clustered in 23 laterally acquired genomic fragments that are up to 170 kb long and have accumulated during the diversification of Alloteropsis. The majority of the 59 LGTs in A. semialata are expressed, and we show that they have added functions to the recipient genome. Functional LGTs were further detected in the genomes of five other grass species, demonstrating that this process is likely widespread in this globally important group of plants. LGT therefore appears to represent a potent evolutionary force capable of spreading functional genes among distantly related grass species.
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31
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Lundgren MR, Dunning LT, Olofsson JK, Moreno‐Villena JJ, Bouvier JW, Sage TL, Khoshravesh R, Sultmanis S, Stata M, Ripley BS, Vorontsova MS, Besnard G, Adams C, Cuff N, Mapaura A, Bianconi ME, Long CM, Christin P, Osborne CP. C 4 anatomy can evolve via a single developmental change. Ecol Lett 2019; 22:302-312. [PMID: 30557904 PMCID: PMC6849723 DOI: 10.1111/ele.13191] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 01/05/2023]
Abstract
C4 photosynthesis is a complex trait that boosts productivity in warm environments. Paradoxically, it evolved independently in numerous plant lineages, despite requiring specialised leaf anatomy. The anatomical modifications underlying C4 evolution have previously been evaluated through interspecific comparisons, which capture numerous changes besides those needed for C4 functionality. Here, we quantify the anatomical changes accompanying the transition between non-C4 and C4 phenotypes by sampling widely across the continuum of leaf anatomical traits in the grass Alloteropsis semialata. Within this species, the only trait that is shared among and specific to C4 individuals is an increase in vein density, driven specifically by minor vein development that yields multiple secondary effects facilitating C4 function. For species with the necessary anatomical preconditions, developmental proliferation of veins can therefore be sufficient to produce a functional C4 leaf anatomy, creating an evolutionary entry point to complex C4 syndromes that can become more specialised.
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Affiliation(s)
- Marjorie R. Lundgren
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
- Present address:
Lancaster Environment CentreLancaster UniversityLancasterLA1 4YQUK
| | - Luke T. Dunning
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Jill K. Olofsson
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Jose J. Moreno‐Villena
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Jacques W. Bouvier
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Tammy L. Sage
- Department of Ecology and Evolutionary BiologyUniversity of Toronto25 Willcocks StreetTorontoONM5S 3B2Canada
| | - Roxana Khoshravesh
- Department of Ecology and Evolutionary BiologyUniversity of Toronto25 Willcocks StreetTorontoONM5S 3B2Canada
| | - Stefanie Sultmanis
- Department of Ecology and Evolutionary BiologyUniversity of Toronto25 Willcocks StreetTorontoONM5S 3B2Canada
| | - Matt Stata
- Department of Ecology and Evolutionary BiologyUniversity of Toronto25 Willcocks StreetTorontoONM5S 3B2Canada
| | - Brad S. Ripley
- Botany DepartmentRhodes UniversityGrahamstown6139South Africa
| | - Maria S. Vorontsova
- Comparative Plant and Fungal BiologyRoyal Botanic GardensKewRichmondSurreyTW9 3ABUK
| | - Guillaume Besnard
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174)Université de ToulouseCNRSENSFEAUPSIRD118 route de Narbonne31062ToulouseFrance
| | - Claire Adams
- Botany DepartmentRhodes UniversityGrahamstown6139South Africa
| | - Nicholas Cuff
- Northern Territory HerbariumDepartment of Environment and Natural ResourcesPO Box 496PalmerstonNT0831Australia
| | | | - Matheus E. Bianconi
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Christine M. Long
- Department of Primary Industry and FisheriesNorthern Territory GovernmentDarwinNT0801Australia
| | - Pascal‐Antoine Christin
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Colin P. Osborne
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
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32
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Pignon CP, Lundgren MR, Osborne CP, Long SP. Bundle sheath chloroplast volume can house sufficient Rubisco to avoid limiting C4 photosynthesis during chilling. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:357-365. [PMID: 30407578 PMCID: PMC6305190 DOI: 10.1093/jxb/ery345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/13/2018] [Indexed: 05/15/2023]
Abstract
C4 leaves confine Rubisco to bundle sheath cells. Thus, the size of bundle sheath compartments and the total volume of chloroplasts within them limit the space available for Rubisco. Rubisco activity limits photosynthesis at low temperatures. C3 plants counter this limitation by increasing leaf Rubisco content, yet few C4 species do the same. Because C3 plants usually outperform C4 plants in chilling environments, it has been suggested that there is insufficient chloroplast volume available in the bundle sheath of C4 leaves to allow such an increase in Rubisco at low temperatures. We investigated this potential limitation by measuring bundle sheath and mesophyll compartment volumes and chloroplast contents, as well as leaf thickness and inter-veinal distance, in three C4 Andropogoneae grasses: two crops (Zea mays and Saccharum officinarum) and a wild, chilling-tolerant grass (Miscanthus × giganteus). A wild C4 Paniceae grass (Alloteropsis semialata) was also included. Despite significant structural differences between species, there was no evidence of increased bundle sheath chloroplast volume per leaf area available to the chilling-tolerant species, relative to the chilling-sensitive ones. Maximal theoretical photosynthetic capacity of the leaf far exceeded the photosynthetic rates achieved even at low temperatures. C4 bundle sheath cells therefore have the chloroplast volume to house sufficient Rubisco to avoid limiting C4 photosynthesis during chilling.
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Affiliation(s)
- Charles P Pignon
- University of Illinois, Carl R. Woese Institute for Genomic Biology and Departments of Crop Sciences and of Plant Biology, Urbana, IL, USA
| | - Marjorie R Lundgren
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, USA
- Arnold Arboretum, Harvard University, Boston, USA
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Colin P Osborne
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield, UK
| | - Stephen P Long
- University of Illinois, Carl R. Woese Institute for Genomic Biology and Departments of Crop Sciences and of Plant Biology, Urbana, IL, USA
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
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33
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Zhou H, Helliker BR, Huber M, Dicks A, Akçay E. C 4 photosynthesis and climate through the lens of optimality. Proc Natl Acad Sci U S A 2018; 115:12057-12062. [PMID: 30401739 PMCID: PMC6255158 DOI: 10.1073/pnas.1718988115] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
CO2, temperature, water availability, and light intensity were all potential selective pressures that determined the competitive advantage and expansion of the C4 photosynthetic carbon-concentrating mechanism over the last ∼30 My. To tease apart how selective pressures varied along the ecological trajectory of C4 expansion and dominance, we coupled hydraulics to photosynthesis models while optimizing photosynthesis over stomatal resistance and leaf/fine-root allocation. We further examined the importance of nitrogen reallocation from the dark to the light reactions. We show here that the primary selective pressures favoring C4 dominance changed through the course of C4 evolution. The higher stomatal resistance and leaf-to-root ratios enabled by C4 led to an advantage without any initial difference in hydraulic properties. We further predict a reorganization of the hydraulic system leading to higher turgor-loss points and possibly lower hydraulic conductance. Selection on nitrogen reallocation varied with CO2 concentration. Through paleoclimate model simulations, we find that water limitation was the primary driver for a C4 advantage, with atmospheric CO2 as high as 600 ppm, thus confirming molecular-based estimates for C4 evolution in the Oligocene. Under these high-CO2 conditions, nitrogen reallocation was necessary. Low CO2 and high light, but not nitrogen reallocation, were the primary drivers for the mid- to late-Miocene global expansion of C4 We also predicted the timing and spatial distribution for origins of C4 ecological dominance. The predicted origins are broadly consistent with prior estimates, but expand upon them to include a center of origin in northwest Africa and a Miocene-long origin in Australia.
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Affiliation(s)
- Haoran Zhou
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104;
| | - Brent R Helliker
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Matthew Huber
- Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, IN 47907
| | - Ashley Dicks
- Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, West Lafayette, IN 47907
| | - Erol Akçay
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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34
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Burke SV, Ungerer MC, Duvall MR. Investigation of mitochondrial-derived plastome sequences in the Paspalum lineage (Panicoideae; Poaceae). BMC PLANT BIOLOGY 2018; 18:152. [PMID: 30075756 PMCID: PMC6091044 DOI: 10.1186/s12870-018-1379-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/30/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND The grass family (Poaceae), ca. 12,075 species, is a focal point of many recent studies that aim to use complete plastomes to reveal and strengthen relationships within the family. The use of Next Generation Sequencing technology has revealed intricate details in many Poaceae plastomes; specifically the trnI - trnL intergenic spacer region. This study investigates this region and the putative mitochondrial inserts within it in complete plastomes of Paspalum and other Poaceae. RESULTS Nine newly sequenced plastomes, seven of which contain an insert within the trnI - trnL intergenic spacer, were combined into plastome phylogenomic and divergence date analyses with 52 other species. A robust Paspalum topology was recovered, originating at 10.6 Ma, with the insert arising at 8.7 Ma. The alignment of the insert across Paspalum reveals 21 subregions with pairwise homology in 19. In an analysis of emergent self-organizing maps of tetranucleotide frequencies, the Paspalum insert grouped with mitochondrial DNA. CONCLUSIONS A hypothetical ancestral insert, 17,685 bp in size, was found in the trnI - trnL intergenic spacer for the Paspalum lineage. A different insert, 2808 bp, was found in the same region for Paraneurachne muelleri. Seven different intrastrand deletion events were found within the Paspalum lineage, suggesting selective pressures to remove large portions of noncoding DNA. Finally, a tetranucleotide frequency analysis was used to determine that the origin of the insert in the Paspalum lineage is mitochondrial DNA.
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Affiliation(s)
- Sean V. Burke
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861 USA
| | - Mark C. Ungerer
- Division of Biology, Kansas State University, 1717 Claflin Rd, Manhattan, KS 66506-4900 USA
| | - Melvin R. Duvall
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861 USA
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Some like it hot: the physiological ecology of C 4 plant evolution. Oecologia 2018; 187:941-966. [PMID: 29955992 DOI: 10.1007/s00442-018-4191-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 06/05/2018] [Indexed: 10/28/2022]
Abstract
The evolution of C4 photosynthesis requires an intermediate phase where photorespiratory glycine produced in the mesophyll cells must flow to the vascular sheath cells for metabolism by glycine decarboxylase. This glycine flux concentrates photorespired CO2 within the sheath cells, allowing it to be efficiently refixed by sheath Rubisco. A modest C4 biochemical cycle is then upregulated, possibly to support the refixation of photorespired ammonia in sheath cells, with subsequent increases in C4 metabolism providing incremental benefits until an optimized C4 pathway is established. 'Why' C4 photosynthesis evolved is largely explained by ancestral C3 species exploiting photorespiratory CO2 to improve carbon gain and thus enhance fitness. While photorespiration depresses C3 performance, it produces a resource (photorespired CO2) that can be exploited to build an evolutionary bridge to C4 photosynthesis. 'Where' C4 evolved is indicated by the habitat of species branching near C3-to-C4 transitions on phylogenetic trees. Consistent with the photorespiratory bridge hypothesis, transitional species show that the large majority of > 60 C4 lineages arose in hot, dry, and/or saline regions where photorespiratory potential is high. 'When' C4 evolved has been clarified by molecular clock analyses using phylogenetic data, coupled with isotopic signatures from fossils. Nearly all C4 lineages arose after 25 Ma when atmospheric CO2 levels had fallen to near current values. This reduction in CO2, coupled with persistent high temperature at low-to-mid-latitudes, met a precondition where photorespiration was elevated, thus facilitating the evolutionary selection pressure that led to C4 photosynthesis.
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36
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Taylor SH, Aspinwall MJ, Blackman CJ, Choat B, Tissue DT, Ghannoum O. CO2 availability influences hydraulic function of C3 and C4 grass leaves. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2731-2741. [PMID: 29538702 PMCID: PMC5920307 DOI: 10.1093/jxb/ery095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/03/2018] [Indexed: 05/12/2023]
Abstract
Atmospheric CO2 (ca) has increased since the last glacial period, increasing photosynthetic water use efficiency and improving plant productivity. Evolution of C4 photosynthesis at low ca led to decreased stomatal conductance (gs), which provided an advantage over C3 plants that may be reduced by rising ca. Using controlled environments, we determined how increasing ca affects C4 water use relative to C3 plants. Leaf gas exchange and mass per area (LMA) were measured for four C3 and four C4 annual, crop-related grasses at glacial (200 µmol mol-1), ambient (400 µmol mol-1), and super-ambient (640 µmol mol-1) ca. C4 plants had lower gs, which resulted in a water use efficiency advantage at all ca and was broadly consistent with slower stomatal responses to shade, indicating less pressure on leaf water status. At glacial ca, net CO2 assimilation and LMA were lower for C3 than for C4 leaves, and C3 and C4 grasses decreased leaf hydraulic conductance (Kleaf) similarly, but only C4 leaves decreased osmotic potential at turgor loss. Greater carbon availability in C4 leaves at glacial ca generated a different hydraulic adjustment relative to C3 plants. At current and future ca, C4 grasses have advantages over C3 grasses due to lower gs, lower stomatal sensitivity, and higher absolute water use efficiency.
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Affiliation(s)
- Samuel H Taylor
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW, Australia
- Lancaster Environment Centre, University of Lancaster, Lancaster, UK
| | - Michael J Aspinwall
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW, Australia
- Department of Biology, University of North Florida, Drive, Jacksonville, FL, USA
| | - Chris J Blackman
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW, Australia
| | - Brendan Choat
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW, Australia
| | - Oula Ghannoum
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith NSW, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Australia
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Bianconi ME, Dunning LT, Moreno-Villena JJ, Osborne CP, Christin PA. Gene duplication and dosage effects during the early emergence of C4 photosynthesis in the grass genus Alloteropsis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1967-1980. [PMID: 29394370 PMCID: PMC6018922 DOI: 10.1093/jxb/ery029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/17/2018] [Indexed: 05/04/2023]
Abstract
The importance of gene duplication for evolutionary diversification has been mainly discussed in terms of genetic redundancy allowing neofunctionalization. In the case of C4 photosynthesis, which evolved via the co-option of multiple enzymes to boost carbon fixation in tropical conditions, the importance of genetic redundancy has not been consistently supported by genomic studies. Here, we test for a different role for gene duplication in the early evolution of C4 photosynthesis, via dosage effects creating rapid step changes in expression levels. Using genome-wide data for accessions of the grass genus Alloteropsis that recently diversified into different photosynthetic types, we estimate gene copy numbers and demonstrate that recurrent duplications in two important families of C4 genes coincided with increases in transcript abundance along the phylogeny, in some cases via a pure dosage effect. While increased gene copy number during the initial emergence of C4 photosynthesis probably offered a rapid route to enhanced expression, we also find losses of duplicates following the acquisition of genes encoding better-suited isoforms. The dosage effect of gene duplication might therefore act as a transient process during the evolution of a C4 biochemistry, rendered obsolete by the fixation of regulatory mutations increasing expression levels.
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Affiliation(s)
- Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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38
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Saarela JM, Burke SV, Wysocki WP, Barrett MD, Clark LG, Craine JM, Peterson PM, Soreng RJ, Vorontsova MS, Duvall MR. A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions. PeerJ 2018; 6:e4299. [PMID: 29416954 PMCID: PMC5798404 DOI: 10.7717/peerj.4299] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/08/2018] [Indexed: 12/23/2022] Open
Abstract
The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.
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Affiliation(s)
- Jeffery M. Saarela
- Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, ON, Canada
| | - Sean V. Burke
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - William P. Wysocki
- Center for Data Intensive Sciences, University of Chicago, Chicago, IL, USA
| | - Matthew D. Barrett
- Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, West Perth, WA, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Lynn G. Clark
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Paul M. Peterson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Robert J. Soreng
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Maria S. Vorontsova
- Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Melvin R. Duvall
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA
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39
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Watcharamongkol T, Christin PA, Osborne CP. C4photosynthesis evolved in warm climates but promoted migration to cooler ones. Ecol Lett 2018; 21:376-383. [DOI: 10.1111/ele.12905] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/01/2017] [Accepted: 11/22/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Teera Watcharamongkol
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | | | - Colin P. Osborne
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
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40
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Moreno-Villena JJ, Dunning LT, Osborne CP, Christin PA. Highly Expressed Genes Are Preferentially Co-Opted for C4 Photosynthesis. Mol Biol Evol 2018. [PMID: 29040657 DOI: 10.1093/molbev/msx269/4457558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Novel adaptations are generally assembled by co-opting pre-existing genetic components, but the factors dictating the suitability of genes for new functions remain poorly known. In this work, we used comparative transcriptomics to determine the attributes that increased the likelihood of some genes being co-opted for C4 photosynthesis, a convergent complex trait that boosts productivity in tropical conditions. We show that independent lineages of grasses repeatedly co-opted the gene lineages that were the most highly expressed in non-C4 ancestors to produce their C4 pathway. Although ancestral abundance in leaves explains which genes were used for the emergence of a C4 pathway, the tissue specificity has surprisingly no effect. Our results suggest that levels of key genes were elevated during the early diversification of grasses and subsequently repeatedly used to trigger a weak C4 cycle via relatively few mutations. The abundance of C4-suitable transcripts therefore facilitated physiological innovation, but the transition to a strong C4 pathway still involved consequent changes in expression levels, leaf specificity, and coding sequences. The direction and amount of changes required for the strong C4 pathway depended on the identity of the genes co-opted, so that ancestral gene expression both facilitates adaptive transitions and constrains subsequent evolutionary trajectories.
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Affiliation(s)
| | - Luke T Dunning
- Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Colin P Osborne
- Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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41
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Linder HP, Lehmann CER, Archibald S, Osborne CP, Richardson DM. Global grass (Poaceae) success underpinned by traits facilitating colonization, persistence and habitat transformation. Biol Rev Camb Philos Soc 2017; 93:1125-1144. [PMID: 29230921 DOI: 10.1111/brv.12388] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 11/02/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022]
Abstract
Poaceae (the grasses) is arguably the most successful plant family, in terms of its global occurrence in (almost) all ecosystems with angiosperms, its ecological dominance in many ecosystems, and high species richness. We suggest that the success of grasses is best understood in context of their capacity to colonize, persist, and transform environments (the "Viking syndrome"). This results from combining effective long-distance dispersal, efficacious establishment biology, ecological flexibility, resilience to disturbance and the capacity to modify environments by changing the nature of fire and mammalian herbivory. We identify a diverse set of functional traits linked to dispersal, establishment and competitive abilities. Enhanced long-distance dispersal is determined by anemochory, epizoochory and endozoochory and is facilitated via the spikelet (and especially the awned lemma) which functions as the dispersal unit. Establishment success could be a consequence of the precocious embryo and large starch reserves, which may underpin the extremely short generation times in grasses. Post-establishment genetic bottlenecks may be mitigated by wind pollination and the widespread occurrence of polyploidy, in combination with gametic self-incompatibility. The ecological competitiveness of grasses is corroborated by their dominance across the range of environmental extremes tolerated by angiosperms, facilitated by both C3 and C4 photosynthesis, well-developed frost tolerance in several clades, and a sympodial growth form that enabled the evolution of both annual and long-lived life forms. Finally, absence of investment in wood (except in bamboos), and the presence of persistent buds at or below ground level, provides tolerance of repeated defoliation (whether by fire, frost, drought or herbivores). Biotic modification of environments via feedbacks with herbivory or fire reinforce grass dominance leading to open ecosystems. Grasses can be both palatable and productive, fostering high biomass and diversity of mammalian herbivores. Many grasses have a suite of architectural and functional traits that facilitate frequent fire, including a tufted growth form, and tannin-like substances in leaves which slow decomposition. We mapped these traits over the phylogeny of the Poales, spanning the grasses and their relatives, and demonstrated the accumulation of traits since monocots originated in the mid-Cretaceous. Although the sympodial growth form is a monocot trait, tillering resulting in the tufted growth form most likely evolved within the grasses. Similarly, although an ovary apparently constructed of a single carpel evolved in the most recent grass ancestor, spikelets and the awned lemma dispersal units evolved within the grasses. Frost tolerance and C4 photosynthesis evolved relatively late (late Palaeogene), and the last significant trait to evolve was probably the production of tannins, associated with pyrophytic savannas. This fits palaeobotanical data, suggesting several phases in the grass success story: from a late Cretaceous origin, to occasional tropical grassland patches in the later Palaeogene, to extensive C3 grassy woodlands in the early-middle Miocene, to the dramatic expansion of the tropical C4 grass savannas and grasslands in the Pliocene, and the C3 steppe grasslands during the Pleistocene glacial periods. Modern grasslands depend heavily on strongly seasonal climates, making them sensitive to climate change.
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Affiliation(s)
- H P Linder
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, Switzerland
| | - Caroline E R Lehmann
- School of GeoSciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.,Centre for African Ecology, School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, Private Bag X3, WITS, 2050, South Africa
| | - Sally Archibald
- Centre for African Ecology, School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, Private Bag X3, WITS, 2050, South Africa
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, U.K
| | - David M Richardson
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Matieland, 7602, South Africa
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42
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Dunning LT, Lundgren MR, Moreno-Villena JJ, Namaganda M, Edwards EJ, Nosil P, Osborne CP, Christin PA. Introgression and repeated co-option facilitated the recurrent emergence of C 4 photosynthesis among close relatives. Evolution 2017; 71:1541-1555. [PMID: 28395112 PMCID: PMC5488178 DOI: 10.1111/evo.13250] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 04/04/2017] [Indexed: 01/16/2023]
Abstract
The origins of novel traits are often studied using species trees and modeling phenotypes as different states of the same character, an approach that cannot always distinguish multiple origins from fewer origins followed by reversals. We address this issue by studying the origins of C4 photosynthesis, an adaptation to warm and dry conditions, in the grass Alloteropsis. We dissect the C4 trait into its components, and show two independent origins of the C4 phenotype via different anatomical modifications, and the use of distinct sets of genes. Further, inference of enzyme adaptation suggests that one of the two groups encompasses two transitions to a full C4 state from a common ancestor with an intermediate phenotype that had some C4 anatomical and biochemical components. Molecular dating of C4 genes confirms the introgression of two key C4 components between species, while the inheritance of all others matches the species tree. The number of origins consequently varies among C4 components, a scenario that could not have been inferred from analyses of the species tree alone. Our results highlight the power of studying individual components of complex traits to reconstruct trajectories toward novel adaptations.
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Affiliation(s)
- Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Jose J Moreno-Villena
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | | | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, 02912
| | - Patrik Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
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43
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Baker TR, Pennington RT, Dexter KG, Fine PVA, Fortune-Hopkins H, Honorio EN, Huamantupa-Chuquimaco I, Klitgård BB, Lewis GP, de Lima HC, Ashton P, Baraloto C, Davies S, Donoghue MJ, Kaye M, Kress WJ, Lehmann CER, Monteagudo A, Phillips OL, Vasquez R. Maximising Synergy among Tropical Plant Systematists, Ecologists, and Evolutionary Biologists. Trends Ecol Evol 2017; 32:258-267. [PMID: 28214038 DOI: 10.1016/j.tree.2017.01.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 11/26/2022]
Abstract
Closer collaboration among ecologists, systematists, and evolutionary biologists working in tropical forests, centred on studies within long-term permanent plots, would be highly beneficial for their respective fields. With a key unifying theme of the importance of vouchered collection and precise identification of species, especially rare ones, we identify four priority areas where improving links between these communities could achieve significant progress in biodiversity and conservation science: (i) increasing the pace of species discovery; (ii) documenting species turnover across space and time; (iii) improving models of ecosystem change; and (iv) understanding the evolutionary assembly of communities and biomes.
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Affiliation(s)
| | | | - Kyle G Dexter
- Royal Botanic Garden Edinburgh, Edinburgh, UK; School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Paul V A Fine
- Department of Integrative Biology and University and Jepson Herbaria, University of California, Berkeley, CA, USA
| | | | | | - Isau Huamantupa-Chuquimaco
- Programa de Pós-Graduação em Botânica, Escola Nacional de Botânica Tropical, Instituto de Pesquisas Jardim Botânico de Rio de Janeiro (ENBT/JBRJ). Rua Pacheco Leão, 2040. RJ, Brazil
| | - Bente B Klitgård
- Department for Identification and Naming, Royal Botanic Gardens, Kew, UK
| | - Gwilym P Lewis
- Department for Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, UK
| | - Haroldo C de Lima
- Programa de Pós-Graduação em Botânica, Escola Nacional de Botânica Tropical, Instituto de Pesquisas Jardim Botânico de Rio de Janeiro (ENBT/JBRJ). Rua Pacheco Leão, 2040. RJ, Brazil
| | | | - Christopher Baraloto
- International Center for Tropical Botany, Florida International University, Miami, USA
| | - Stuart Davies
- Center for Tropical Forest Science - Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Washington, DC, USA; National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Michael J Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Maria Kaye
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - W John Kress
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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Mahelka V, Krak K, Kopecký D, Fehrer J, Šafář J, Bartoš J, Hobza R, Blavet N, Blattner FR. Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages. Proc Natl Acad Sci U S A 2017; 114:1726-1731. [PMID: 28137844 PMCID: PMC5320982 DOI: 10.1073/pnas.1613375114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley (Hordeum) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some current Hordeum sp. individuals harbor up to five different panicoid rDNA units in addition to the native Hordeum rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a Panicum sp. rDNA unit present in H. bogdanii had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral.
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MESH Headings
- Cell Nucleus/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Diploidy
- Evolution, Molecular
- Gene Transfer, Horizontal
- Genes, Plant/genetics
- Hordeum/classification
- Hordeum/genetics
- Phylogeny
- Poaceae/classification
- Poaceae/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Václav Mahelka
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic;
| | - Karol Krak
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague 6 16500, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Judith Fehrer
- Institute of Botany, The Czech Academy of Sciences, Průhonice 25243, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Roman Hobza
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
- Institute of Biophysics, The Czech Academy of Sciences, Brno 61265, Czech Republic
| | - Nicolas Blavet
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc 78371, Czech Republic
| | - Frank R Blattner
- Experimental Taxonomy, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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45
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Sage RF. A portrait of the C4 photosynthetic family on the 50th anniversary of its discovery: species number, evolutionary lineages, and Hall of Fame. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4039-4056. [PMID: 28110278 DOI: 10.1093/jxb/erx005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Fifty years ago, the C4 photosynthetic pathway was first characterized. In the subsequent five decades, much has been learned about C4 plants, such that it is now possible to place nearly all C4 species into their respective evolutionary lineages. Sixty-one independent lineages of C4 photosynthesis are identified, with additional, ancillary C4 origins possible in 12 of these principal lineages. The lineages produced ~8100 C4 species (5044 grasses, 1322 sedges, and 1777 eudicots). Using midpoints of stem and crown node dates in their respective phylogenies, the oldest and most speciose C4 lineage is the grass lineage Chloridoideae, estimated to be near 30 million years old. Most C4 lineages are estimated to be younger than 15 million years. Older C4 lineages tend to be more speciose, while those younger than 7 million years have <43 species each. To further highlight C4 photosynthesis for a 50th anniversary snapshot, a Hall of Fame comprised of the 40 most significant C4 species is presented. Over the next 50 years, preservation of the Earth's C4 diversity is a concern, largely because of habitat loss due to elevated CO2 effects, invasive species, and expanded agricultural activities. Ironically, some members of the C4 Hall of Fame are leading threats to the natural C4 flora due to their association with human activities on landscapes where most C4 plants occur.
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Affiliation(s)
- Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5R3C6
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Lundgren MR, Christin PA. Despite phylogenetic effects, C3-C4 lineages bridge the ecological gap to C4 photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:241-254. [PMID: 28025316 PMCID: PMC5853900 DOI: 10.1093/jxb/erw451] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/09/2016] [Indexed: 05/25/2023]
Abstract
C4 photosynthesis is a physiological innovation involving several anatomical and biochemical components that emerged recurrently in flowering plants. This complex trait evolved via a series of physiological intermediates, broadly termed 'C3-C4', which have been widely studied to understand C4 origins. While this research program has focused on biochemistry, physiology, and anatomy, the ecology of these intermediates remains largely unexplored. Here, we use global occurrence data and local habitat descriptions to characterize the niches of multiple C3-C4 lineages, as well as their close C3 and C4 relatives. While C3-C4 taxa tend to occur in warm climates, their abiotic niches are spread along other dimensions, making it impossible to define a universal C3-C4 niche. Phylogeny-based comparisons suggest that, despite shifts associated with photosynthetic types, the precipitation component of the C3-C4 niche is particularly lineage specific, being highly correlated with that of closely related C3 and C4 taxa. Our large-scale analyses suggest that C3-C4 lineages converged toward warm habitats, which may have facilitated the transition to C4 photosynthesis, effectively bridging the ecological gap between C3 and C4 plants. The intermediates retained some precipitation aspects of their C3 ancestors' habitat, and likely transmitted them to their C4 descendants, contributing to the diversity among C4 lineages seen today.
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Affiliation(s)
- Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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Olofsson JK, Bianconi M, Besnard G, Dunning LT, Lundgren MR, Holota H, Vorontsova MS, Hidalgo O, Leitch IJ, Nosil P, Osborne CP, Christin P. Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait. Mol Ecol 2016; 25:6107-6123. [PMID: 27862505 PMCID: PMC6849575 DOI: 10.1111/mec.13914] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 10/27/2016] [Accepted: 11/09/2016] [Indexed: 01/17/2023]
Abstract
Physiological novelties are often studied at macro-evolutionary scales such that their micro-evolutionary origins remain poorly understood. Here, we test the hypothesis that key components of a complex trait can evolve in isolation and later be combined by gene flow. We use C4 photosynthesis as a study system, a derived physiology that increases plant productivity in warm, dry conditions. The grass Alloteropsis semialata includes C4 and non-C4 genotypes, with some populations using laterally acquired C4 -adaptive loci, providing an outstanding system to track the spread of novel adaptive mutations. Using genome data from C4 and non-C4 A. semialata individuals spanning the species' range, we infer and date past migrations of different parts of the genome. Our results show that photosynthetic types initially diverged in isolated populations, where key C4 components were acquired. However, rare but recurrent subsequent gene flow allowed the spread of adaptive loci across genetic pools. Indeed, laterally acquired genes for key C4 functions were rapidly passed between populations with otherwise distinct genomic backgrounds. Thus, our intraspecific study of C4 -related genomic variation indicates that components of adaptive traits can evolve separately and later be combined through secondary gene flow, leading to the assembly and optimization of evolutionary innovations.
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Affiliation(s)
- Jill K. Olofsson
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Matheus Bianconi
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Guillaume Besnard
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174)Université de ToulouseCNRS, ENSFEA, UPS118 route de NarbonneF‐31062ToulouseFrance
| | - Luke T. Dunning
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Marjorie R. Lundgren
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Helene Holota
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174)Université de ToulouseCNRS, ENSFEA, UPS118 route de NarbonneF‐31062ToulouseFrance
| | | | | | | | - Patrik Nosil
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Colin P. Osborne
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Pascal‐Antoine Christin
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
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Bellasio C, Lundgren MR. Anatomical constraints to C4 evolution: light harvesting capacity in the bundle sheath. THE NEW PHYTOLOGIST 2016; 212:485-496. [PMID: 27375085 DOI: 10.1111/nph.14063] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/10/2016] [Indexed: 06/06/2023]
Abstract
In C4 photosynthesis CO2 assimilation and reduction are typically coordinated across mesophyll (M) and bundle sheath (BS) cells, respectively. This system consequently requires sufficient light to reach BS to generate enough ATP to allow ribulose-1,5-bisphosphate (RuBP) regeneration in BS. Leaf anatomy influences BS light penetration and therefore constrains C4 cycle functionality. Using an absorption scattering model (coded in Excel, and freely downloadable) we simulate light penetration profiles and rates of ATP production in BS across the C3 , C3 -C4 and C4 anatomical continua. We present a trade-off for light absorption between BS pigment concentration and space allocation. C3 BS anatomy limits light absorption and benefits little from high pigment concentrations. Unpigmented BS extensions increase BS light penetration. C4 and C3 -C4 anatomies have the potential to generate sufficient ATP in the BS, whereas typical C3 anatomy does not, except some C3 taxa closely related to C4 groups. Insufficient volume of BS, relative to M, will hamper a C4 cycle via insufficient BS light absorption. Thus, BS ATP production and RuBP regeneration, coupled with increased BS investments, allow greater operational plasticity. We propose that larger BS in C3 lineages may be co-opted for C3 -C4 and C4 biochemistry requirements.
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Affiliation(s)
- Chandra Bellasio
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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Reeves G, Hibberd JM. Broadening the spectrum of photosynthesis in the grass, Alloteropsis semialata. PLANT, CELL & ENVIRONMENT 2016; 39:1871-1873. [PMID: 26641208 DOI: 10.1111/pce.12685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 06/05/2023]
Abstract
This article comments on: Evolutionary implications of C3 -C4 intermediates in the grass Alloteropsis semialata.
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Affiliation(s)
- Gregory Reeves
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA, UK
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA, UK
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Lundgren MR, Christin PA, Escobar EG, Ripley BS, Besnard G, Long CM, Hattersley PW, Ellis RP, Leegood RC, Osborne CP. Evolutionary implications of C3 -C4 intermediates in the grass Alloteropsis semialata. PLANT, CELL & ENVIRONMENT 2016; 39:1874-1885. [PMID: 26524631 DOI: 10.1111/pce.12665] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 10/21/2015] [Accepted: 10/25/2015] [Indexed: 06/05/2023]
Abstract
C4 photosynthesis is a complex trait resulting from a series of anatomical and biochemical modifications to the ancestral C3 pathway. It is thought to evolve in a stepwise manner, creating intermediates with different combinations of C4 -like components. Determining the adaptive value of these components is key to understanding how C4 photosynthesis can gradually assemble through natural selection. Here, we decompose the photosynthetic phenotypes of numerous individuals of the grass Alloteropsis semialata, the only species known to include both C3 and C4 genotypes. Analyses of δ(13) C, physiology and leaf anatomy demonstrate for the first time the existence of physiological C3 -C4 intermediate individuals in the species. Based on previous phylogenetic analyses, the C3 -C4 individuals are not hybrids between the C3 and C4 genotypes analysed, but instead belong to a distinct genetic lineage, and might have given rise to C4 descendants. C3 A. semialata, present in colder climates, likely represents a reversal from a C3 -C4 intermediate state, indicating that, unlike C4 photosynthesis, evolution of the C3 -C4 phenotype is not irreversible.
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Affiliation(s)
- Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Emmanuel Gonzalez Escobar
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Brad S Ripley
- Botany Department, Rhodes University, Grahamstown, 6139, South Africa
| | - Guillaume Besnard
- CNRS, Université de Toulouse, ENFA, UMR5174 EDB (Laboratoire Évolution and Diversité Biologique), 118 Route de Narbonne, Toulouse, 31062, France
| | - Christine M Long
- Department of Primary Industry and Fisheries, Northern Territory Government, Darwin, NT, 0801, Australia
| | - Paul W Hattersley
- School of Chemistry and Biochemistry (honorary research fellow), University of Western Australia, Crawley, WA, 6009, Australia
| | | | - Richard C Leegood
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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