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Laspisa D, Illa-Berenguer E, Bang S, Schmitz RJ, Parrott W, Wallace J. Mining the Utricularia gibba genome for insulator-like elements for genetic engineering. FRONTIERS IN PLANT SCIENCE 2023; 14:1279231. [PMID: 38023853 PMCID: PMC10663240 DOI: 10.3389/fpls.2023.1279231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Introduction Gene expression is often controlled via cis-regulatory elements (CREs) that modulate the production of transcripts. For multi-gene genetic engineering and synthetic biology, precise control of transcription is crucial, both to insulate the transgenes from unwanted native regulation and to prevent readthrough or cross-regulation of transgenes within a multi-gene cassette. To prevent this activity, insulator-like elements, more properly referred to as transcriptional blockers, could be inserted to separate the transgenes so that they are independently regulated. However, only a few validated insulator-like elements are available for plants, and they tend to be larger than ideal. Methods To identify additional potential insulator-like sequences, we conducted a genome-wide analysis of Utricularia gibba (humped bladderwort), one of the smallest known plant genomes, with genes that are naturally close together. The 10 best insulator-like candidates were evaluated in vivo for insulator-like activity. Results We identified a total of 4,656 intergenic regions with expression profiles suggesting insulator-like activity. Comparisons of these regions across 45 other plant species (representing Monocots, Asterids, and Rosids) show low levels of syntenic conservation of these regions. Genome-wide analysis of unmethylated regions (UMRs) indicates ~87% of the targeted regions are unmethylated; however, interpretation of this is complicated because U. gibba has remarkably low levels of methylation across the genome, so that large UMRs frequently extend over multiple genes and intergenic spaces. We also could not identify any conserved motifs among our selected intergenic regions or shared with existing insulator-like elements for plants. Despite this lack of conservation, however, testing of 10 selected intergenic regions for insulator-like activity found two elements on par with a previously published element (EXOB) while being significantly smaller. Discussion Given the small number of insulator-like elements currently available for plants, our results make a significant addition to available tools. The high hit rate (2 out of 10) also implies that more useful sequences are likely present in our selected intergenic regions; additional validation work will be required to identify which will be most useful for plant genetic engineering.
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Affiliation(s)
- Daniel Laspisa
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Eudald Illa-Berenguer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Sohyun Bang
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Wayne Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Science & Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Jason Wallace
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Department of Crop & Soil Science & Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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Fleck SJ, Jobson RW. Molecular Phylogenomics Reveals the Deep Evolutionary History of Carnivory across Land Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3356. [PMID: 37836100 PMCID: PMC10574757 DOI: 10.3390/plants12193356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023]
Abstract
Plastid molecular phylogenies that broadly sampled angiosperm lineages imply that carnivorous plants evolved at least 11 times independently in 13 families and 6 orders. Within and between these clades, the different prey capture strategies involving flypaper and pitfall structures arose in parallel with the subsequent evolution of snap traps and suction bladders. Attempts to discern the deep ontological history of carnivorous structures using multigene phylogenies have provided a plastid-level picture of sister relationships at the family level. Here, we present a molecular phylogeny of the angiosperms based on nuclear target sequence capture data (Angiosperms-353 probe set), assembled by the Kew Plant Trees of Life initiative, which aims to complete the tree of life for plants. This phylogeny encompasses all carnivorous and protocarnivorous families, although certain genera such as Philcoxia (Plantaginaceae) are excluded. This study offers a novel nuclear gene-based overview of relationships within and between carnivorous families and genera. Consistent with previous broadly sampled studies, we found that most carnivorous families are not affiliated with any single family. Instead, they emerge as sister groups to large clades comprising multiple non-carnivorous families. Additionally, we explore recent genomic studies across various carnivorous clades that examine the evolution of the carnivorous syndrome in relation to whole-genome duplication, subgenome dominance, small-scale gene duplication, and convergent evolution. Furthermore, we discuss insights into genome size evolution through the lens of carnivorous plant genomes.
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Affiliation(s)
- Steven J. Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Richard W. Jobson
- National Herbarium of New South Wales, Botanic Gardens of Sydney, Locked Bag 6002, Mount Annan, NSW 2567, Australia
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3
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Smith SA, Walker-Hale N, Parins-Fukuchi CT. Compositional shifts associated with major evolutionary transitions in plants. THE NEW PHYTOLOGIST 2023; 239:2404-2415. [PMID: 37381083 DOI: 10.1111/nph.19099] [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: 03/10/2023] [Accepted: 06/04/2023] [Indexed: 06/30/2023]
Abstract
Heterogeneity in gene trees, morphological characters, and composition has been associated with several major plant clades. Here, we examine heterogeneity in composition across a large transcriptomic dataset of plants to better understand whether locations of shifts in composition are shared across gene regions and whether directions of shifts within clades are shared across gene regions. We estimate mixed models of composition for both nucleotide and amino acids across a recent large-scale transcriptomic dataset for plants. We find shifts in composition across both nucleotide and amino acid datasets, with more shifts detected in nucleotides. We find that Chlorophytes and lineages within experience the most shifts. However, many shifts occur at the origins of land, vascular, and seed plants. While genes in these clades do not typically share the same composition, they tend to shift in the same direction. We discuss potential causes of these patterns. Compositional heterogeneity has been highlighted as a potential problem for phylogenetic analysis, but the variation presented here highlights the need to further investigate these patterns for the signal of biological processes.
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Affiliation(s)
- Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48103, USA
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Silva SR, Miranda VFO, Michael TP, Płachno BJ, Matos RG, Adamec L, Pond SLK, Lucaci AG, Pinheiro DG, Varani AM. The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae). Mol Phylogenet Evol 2023; 181:107711. [PMID: 36693533 DOI: 10.1016/j.ympev.2023.107711] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT) and mitochondrial (MT) genes of 26 Utricularia and six Genlisea species, with representatives of all subgenera and growth habits. All PT genomes maintain similar gene content, showing minor variation across the genes located between the PT junctions. One exception is a major variation related to different patterns in the presence and absence of ndh genes in the small single copy region, which appears to follow the phylogenetic history of the species rather than their lifestyle. All MT genomes exhibit similar gene content, with most differences related to a lineage-specific pseudogenes. We find evidence for episodic positive diversifying selection in PT and for most of the Utricularia MT genes that may be related to the current hypothesis that bladderworts' nuclear DNA is under constant ROS oxidative DNA damage and unusual DNA repair mechanisms, or even low fidelity polymerase that bypass lesions which could also be affecting the organellar genomes. Finally, both PT and MT phylogenetic trees were well resolved and highly supported, providing a congruent phylogenomic hypothesis for Utricularia and Genlisea clade given the study sampling.
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Affiliation(s)
- Saura R Silva
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Vitor F O Miranda
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Biology, Laboratory of Plant Systematics, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, Gronostajowa 9 St., 30-387 Cracow, Poland.
| | - Ramon G Matos
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Biology, Laboratory of Plant Systematics, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Lubomir Adamec
- Department of Experimental and Functional Morphology, Institute of Botany CAS, Dukelská 135, CZ-379 01 Třeboň, Czech Republic.
| | - Sergei L K Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
| | - Daniel G Pinheiro
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Alessandro M Varani
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
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Elliott TL, Zedek F, Barrett RL, Bruhl JJ, Escudero M, Hroudová Z, Joly S, Larridon I, Luceño M, Márquez-Corro JI, Martín-Bravo S, Muasya AM, Šmarda P, Thomas WW, Wilson KL, Bureš P. Chromosome size matters: genome evolution in the cyperid clade. ANNALS OF BOTANY 2022; 130:999-1014. [PMID: 36342743 PMCID: PMC9851305 DOI: 10.1093/aob/mcac136] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/03/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS While variation in genome size and chromosome numbers and their consequences are often investigated in plants, the biological relevance of variation in chromosome size remains poorly known. Here, we examine genome and mean chromosome size in the cyperid clade (families Cyperaceae, Juncaceae and Thurniaceae), which is the largest vascular plant lineage with predominantly holocentric chromosomes. METHODS We measured genome size in 436 species of cyperids using flow cytometry, and augment these data with previously published datasets. We then separately compared genome and mean chromosome sizes (2C/2n) amongst the major lineages of cyperids and analysed how these two genomic traits are associated with various environmental factors using phylogenetically informed methods. KEY RESULTS We show that cyperids have the smallest mean chromosome sizes recorded in seed plants, with a large divergence between the smallest and largest values. We found that cyperid species with smaller chromosomes have larger geographical distributions and that there is a strong inverse association between mean chromosome size and number across this lineage. CONCLUSIONS The distinct patterns in genome size and mean chromosome size across the cyperids might be explained by holokinetic drive. The numerous small chromosomes might function to increase genetic diversity in this lineage where crossovers are limited during meiosis.
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Affiliation(s)
- Tammy L Elliott
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Institute of Botanical Science, Australian Botanic Garden, Locked Bag 6002, Mount Annan, New South Wales 2567, Australia
| | - Jeremy J Bruhl
- Botany and N.C.W. Beadle Herbarium, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Reina Mercedes 6, 41012 Seville, Spain
| | - Zdenka Hroudová
- Institute of Botany of the Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
- National Museum, Department of Botany, Cirkusová 1740, 193 00 Prague 9, Czech Republic
| | - Simon Joly
- Montreal Botanical Garden, 4101, Sherbrooke East, Montreal, QC H1X 2B2, Canada
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101, Sherbrooke East, Montreal, QC H1X 2B2, Canada
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Modesto Luceño
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km. 1, 41013, Seville, Spain
| | - José Ignacio Márquez-Corro
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km. 1, 41013, Seville, Spain
| | - Santiago Martín-Bravo
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km. 1, 41013, Seville, Spain
| | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africaand
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | | | - Karen L Wilson
- National Herbarium of New South Wales, Australian Institute of Botanical Science, Australian Botanic Garden, Locked Bag 6002, Mount Annan, New South Wales 2567, Australia
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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Sliwinska E, Loureiro J, Leitch IJ, Šmarda P, Bainard J, Bureš P, Chumová Z, Horová L, Koutecký P, Lučanová M, Trávníček P, Galbraith DW. Application-based guidelines for best practices in plant flow cytometry. Cytometry A 2021; 101:749-781. [PMID: 34585818 DOI: 10.1002/cyto.a.24499] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/10/2021] [Accepted: 08/26/2021] [Indexed: 12/15/2022]
Abstract
Flow cytometry (FCM) is currently the most widely-used method to establish nuclear DNA content in plants. Since simple, 1-3-parameter, flow cytometers, which are sufficient for most plant applications, are commercially available at a reasonable price, the number of laboratories equipped with these instruments, and consequently new FCM users, has greatly increased over the last decade. This paper meets an urgent need for comprehensive recommendations for best practices in FCM for different plant science applications. We discuss advantages and limitations of establishing plant ploidy, genome size, DNA base composition, cell cycle activity, and level of endoreduplication. Applications of such measurements in plant systematics, ecology, molecular biology research, reproduction biology, tissue cultures, plant breeding, and seed sciences are described. Advice is included on how to obtain accurate and reliable results, as well as how to manage troubleshooting that may occur during sample preparation, cytometric measurements, and data handling. Each section is followed by best practice recommendations; tips as to what specific information should be provided in FCM papers are also provided.
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Affiliation(s)
- Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Bydgoszcz, Poland
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ilia J Leitch
- Kew Science Directorate, Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jillian Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zuzana Chumová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Magdalena Lučanová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Pavel Trávníček
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - David W Galbraith
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA.,Henan University, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, Kaifeng, China
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Adamec L, Matušíková I, Pavlovič A. Recent ecophysiological, biochemical and evolutional insights into plant carnivory. ANNALS OF BOTANY 2021; 128:241-259. [PMID: 34111238 PMCID: PMC8389183 DOI: 10.1093/aob/mcab071] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/07/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Carnivorous plants are an ecological group of approx. 810 vascular species which capture and digest animal prey, absorb prey-derived nutrients and utilize them to enhance their growth and development. Extant carnivorous plants have evolved in at least ten independent lineages, and their adaptive traits represent an example of structural and functional convergence. Plant carnivory is a result of complex adaptations to mostly nutrient-poor, wet and sunny habitats when the benefits of carnivory exceed the costs. With a boost in interest and extensive research in recent years, many aspects of these adaptations have been clarified (at least partly), but many remain unknown. SCOPE We provide some of the most recent insights into substantial ecophysiological, biochemical and evolutional particulars of plant carnivory from the functional viewpoint. We focus on those processes and traits in carnivorous plants associated with their ecological characterization, mineral nutrition, cost-benefit relationships, functioning of digestive enzymes and regulation of the hunting cycle in traps. We elucidate mechanisms by which uptake of prey-derived nutrients leads to stimulation of photosynthesis and root nutrient uptake. CONCLUSIONS Utilization of prey-derived mineral (mainly N and P) and organic nutrients is highly beneficial for plants and increases the photosynthetic rate in leaves as a prerequisite for faster plant growth. Whole-genome and tandem gene duplications brought gene material for diversification into carnivorous functions and enabled recruitment of defence-related genes. Possible mechanisms for the evolution of digestive enzymes are summarized, and a comprehensive picture on the biochemistry and regulation of prey decomposition and prey-derived nutrient uptake is provided.
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Affiliation(s)
- Lubomír Adamec
- Institute of Botany of the Czech Academy of Sciences, Dukelská 135, CZ-379 01 Třeboň, Czech Republic
| | - Ildikó Matušíková
- University of Ss. Cyril and Methodius, Department of Ecochemistry and Radioecology, J. Herdu 2, SK-917 01 Trnava, Slovak Republic
| | - Andrej Pavlovič
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
- For correspondence. E-mail
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8
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Veleba A, Zedek F, Horová L, Veselý P, Srba M, Šmarda P, Bureš P. Is the evolution of carnivory connected with genome size reduction? AMERICAN JOURNAL OF BOTANY 2020; 107:1253-1259. [PMID: 32882073 DOI: 10.1002/ajb2.1526] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/13/2020] [Indexed: 05/24/2023]
Abstract
PREMISE As repeatedly shown, the remarkable variation in the genome size of angiosperms can be shaped by extrinsic selective pressures, including nutrient availability. Carnivory has evolved independently in 10 angiosperm clades, but all carnivorous plants share a common affinity to nutrient-poor habitats. As such, carnivory and genome reduction could be responses to the same environmental pressure. Indeed, the smallest genomes among flowering plants are found in the carnivorous family Lentibulariaceae, where a unique mutation in cytochrome c oxidase (COX) is suspected to promote genome miniaturization. Despite these hypotheses, a phylogenetically informed test of genome size and nutrient availability across carnivorous clades has so far been missing. METHODS Using linear mixed models, we compared genome sizes of 127 carnivorous plants from 7 diverse angiosperm clades with 1072 of their noncarnivorous relatives. We also tested whether genome size in Lentibulariaceae reflects the presence of the COX mutation. RESULTS The genome sizes of carnivorous plants do not differ significantly from those of their noncarnivorous relatives. Based on available data, no significant association between the COX mutation and genome miniaturization could be confirmed, not even when considering polyploidy. CONCLUSIONS Carnivory alone does not seem to significantly affect genome size decrease. Plausibly, it might actually counterbalance the effect of nutrient limitation on genome size evolution. The role of the COX mutation in genome miniaturization needs to be evaluated by analysis of a broader data set because current knowledge of its presence across Lentibulariaceae covers less than 10% of the species diversity in this family.
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Affiliation(s)
- Adam Veleba
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Pavel Veselý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Miroslav Srba
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, CZ, 12844, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ, 61137, Czech Republic
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9
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Reut MS, Płachno BJ. Unusual developmental morphology and anatomy of vegetative organs in Utricularia dichotoma-leaf, shoot and root dynamics. PROTOPLASMA 2020; 257:371-390. [PMID: 31659470 PMCID: PMC7039851 DOI: 10.1007/s00709-019-01443-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/19/2019] [Indexed: 05/05/2023]
Abstract
The terrestrial carnivorous species Utricularia dichotoma is known for a great phenotypic plasticity and unusual vegetative organs. Our investigation on 22 sources/populations revealed that after initiation of a leaf and two bladders on a stolon, a bud was formed in the proximal axil of the leaf, developing into a rosette with up to seven organs. The first two primordia of the bud grew into almost every possible combination of organs, but often into two anchor stolons. The patterns were generally not population specific. The interchangeability of organs increased with increasing rank in the succession of organs on stolon nodes. A high potential of switching developmental programs may be successful in a fluctuating environment. In this respect, we were able to show that bladders developed from anchor stolons experimentally when raising the water table. Anatomical structures were simple, lacunate and largely homogenous throughout all organs. They showed similarities with many hydrophytes, reflecting the plant's adaptation to (temporarily) submerged conditions. The principal component analysis was used in the context of dynamic morphology to illustrate correlations between organ types in the morphospace of U. dichotoma, revealing an organ specific patchwork of developmental processes for typical leaves and shoots, and less pronounced for a typical root. The concept and methods we applied may prove beneficial for future studies on the evolution of Lentibulariaceae, and on developmental morphology and genetics of unusual structures in plants.
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Affiliation(s)
- Markus S Reut
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, 9 Gronostajowa St, 30-387, Cracow, Poland.
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, 9 Gronostajowa St, 30-387, Cracow, Poland
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10
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Silva SR, Moraes AP, Penha HA, Julião MHM, Domingues DS, Michael TP, Miranda VFO, Varani AM. The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity. Int J Mol Sci 2019; 21:E3. [PMID: 31861318 PMCID: PMC6982007 DOI: 10.3390/ijms21010003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/13/2019] [Accepted: 12/15/2019] [Indexed: 12/22/2022] Open
Abstract
Utricularia belongs to Lentibulariaceae, a widespread family of carnivorous plants that possess ultra-small and highly dynamic nuclear genomes. It has been shown that the Lentibulariaceae genomes have been shaped by transposable elements expansion and loss, and multiple rounds of whole-genome duplications (WGD), making the family a platform for evolutionary and comparative genomics studies. To explore the evolution of Utricularia, we estimated the chromosome number and genome size, as well as sequenced the terrestrial bladderwort Utricularia reniformis (2n = 40, 1C = 317.1-Mpb). Here, we report a high quality 304 Mb draft genome, with a scaffold NG50 of 466-Kb, a BUSCO completeness of 87.8%, and 42,582 predicted genes. Compared to the smaller and aquatic U. gibba genome (101 Mb) that has a 32% repetitive sequence, the U. reniformis genome is highly repetitive (56%). The structural differences between the two genomes are the result of distinct fractionation and rearrangements after WGD, and massive proliferation of LTR-retrotransposons. Moreover, GO enrichment analyses suggest an ongoing gene birth-death-innovation process occurring among the tandem duplicated genes, shaping the evolution of carnivory-associated functions. We also identified unique patterns of developmentally related genes that support the terrestrial life-form and body plan of U. reniformis. Collectively, our results provided additional insights into the evolution of the plastic and specialized Lentibulariaceae genomes.
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Affiliation(s)
- Saura R. Silva
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
| | - Ana Paula Moraes
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo 09606-070, Brazil;
| | - Helen A. Penha
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
| | - Maria H. M. Julião
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
| | - Douglas S. Domingues
- Departamento de Botânica, Instituto de Biociências, UNESP—Universidade Estadual Paulista, Rio Claro 13506-900, Brazil;
| | | | - Vitor F. O. Miranda
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil
| | - Alessandro M. Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP—Universidade Estadual Paulista, Jaboticabal 14884-900, Brazil; (S.R.S.); (H.A.P.); (M.H.M.J.)
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11
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Silva SR, Pinheiro DG, Penha HA, Płachno BJ, Michael TP, Meer EJ, Miranda VFO, Varani AM. Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes. Int J Mol Sci 2019; 20:E6130. [PMID: 31817365 PMCID: PMC6940893 DOI: 10.3390/ijms20246130] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/09/2019] [Accepted: 11/27/2019] [Indexed: 01/09/2023] Open
Abstract
Utricularia amethystina Salzm. ex A.St.-Hil. & Girard (Lentibulariaceae) is a highly polymorphic carnivorous plant taxonomically rearranged many times throughout history. Herein, the complete chloroplast genomes (cpDNA) of three U. amethystina morphotypes: purple-, white-, and yellow-flowered, were sequenced, compared, and putative markers for systematic, populations, and evolutionary studies were uncovered. In addition, RNA-Seq and RNA-editing analysis were employed for functional cpDNA evaluation. The cpDNA of three U. amethystina morphotypes exhibits typical quadripartite structure. Fine-grained sequence comparison revealed a high degree of intraspecific genetic variability in all morphotypes, including an exclusive inversion in the psbM and petN genes in U. amethystina yellow. Phylogenetic analyses indicate that U. amethystina morphotypes are monophyletic. Furthermore, in contrast to the terrestrial Utricularia reniformis cpDNA, the U. amethystina morphotypes retain all the plastid NAD(P)H-dehydrogenase (ndh) complex genes. This observation supports the hypothesis that the ndhs in terrestrial Utricularia were independently lost and regained, also suggesting that different habitats (aquatic and terrestrial) are not related to the absence of Utricularia ndhs gene repertoire as previously assumed. Moreover, RNA-Seq analyses recovered similar patterns, including nonsynonymous RNA-editing sites (e.g., rps14 and petB). Collectively, our results bring new insights into the chloroplast genome architecture and evolution of the photosynthesis machinery in the Lentibulariaceae.
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Affiliation(s)
- Saura R. Silva
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
| | - Daniel G. Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
| | - Helen A. Penha
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
| | - Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 30-387 Krakow, Poland;
| | | | | | - Vitor F. O. Miranda
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil
| | - Alessandro M. Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Universidade Estadual Paulista (Unesp), Sao Paulo 14884-900, Brazil; (D.G.P.); (H.A.P.)
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12
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Trávníček P, Čertner M, Ponert J, Chumová Z, Jersáková J, Suda J. Diversity in genome size and GC content shows adaptive potential in orchids and is closely linked to partial endoreplication, plant life-history traits and climatic conditions. THE NEW PHYTOLOGIST 2019; 224:1642-1656. [PMID: 31215648 DOI: 10.1111/nph.15996] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 05/21/2023]
Abstract
In angiosperms, genome size and nucleobase composition (GC content) exhibit pronounced variation with possible adaptive consequences. The hyperdiverse orchid family possessing the unique phenomenon of partial endoreplication (PE) provides a great opportunity to search for interactions of both genomic traits with the evolutionary history of the family. Using flow cytometry, we report values of both genomic traits and the type of endoreplication for 149 orchid species and compare these with a suite of life-history traits and climatic niche data using phylogeny-based statistics. The evolution of genomic traits was further studied using the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to access their adaptive potential. Pronounced variation in genome size (341-54 878 Mb), and especially in GC content (23.9-50.5%), was detected among orchids. Diversity in both genomic traits was closely related to the type of endoreplication, plant growth form and climatic conditions. GC content was also associated with the type of dormancy. In all tested scenarios, OU models always outperformed BM models. Unparalleled GC content variation was discovered in orchids, setting new limits for plants. Our study indicates that diversity in both genome size and GC content has adaptive consequences and is tightly linked with evolutionary transitions to PE.
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Affiliation(s)
- Pavel Trávníček
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Martin Čertner
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12801, Czech Republic
| | - Jan Ponert
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Prague Botanical Garden, Trojská 800/196, Prague, CZ-17100, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, CZ-12844, Czech Republic
| | - Zuzana Chumová
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12801, Czech Republic
| | - Jana Jersáková
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
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13
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Lee KJI, Bushell C, Koide Y, Fozard JA, Piao C, Yu M, Newman J, Whitewoods C, Avondo J, Kennaway R, Marée AFM, Cui M, Coen E. Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism. PLoS Biol 2019; 17:e3000427. [PMID: 31600203 PMCID: PMC6786542 DOI: 10.1371/journal.pbio.3000427] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/05/2019] [Indexed: 11/18/2022] Open
Abstract
Leaves display a remarkable range of forms, from flat sheets with simple outlines to cup-shaped traps. Although much progress has been made in understanding the mechanisms of planar leaf development, it is unclear whether similar or distinctive mechanisms underlie shape transformations during development of more complex curved forms. Here, we use 3D imaging and cellular and clonal analysis, combined with computational modelling, to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. We show that the transformation from a near-spherical form at early developmental stages to an oblate spheroid with a straightened ventral midline in the mature form can be accounted for by spatial variations in rates and orientations of growth. Different hypotheses regarding spatiotemporal control predict distinct patterns of cell shape and size, which were tested experimentally by quantifying cellular and clonal anisotropy. We propose that orientations of growth are specified by a proximodistal polarity field, similar to that hypothesised to account for Arabidopsis leaf development, except that in Utricularia, the field propagates through a highly curved tissue sheet. Independent evidence for the polarity field is provided by the orientation of glandular hairs on the inner surface of the trap. Taken together, our results show that morphogenesis of complex 3D leaf shapes can be accounted for by similar mechanisms to those for planar leaves, suggesting that simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies. Many plant and animal organs derive from tissue sheets, but how are they shaped to create the diversity of forms observed in nature? This study uses a combination of imaging and mathematical modelling to show how carnivorous plant traps shape themselves in 3D by a growth framework oriented by tissue polarity, similar to that found in planar leaves.
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Affiliation(s)
- Karen J. I. Lee
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Claire Bushell
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Yohei Koide
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - John A. Fozard
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Chunlan Piao
- College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Linan, Zhejiang, China
| | - Man Yu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Jacob Newman
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Christopher Whitewoods
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Jerome Avondo
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Richard Kennaway
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Athanasius F. M. Marée
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Minlong Cui
- College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Linan, Zhejiang, China
- * E-mail: (EC); (MC)
| | - Enrico Coen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (EC); (MC)
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Qiu F, Baack EJ, Whitney KD, Bock DG, Tetreault HM, Rieseberg LH, Ungerer MC. Phylogenetic trends and environmental correlates of nuclear genome size variation in Helianthus sunflowers. THE NEW PHYTOLOGIST 2019; 221:1609-1618. [PMID: 30368824 DOI: 10.1111/nph.15465] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Flowering plants serve as a powerful model for studying the evolution of nuclear genome size (GS) given the tremendous GS variation that exists both within and across angiosperm lineages. Helianthus sunflowers consist of c. 50 species native to North America that occupy diverse habitats and vary in ploidy level. In the current study, we generated a comprehensive GS database for 49 Helianthus species using flow cytometric approaches. We examined variability across the genus and present a comparative phylogenetic analysis of GS evolution in diploid Helianthus species. Results demonstrated that different clades of diploid Helianthus species showed evolutionary patterns of GS contraction, expansion and relative stasis, with annual diploid species evolving smaller GS with the highest rate of evolution. Phylogenetic comparative analyses of diploids revealed significant negative associations of GS with temperature seasonality and cell production rate, indicating that the evolution of larger GS in Helianthus diploids may be more permissible in habitats with longer growing seasons where selection for more rapid growth may be relaxed. The Helianthus GS database presented here and corresponding analyses of environmental and phenotypic correlates will facilitate ongoing and future research on the ultimate drivers of GS evolution in this well-studied North American plant genus.
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Affiliation(s)
- Fan Qiu
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Eric J Baack
- Department of Biology, Luther College, Decorah, IA, 52101, USA
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Dan G Bock
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark C Ungerer
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
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Karyotype heterogeneity in Philodendron s.l. (Araceae) revealed by chromosome mapping of rDNA loci. PLoS One 2018; 13:e0207318. [PMID: 30440003 PMCID: PMC6237374 DOI: 10.1371/journal.pone.0207318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/29/2018] [Indexed: 12/18/2022] Open
Abstract
Philodendron s.l. (Araceae) has been recently focus of taxonomic and phylogenetic studies, but karyotypic data are limited to chromosome numbers and a few published genome sizes. In this work, karyotypes of 34 species of Philodendron s.l. (29 species of Philodendron and five of Thaumatophyllum), ranging from 2n = 28 to 36 chromosomes, were analyzed by fluorescence in situ hybridization (FISH) with rDNA and telomeric probes, aiming to understand the evolution of the karyotype diversity of the group. Philodendron presented a high number variation of 35S rDNA, ranging from two to 16 sites, which were mostly in the terminal region of the short arms, with nine species presenting heteromorphisms. In the case of Thaumatophyllum species, we observed a considerably lower variation, which ranged from two to four terminal sites. The distribution of the 5S rDNA clusters was more conserved, with two sites for most species, being preferably located interstitially in the long chromosome arms. For the telomeric probe, while exclusively terminal sites were observed for P. giganteum (2n = 30) chromosomes, P. callosum (2n = 28) presented an interstitial distribution associated with satellite DNA. rDNA sites of the analyzed species of Philodendron s.l. species were randomly distributed considering the phylogenetic context, probably due to rapid evolution and great diversity of these genomes. The observed heteromorphisms suggest the accumulation of repetitive DNA in the genomes of some species and the occurrence of chromosomal rearrangements along the karyotype evolution of the group.
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Silva SR, Gibson R, Adamec L, Domínguez Y, Miranda VF. Molecular phylogeny of bladderworts: A wide approach of Utricularia (Lentibulariaceae) species relationships based on six plastidial and nuclear DNA sequences. Mol Phylogenet Evol 2018; 118:244-264. [DOI: 10.1016/j.ympev.2017.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023]
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17
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Płachno BJ, Świątek P, Jobson RW, Małota K, Brutkowski W. Serial block face SEM visualization of unusual plant nuclear tubular extensions in a carnivorous plant (Utricularia, Lentibulariaceae). ANNALS OF BOTANY 2017; 120:673-680. [PMID: 28541416 PMCID: PMC5691799 DOI: 10.1093/aob/mcx042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 02/09/2017] [Accepted: 03/23/2017] [Indexed: 05/22/2023]
Abstract
Background and Aims In Utricularia nelumbifolia , the nuclei of placental nutritive tissue possess unusually shaped projections not known to occur in any other flowering plant. The main aim of the study was to document the morphology and ultrastructure of these unusual nuclei. In addition, the literature was searched to find examples of nuclear tubular projections in other plant groups, and the nuclei of closely related species of Utricularia (i.e. sects Iperua , Orchidioides , Foliosa and Utricularia ) were examined. Methods To visualize the complexity of the nuclear structures, transmission electron microscopy (TEM) was used, and 3-D ultrastructural reconstructions were made using the serial block face scanning electron microscopy (SBEM) technique. The nuclei of 11 Utricularia species, i.e. U. nelumbifolia , U. reniformis , U. cornigera , U. nephrophylla (sect. Iperua ), U. asplundii , U. alpina , U. quelchii (sect. Orchidioides ), U. longifolia (sect. Foliosa ), U. intermedia , U. minor and U. gibba (sect. Utricularia ) were examined. Key Results Of the 11 Utricularia species examined, the spindle-like tubular projections (approx. 5 μm long) emanating from resident nuclei located in placental nutritive tissues were observed only in U. nelumbifolia . These tubular nuclear extensions contained chromatin distributed along hexagonally shaped tubules. The apices of the projections extended into the cell plasma membrane, and in many cases also made contact at the two opposing cellular poles, and with plasmodesmata via a short cisterna of the cortical endoplasmic reticulum. Images from the SBEM provide some evidence that the nuclear projections are making contact with those of neighbouring cells. Conclusions The term chromatubules (chromatin-filled tubules) for the nuclear projections of U. nelumbifolia placental tissue was proposed here. Due to the apparent association with the plasma membrane and plasmodesmata, it was also speculated that chromatubules are involved in nucleus-cell-cell communication. However, further experimental evidence is required before any functional hypothesis can be entertained.
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Affiliation(s)
- Bartosz J Płachno
- Department of Plant Cytology and Embryology, Jagiellonian University in Kraków, 9 Gronostajowa St., Cracow, Poland
| | - Piotr Świątek
- Department of Animal Histology and Embryology, University of Silesia in Katowice, 9 Bankowa St., 40-007 Katowice, Poland
| | - Richard W Jobson
- National Herbarium of New South Wales, Mrs Macquaries Road, Sydney, NSW 2000 Australia
| | - Karol Małota
- Department of Animal Histology and Embryology, University of Silesia in Katowice, 9 Bankowa St., 40-007 Katowice, Poland
| | - Wojciech Brutkowski
- Laboratory for Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warszawa, Poland
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18
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Gomes Rodrigues F, Franco Marulanda N, Silva SR, Płachno BJ, Adamec L, Miranda VFO. Phylogeny of the 'orchid-like' bladderworts (gen. Utricularia sect. Orchidioides and Iperua: Lentibulariaceae) with remarks on the stolon-tuber system. ANNALS OF BOTANY 2017; 120:709-723. [PMID: 28673037 PMCID: PMC5691873 DOI: 10.1093/aob/mcx056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 03/22/2017] [Accepted: 04/13/2017] [Indexed: 05/11/2023]
Abstract
Background and Aims The 'orchid-like' bladderworts ( Utricularia ) comprise 15 species separated into two sections: Orchidioides and Iperua . These robust and mostly epiphytic species were originally grouped within the section Orchidioides by the first taxonomical systems. These species were later split into two sections when sect. Iperua was proposed. Due to the lack of strong evidence based on a robust phylogenetic perspective, this study presents a phylogenetic proposal based on four different DNA sequences (plastid and nuclear) and morphology to test the monophyly of the two sections. Methods In comparison with all previous phylogenetic studies, the largest number of species across the sections was covered: 11 species from sections Orchidioides and Iperua with 14 species as an external group. Maximum likelihood and Bayesian inferences were applied to DNA sequences of rps16 , trnL-F , matK , the internal transcribed spacer (ITS) and three morphological characters: (1) the crest of the corolla; (2) the primary organs in the embryo; and (3) tubers. Additionally, a histochemical analysis of the stolons and tubers is presented from an evolutionary perspective. Key Results The analyses showed the paraphyly of sect. Iperua , since Utricularia humboldtii is more related to the clade of sect. Orchidioides . Utricularia cornigera is grouped in the sect. Iperua clade based on chloroplast DNA sequences, but it is nested to sect. Orchidioides according to ITS dataset. Morphological characters do not support the breaking up of the 'orchid-like' species into two sections, either. Moreover, the stolon-tuber systems of both sections serve exclusively for water storage, according to histological analyses. Conclusions This study provides strong evidence, based on DNA sequences from two genomic compartments (plastid and nucleus) and morphology to group the Utricularia sect. Orchidioides into the sect. Iperua . The tubers are important adaptations for water storage and have been derived from stolons at least twice in the phylogenetic history of 'orchid-like' bladderworts.
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Affiliation(s)
- Fernanda Gomes Rodrigues
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Biologia Aplicada à Agropecuária, São Paulo, Brazil
| | - Néstor Franco Marulanda
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Biologia Aplicada à Agropecuária, São Paulo, Brazil
| | - Saura R Silva
- Universidade Estadual Paulista (Unesp), Instituto de Biociências, Botucatu, São Paulo, Brazil
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Jagiellonian University in Kraków, 9 Gronostajowa St., 30-387 Kraków, Poland
| | - Lubomír Adamec
- Institute of Botany of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - Vitor F O Miranda
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Biologia Aplicada à Agropecuária, São Paulo, Brazil
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Westermeier AS, Fleischmann A, Müller K, Schäferhoff B, Rubach C, Speck T, Poppinga S. Trap diversity and character evolution in carnivorous bladderworts (Utricularia, Lentibulariaceae). Sci Rep 2017; 7:12052. [PMID: 28935893 PMCID: PMC5608911 DOI: 10.1038/s41598-017-12324-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/07/2017] [Indexed: 01/12/2023] Open
Abstract
Bladderworts (Utricularia, Lentibulariaceae, Lamiales) constitute the largest genus of carnivorous plants but only aquatic species (about one fifth of the genus) have so far been thoroughly studied as to their suction trap functioning. In this study, we comparatively investigated trap biomechanics in 19 Utricularia species to examine correlations between life-forms, trapping mechanisms, and functional-morphological traits. Our investigations show the existence of two functional trap principles (passive trap in U. multifida vs. active suction traps), and - in active suction traps - three main trapdoor movement types (with several subtypes). The trapdoor movement types and their corresponding functional-morphological features most presumably represent adaptations to the respective habitat. We furthermore give insights into fluid dynamics during suction in three representatives of the main types of trapdoor movement. The results on functional morphology and trapdoor movement were mapped onto a new phylogenetic reconstruction of the genus, derived from the rapidly evolving chloroplast regions trnK, rps16 and trnQ-rps16 and a sampling of 105 Utricularia species in total. We discuss potential scenarios of trap character evolution and species radiation, highlighting possible key innovations that enable such a unique carnivorous lifestyle in different habitats.
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Affiliation(s)
- Anna Sofia Westermeier
- Plant Biomechanics Group, Botanic Garden, University of Freiburg, Schänzlestraße 1, D-79104, Freiburg im Breisgau, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, D-79110, Freiburg im Breisgau, Germany
| | - Andreas Fleischmann
- Botanische Staatssammlung München, Menzinger Straße 67, D-80638, München, Germany
- GeoBio-Center LMU, Center of Geobiology and Biodiversity Research, Ludwig-Maximilians-University, München, Germany
| | - Kai Müller
- Westfälische Wilhelms-Universität Münster, Institut für Evolution und Biodiversität, AG Evolution und Biodiversität der Pflanzen, Hüfferstraße 1, D-48149, Münster, Germany
| | - Bastian Schäferhoff
- Westfälische Wilhelms-Universität Münster, Institut für Evolution und Biodiversität, AG Evolution und Biodiversität der Pflanzen, Hüfferstraße 1, D-48149, Münster, Germany
- PAN Institut für Endokrinologie und Reproduktionsmedizin, Zeppelinstraße 1, D-50667, Köln, Germany
| | - Carmen Rubach
- Plant Biomechanics Group, Botanic Garden, University of Freiburg, Schänzlestraße 1, D-79104, Freiburg im Breisgau, Germany
| | - Thomas Speck
- Plant Biomechanics Group, Botanic Garden, University of Freiburg, Schänzlestraße 1, D-79104, Freiburg im Breisgau, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, D-79110, Freiburg im Breisgau, Germany
| | - Simon Poppinga
- Plant Biomechanics Group, Botanic Garden, University of Freiburg, Schänzlestraße 1, D-79104, Freiburg im Breisgau, Germany.
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Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome. Proc Natl Acad Sci U S A 2017; 114:E4435-E4441. [PMID: 28507139 DOI: 10.1073/pnas.1702072114] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.
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Veleba A, Šmarda P, Zedek F, Horová L, Šmerda J, Bureš P. Evolution of genome size and genomic GC content in carnivorous holokinetics (Droseraceae). ANNALS OF BOTANY 2017; 119:409-416. [PMID: 28025291 PMCID: PMC5314647 DOI: 10.1093/aob/mcw229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/06/2016] [Accepted: 09/26/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Studies in the carnivorous family Lentibulariaceae in the last years resulted in the discovery of the smallest plant genomes and an unusual pattern of genomic GC content evolution. However, scarcity of genomic data in other carnivorous clades still prevents a generalization of the observed patterns. Here the aim was to fill this gap by mapping genome evolution in the second largest carnivorous family, Droseraceae, where this evolution may be affected by chromosomal holokinetism in Drosera METHODS: The genome size and genomic GC content of 71 Droseraceae species were measured by flow cytometry. A dated phylogeny was constructed, and the evolution of both genomic parameters and their relationship to species climatic niches were tested using phylogeny-based statistics. KEY RESULTS The 2C genome size of Droseraceae varied between 488 and 10 927 Mbp, and the GC content ranged between 37·1 and 44·7 %. The genome sizes and genomic GC content of carnivorous and holocentric species did not differ from those of their non-carnivorous and monocentric relatives. The genomic GC content positively correlated with genome size and annual temperature fluctuations. The genome size and chromosome numbers were inversely correlated in the Australian clade of Drosera CONCLUSIONS: Our results indicate that neither carnivory (nutrient scarcity) nor the holokinetism have a prominent effect on size and DNA base composition of Droseraceae genomes. However, the holokinetic drive seems to affect karyotype evolution in one of the major clades of Drosera Our survey confirmed that the evolution of GC content is tightly connected with the evolution of genome size and also with environmental conditions.
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Affiliation(s)
- Adam Veleba
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
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Chen Q, Zobel J, Verspoor K. Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:baw163. [PMID: 28077566 PMCID: PMC5225397 DOI: 10.1093/database/baw163] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 01/22/2023]
Abstract
GenBank, the EMBL European Nucleotide Archive and the DNA DataBank of Japan, known collectively as the International Nucleotide Sequence Database Collaboration or INSDC, are the three most significant nucleotide sequence databases. Their records are derived from laboratory work undertaken by different individuals, by different teams, with a range of technologies and assumptions and over a period of decades. As a consequence, they contain a great many duplicates, redundancies and inconsistencies, but neither the prevalence nor the characteristics of various types of duplicates have been rigorously assessed. Existing duplicate detection methods in bioinformatics only address specific duplicate types, with inconsistent assumptions; and the impact of duplicates in bioinformatics databases has not been carefully assessed, making it difficult to judge the value of such methods. Our goal is to assess the scale, kinds and impact of duplicates in bioinformatics databases, through a retrospective analysis of merged groups in INSDC databases. Our outcomes are threefold: (1) We analyse a benchmark dataset consisting of duplicates manually identified in INSDC—a dataset of 67 888 merged groups with 111 823 duplicate pairs across 21 organisms from INSDC databases – in terms of the prevalence, types and impacts of duplicates. (2) We categorize duplicates at both sequence and annotation level, with supporting quantitative statistics, showing that different organisms have different prevalence of distinct kinds of duplicate. (3) We show that the presence of duplicates has practical impact via a simple case study on duplicates, in terms of GC content and melting temperature. We demonstrate that duplicates not only introduce redundancy, but can lead to inconsistent results for certain tasks. Our findings lead to a better understanding of the problem of duplication in biological databases. Database URL: the merged records are available at https://cloudstor.aarnet.edu.au/plus/index.php/s/Xef2fvsebBEAv9w
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Affiliation(s)
- Qingyu Chen
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Justin Zobel
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Karin Verspoor
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
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De Castro O, Innangi M, Di Maio A, Menale B, Bacchetta G, Pires M, Noble V, Gestri G, Conti F, Peruzzi L. Disentangling Phylogenetic Relationships in a Hotspot of Diversity: The Butterworts (Pinguicula L., Lentibulariaceae) Endemic to Italy. PLoS One 2016; 11:e0167610. [PMID: 28030566 PMCID: PMC5193322 DOI: 10.1371/journal.pone.0167610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 11/04/2016] [Indexed: 11/20/2022] Open
Abstract
The genus Pinguicula (Lentibulariaceae) consists of about 100 carnivorous species, also known as butterworts. Eleven taxa are endemic to Italy, which represents a biodiversity hotspot for butterworts in Europe. The aim of our study was to provide a phylogenetic framework for the Italian endemics, in order to: a) investigate the relationships between species in this group; b) evaluate their actual taxonomic value. To achieve this, we analysed all the taxa endemic to Italy, along with several other species, by means of ITS nrDNA analysis. Our results clarify the relationships between Italian endemics and other Pinguicula taxa identifying a basal polytomy defined by five clades. All of the Italian endemics (with the exception of P. lavalvae) fall within a single large clade, which includes P. vulgaris and allied species. Among them, P. poldinii represents the most isolated lineage. Other taxa show strong molecular similarities and form a single subclade, although their taxonomic ranks can be retained. Pinguicula lattanziae sp. nov., seemingly endemic to Liguria (NW Italy), is also described.
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Affiliation(s)
- Olga De Castro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Michele Innangi
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università degli Studi di Napoli, Caserta, Italy
| | - Antonietta Di Maio
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Bruno Menale
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Gianluigi Bacchetta
- Centro Conservazione Biodiversità, Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cagliari, Italy
| | - Mathias Pires
- Conservatoire Botanique National Méditerranéen, Hyères, France
| | - Virgile Noble
- Conservatoire Botanique National Méditerranéen, Hyères, France
| | | | - Fabio Conti
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino—Centro Ricerche Floristiche dell’Appennino, Parco Nazionale del Gran Sasso e Monti della Laga, Barisciano (L’Aquila), Italy
| | - Lorenzo Peruzzi
- Dipartimento di Biologia, Università degli Studi di Pisa, Pisa, Italy
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Silva SR, Pinheiro DG, Meer EJ, Michael TP, Varani AM, Miranda VFO. The complete chloroplast genome sequence of the leafy bladderwort, Utricularia foliosa L. (Lentibulariaceae). CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0653-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Baniaga AE, Arrigo N, Barker MS. The Small Nuclear Genomes of Selaginella Are Associated with a Low Rate of Genome Size Evolution. Genome Biol Evol 2016; 8:1516-25. [PMID: 27189987 PMCID: PMC4898805 DOI: 10.1093/gbe/evw091] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2016] [Indexed: 02/07/2023] Open
Abstract
The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome.
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Affiliation(s)
| | - Nils Arrigo
- Department of Ecology & Evolutionary Biology, University of Arizona Department of Ecology & Evolution, University of Lausanne, Switzerland
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona
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Rutishauser R. Evolution of unusual morphologies in Lentibulariaceae (bladderworts and allies) and Podostemaceae (river-weeds): a pictorial report at the interface of developmental biology and morphological diversification. ANNALS OF BOTANY 2016; 117:811-32. [PMID: 26589968 PMCID: PMC4845801 DOI: 10.1093/aob/mcv172] [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: 07/30/2015] [Revised: 08/19/2015] [Accepted: 09/25/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND Various groups of flowering plants reveal profound ('saltational') changes of their bauplans (architectural rules) as compared with related taxa. These plants are known as morphological misfits that appear as rather large morphological deviations from the norm. Some of them emerged as morphological key innovations (perhaps 'hopeful monsters') that gave rise to new evolutionary lines of organisms, based on (major) genetic changes. SCOPE This pictorial report places emphasis on released bauplans as typical for bladderworts (Utricularia, approx. 230 secies, Lentibulariaceae) and river-weeds (Podostemaceae, three subfamilies, approx. 54 genera, approx. 310 species). Bladderworts (Utricularia) are carnivorous, possessing sucking traps. They live as submerged aquatics (except for their flowers), as humid terrestrials or as epiphytes. Most Podostemaceae are restricted to rocks in tropical river-rapids and waterfalls. They survive as submerged haptophytes in these extreme habitats during the rainy season, emerging with their flowers afterwards. The recent scientific progress in developmental biology and evolutionary history of both Lentibulariaceae and Podostemaceae is summarized. CONCLUSIONS Lentibulariaceae and Podostemaceae follow structural rules that are different from but related to those of more typical flowering plants. The roots, stems and leaves - as still distinguishable in related flowering plants - are blurred ('fuzzy'). However, both families have stable floral bauplans. The developmental switches to unusual vegetative morphologies facilitated rather than prevented the evolution of species diversity in both families. The lack of one-to-one correspondence between structural categories and gene expression may have arisen from the re-use of existing genetic resources in novel contexts. Understanding what developmental patterns are followed in Lentibulariaceae and Podostemaceae is a necessary prerequisite to discover the genetic alterations that led to the evolution of these atypical plants. Future molecular genetic work on morphological misfits such as bladderworts and river-weeds will provide insight into developmental and evolutionary aspects of more typical vascular plants.
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Affiliation(s)
- Rolf Rutishauser
- Institute of Systematic Botany, University of Zurich, Zurich, Switzerland
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Carta A, Peruzzi L. Testing the large genome constraint hypothesis: plant traits, habitat and climate seasonality in Liliaceae. THE NEW PHYTOLOGIST 2016; 210:709-16. [PMID: 26595257 DOI: 10.1111/nph.13769] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/20/2015] [Indexed: 05/08/2023]
Abstract
The factors driving genome size evolution in Liliaceae were examined. In particular, we investigated whether species with larger genomes are confined to less stressful environments with a longer vegetative season. We tested our hypotheses by correlating the genome size with other plant traits and environmental variables. To determine the adaptive nature of the genome size, we also compared the performances of Brownian motion (BM) processes with those inferred by Ornstein-Uhlenbeck (OU) models of trait evolution. A positive correlation of genome size with plant size, mean temperature and habitat moisture and a negative correlation with altitude and precipitation seasonality were found. Models of trait evolution revealed a deviation from a drift process or BM. Instead, changes in genome size were significantly associated with precipitation regimes according to an OU process. Specifically, the evolutionary optima towards which the genome size evolves were higher for humid climates and lower for drier ones. Taken together, our results indicate that the genome size increase in Liliaceae is constrained by climate seasonality.
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Affiliation(s)
- Angelino Carta
- Unit of Botany, Department of Biology, Università of Pisa, via Derna 1, Pisa, 56126, Italy
| | - Lorenzo Peruzzi
- Unit of Botany, Department of Biology, Università of Pisa, via Derna 1, Pisa, 56126, Italy
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Tran TD, Cao HX, Jovtchev G, Neumann P, Novák P, Fojtová M, Vu GTH, Macas J, Fajkus J, Schubert I, Fuchs J. Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:1087-99. [PMID: 26485466 DOI: 10.1111/tpj.13058] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 10/07/2015] [Accepted: 10/15/2015] [Indexed: 05/25/2023]
Abstract
Linear chromosomes of eukaryotic organisms invariably possess centromeres and telomeres to ensure proper chromosome segregation during nuclear divisions and to protect the chromosome ends from deterioration and fusion, respectively. While centromeric sequences may differ between species, with arrays of tandemly repeated sequences and retrotransposons being the most abundant sequence types in plant centromeres, telomeric sequences are usually highly conserved among plants and other organisms. The genome size of the carnivorous genus Genlisea (Lentibulariaceae) is highly variable. Here we study evolutionary sequence plasticity of these chromosomal domains at an intrageneric level. We show that Genlisea nigrocaulis (1C = 86 Mbp; 2n = 40) and G. hispidula (1C = 1550 Mbp; 2n = 40) differ as to their DNA composition at centromeres and telomeres. G. nigrocaulis and its close relative G. pygmaea revealed mainly 161 bp tandem repeats, while G. hispidula and its close relative G. subglabra displayed a combination of four retroelements at centromeric positions. G. nigrocaulis and G. pygmaea chromosome ends are characterized by the Arabidopsis-type telomeric repeats (TTTAGGG); G. hispidula and G. subglabra instead revealed two intermingled sequence variants (TTCAGG and TTTCAGG). These differences in centromeric and, surprisingly, also in telomeric DNA sequences, uncovered between groups with on average a > 9-fold genome size difference, emphasize the fast genome evolution within this genus. Such intrageneric evolutionary alteration of telomeric repeats with cytosine in the guanine-rich strand, not yet known for plants, might impact the epigenetic telomere chromatin modification.
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Affiliation(s)
- Trung D Tran
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Gabriele Jovtchev
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Pavel Neumann
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Petr Novák
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Miloslava Fojtová
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Jiří Macas
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Jiří Fajkus
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 61265, Brno, Czech Republic
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, D-06466, Stadt Seeland, Germany
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Poppinga S, Weisskopf C, Westermeier AS, Masselter T, Speck T. Fastest predators in the plant kingdom: functional morphology and biomechanics of suction traps found in the largest genus of carnivorous plants. AOB PLANTS 2015; 8:plv140. [PMID: 26602984 PMCID: PMC4717191 DOI: 10.1093/aobpla/plv140] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/07/2015] [Indexed: 05/18/2023]
Abstract
Understanding the physics of plant movements, which describe the interplay between plant architecture, movement speed and actuation principles, is essential for the comprehension of important processes like plant morphogenesis. Recent investigations especially on rapid plant movements at the interface of biology, physics and engineering sciences highlight how such fast motions can be achieved without the presence of muscles, nerves and technical hinge analogies. The suction traps (bladders) of carnivorous bladderworts (Utricularia spp., Lentibulariaceae, Lamiales) are considered as some of the most elaborate moving structures in the plant kingdom. A complex interplay of morphological and physiological adaptations allows the traps to pump water out of their body and to store elastic energy in the deformed bladder walls. Mechanical stimulation by prey entails opening of the otherwise watertight trapdoor, followed by trap wall relaxation, sucking in of water and prey, and consecutive trapdoor closure. Suction can also occur spontaneously in non-stimulated traps. We review the current state of knowledge about the suction trap mechanism with a focus on architectonically homogeneous traps of aquatic bladderwort species from section Utricularia (the so-called 'Utricularia vulgaris trap type'). The functional morphology and biomechanics of the traps are described in detail. We discuss open questions and propose promising aspects for future studies on these sophisticated ultra-fast trapping devices.
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Affiliation(s)
- Simon Poppinga
- Plant Biomechanics Group, University of Freiburg, Botanic Garden, Schänzlestrasse 1, 79104 Freiburg im Breisgau, Germany Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg im Breisgau, Germany
| | - Carmen Weisskopf
- Plant Biomechanics Group, University of Freiburg, Botanic Garden, Schänzlestrasse 1, 79104 Freiburg im Breisgau, Germany Present address: Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Anna Sophia Westermeier
- Plant Biomechanics Group, University of Freiburg, Botanic Garden, Schänzlestrasse 1, 79104 Freiburg im Breisgau, Germany
| | - Tom Masselter
- Plant Biomechanics Group, University of Freiburg, Botanic Garden, Schänzlestrasse 1, 79104 Freiburg im Breisgau, Germany
| | - Thomas Speck
- Plant Biomechanics Group, University of Freiburg, Botanic Garden, Schänzlestrasse 1, 79104 Freiburg im Breisgau, Germany Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg im Breisgau, Germany
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Vu GTH, Schmutzer T, Bull F, Cao HX, Fuchs J, Tran TD, Jovtchev G, Pistrick K, Stein N, Pecinka A, Neumann P, Novak P, Macas J, Dear PH, Blattner FR, Scholz U, Schubert I. Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus. THE PLANT GENOME 2015; 8:eplantgenome2015.04.0021. [PMID: 33228273 DOI: 10.3835/plantgenome2015.04.0021] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/19/2015] [Indexed: 06/11/2023]
Abstract
The C-value paradox remains incompletely resolved after >40 yr and is exemplified by 2,350-fold variation in genome sizes of flowering plants. The carnivorous Lentibulariaceae genus Genlisea, displaying a 25-fold range of genome sizes, is a promising subject to study mechanisms and consequences of evolutionary genome size variation. Applying genomic, phylogenetic, and cytogenetic approaches, we uncovered bidirectional genome size evolution within the genus Genlisea. The Genlisea nigrocaulis Steyerm. genome (86 Mbp) has probably shrunk by retroelement silencing and deletion-biased double-strand break (DSB) repair, from an ancestral size of 400 to 800 Mbp to become one of the smallest among flowering plants. The G. hispidula Stapf genome has expanded by whole-genome duplication (WGD) and retrotransposition to 1550 Mbp. Genlisea hispidula became allotetraploid after the split from the G. nigrocaulis clade ∼29 Ma. Genlisea pygmaea A. St.-Hil. (179 Mbp), a close relative of G. nigrocaulis, proved to be a recent (auto)tetraploid. Our analyses suggest a common ancestor of the genus Genlisea with an intermediate 1C value (400-800 Mbp) and subsequent rapid genome size evolution in opposite directions. Many abundant repeats of the larger genome are absent in the smaller, casting doubt on their functionality for the organism, while recurrent WGD seems to safeguard against the loss of essential elements in the face of genome shrinkage. We cannot identify any consistent differences in habitat or life strategy that correlate with genome size changes, raising the possibility that these changes may be selectively neutral.
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Affiliation(s)
- Giang T H Vu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- Max Planck Institute for Plant Breeding Research (MPIPZ), Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Fabian Bull
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Hieu X Cao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Trung D Tran
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Gabriele Jovtchev
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- Institute for Biodiversity and Ecosystem Research, 2 Yurii Gagarin Street, Sofia, 1113, Bulgaria
| | - Klaus Pistrick
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Ales Pecinka
- Max Planck Institute for Plant Breeding Research (MPIPZ), Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Pavel Neumann
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05, Cˇeske Budejovicé, Czech Republic
| | - Petr Novak
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05, Cˇeske Budejovicé, Czech Republic
| | - Jiri Macas
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05, Cˇeske Budejovicé, Czech Republic
| | - Paul H Dear
- MRC Lab. of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
- Faculty of Science and Central European Institute of Technology, Masaryk Univ., 61137, Brno, Czech Republic
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Tran TD, Cao HX, Jovtchev G, Novák P, Vu GTH, Macas J, Schubert I, Fuchs J. Chromatin organization and cytological features of carnivorous Genlisea species with large genome size differences. FRONTIERS IN PLANT SCIENCE 2015; 6:613. [PMID: 26347752 PMCID: PMC4542322 DOI: 10.3389/fpls.2015.00613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/24/2015] [Indexed: 05/07/2023]
Abstract
The monophyletic carnivorous genus Genlisea (Lentibulariaceae) is characterized by a bi-directional genome size evolution resulting in a 25-fold difference in nuclear DNA content. This is one of the largest ranges found within a genus so far and makes Genlisea an interesting subject to study mechanisms of genome and karyotype evolution. Genlisea nigrocaulis, with 86 Mbp one of the smallest plant genomes, and the 18-fold larger genome of G. hispidula (1,550 Mbp) possess identical chromosome numbers (2n = 40) but differ considerably in chromatin organization, nuclear and cell size. Interphase nuclei of G. nigrocaulis and of related species with small genomes, G. aurea (133 Mbp, 2n ≈ 104) and G. pygmaea (179 Mbp, 2n = 80), are hallmarked by intensely DAPI-stained chromocenters, carrying typical heterochromatin-associated methylation marks (5-methylcytosine, H3K9me2), while in G. hispidula and surprisingly also in the small genome of G. margaretae (184 Mbp, 2n = 38) the heterochromatin marks are more evenly distributed. Probes of tandem repetitive sequences together with rDNA allow the unequivocal discrimination of 13 out of 20 chromosome pairs of G. hispidula. One of the repetitive sequences labeled half of the chromosome set almost homogenously supporting an allopolyploid status of G. hispidula and its close relative G. subglabra (1,622 Mbp, 2n = 40). In G. nigrocaulis 11 chromosome pairs could be individualized using a combination of rDNA and unique genomic probes. The presented data provide a basis for future studies of karyotype evolution within the genus Genlisea.
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Affiliation(s)
- Trung D. Tran
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Hieu X. Cao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Gabriele Jovtchev
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Petr Novák
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of SciencesČeské Budějovice, Czech Republic
| | - Giang T. H. Vu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Jiří Macas
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of SciencesČeské Budějovice, Czech Republic
| | - Ingo Schubert
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
- Central European Institute of Technology and Faculty of Science, Masaryk UniversityBrno, Czech Republic
| | - Joerg Fuchs
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
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Bárta J, Stone JD, Pech J, Sirová D, Adamec L, Campbell MA, Štorchová H. The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba. BMC PLANT BIOLOGY 2015; 15:78. [PMID: 25848894 PMCID: PMC4358910 DOI: 10.1186/s12870-015-0467-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/23/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND The species of Utricularia attract attention not only owing to their carnivorous lifestyle, but also due to an elevated substitution rate and a dynamic evolution of genome size leading to its dramatic reduction. To better understand the evolutionary dynamics of genome size and content as well as the great physiological plasticity in this mostly aquatic carnivorous genus, we analyzed the transcriptome of Utricularia vulgaris, a temperate species with well characterized physiology and ecology. We compared its transcriptome, namely gene content and overall transcript profile, with a previously described transcriptome of Utricularia gibba, a congener possessing one of the smallest angiosperm genomes. RESULTS We sequenced a normalized cDNA library prepared from total RNA extracted from shoots of U. vulgaris including leaves and traps, cultivated under sterile or outdoor conditions. 454 pyrosequencing resulted in more than 1,400,000 reads which were assembled into 41,407 isotigs in 19,522 isogroups. We observed high transcript variation in several isogroups explained by multiple loci and/or alternative splicing. The comparison of U. vulgaris and U. gibba transcriptomes revealed a similar distribution of GO categories among expressed genes, despite the differences in transcriptome preparation. We also found a strong correspondence in the presence or absence of root-associated genes between the U. vulgaris transcriptome and U. gibba genome, which indicated that the loss of some root-specific genes had occurred before the divergence of the two rootless species. CONCLUSIONS The species-rich genus Utricularia offers a unique opportunity to study adaptations related to the environment and carnivorous habit and also evolutionary processes responsible for considerable genome reduction. We show that a transcriptome may approximate the genome for gene content or gene duplication estimation. Our study is the first comparison of two global sequence data sets in Utricularia.
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Affiliation(s)
- Jiří Bárta
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - James D Stone
- />Institute of Experimental Botany CAS, Rozvojová 263 6- Lysolaje, Praha, 16502 Czech Republic
- />Institute of Botany CAS, Zámek 1, Průhonice, 25243 Czech Republic
| | - Jiří Pech
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - Dagmara Sirová
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - Lubomír Adamec
- />Institute of Botany CAS, Section of Plant Ecology, Dukelská 135, Treboň, 37982 Czech Republic
| | - Matthew A Campbell
- />Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, 4442 New Zealand
| | - Helena Štorchová
- />Institute of Experimental Botany CAS, Rozvojová 263 6- Lysolaje, Praha, 16502 Czech Republic
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Carretero-Paulet L, Librado P, Chang TH, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA. High Gene Family Turnover Rates and Gene Space Adaptation in the Compact Genome of the Carnivorous Plant Utricularia gibba. Mol Biol Evol 2015; 32:1284-95. [PMID: 25637935 DOI: 10.1093/molbev/msv020] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Utricularia gibba is an aquatic carnivorous plant with highly specialized morphology, featuring fibrous floating networks of branches and leaf-like organs, no recognizable roots, and bladder traps that capture and digest prey. We recently described the compressed genome of U. gibba as sufficient to control the development and reproduction of a complex organism. We hypothesized intense deletion pressure as a mechanism whereby most noncoding DNA was deleted, despite evidence for three independent whole-genome duplications (WGDs). Here, we explore the impact of intense genome fractionation in the evolutionary dynamics of U. gibba's functional gene space. We analyze U. gibba gene family turnover by modeling gene gain/death rates under a maximum-likelihood statistical framework. In accord with our deletion pressure hypothesis, we show that the U. gibba gene death rate is significantly higher than those of four other eudicot species. Interestingly, the gene gain rate is also significantly higher, likely reflecting the occurrence of multiple WGDs and possibly also small-scale genome duplications. Gene ontology enrichment analyses of U. gibba-specific two-gene orthogroups, multigene orthogroups, and singletons highlight functions that may represent adaptations in an aquatic carnivorous plant. We further discuss two homeodomain transcription factor gene families (WOX and HDG/HDZIP-IV) showing conspicuous differential expansions and contractions in U. gibba. Our results 1) reconcile the compactness of the U. gibba genome with its accommodation of a typical number of genes for a plant genome, and 2) highlight the role of high gene family turnover in the evolutionary diversification of U. gibba's functional gene space and adaptations to its unique lifestyle and highly specialized body plan.
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Affiliation(s)
| | - Pablo Librado
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Tien-Hao Chang
- Department of Biological Sciences, University at Buffalo, Buffalo, NY
| | - Enrique Ibarra-Laclette
- Laboratorio Nacional de Genómica Para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, Irapuato, Guanajuato, México
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica Para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, Irapuato, Guanajuato, México
| | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY
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34
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Fleischmann A, Michael TP, Rivadavia F, Sousa A, Wang W, Temsch EM, Greilhuber J, Müller KF, Heubl G. Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms. ANNALS OF BOTANY 2014; 114:1651-63. [PMID: 25274549 PMCID: PMC4649684 DOI: 10.1093/aob/mcu189] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/07/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Some species of Genlisea possess ultrasmall nuclear genomes, the smallest known among angiosperms, and some have been found to have chromosomes of diminutive size, which may explain why chromosome numbers and karyotypes are not known for the majority of species of the genus. However, other members of the genus do not possess ultrasmall genomes, nor do most taxa studied in related genera of the family or order. This study therefore examined the evolution of genome sizes and chromosome numbers in Genlisea in a phylogenetic context. The correlations of genome size with chromosome number and size, with the phylogeny of the group and with growth forms and habitats were also examined. METHODS Nuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes. KEY RESULTS Genome sizes of 15 taxa of Genlisea are presented and interpreted in a phylogenetic context. A high degree of congruence was found between genome size distribution and the major phylogenetic lineages. Ultrasmall genomes with 1C values of <100 Mbp were almost exclusively found in a derived lineage of South American species. The ancestral haploid chromosome number was inferred to be n = 8. Chromosome numbers in Genlisea ranged from 2n = 2x = 16 to 2n = 4x = 32. Ascendant dysploid series (2n = 36, 38) are documented for three derived taxa. The different ploidy levels corresponded to the two subgenera, but were not directly correlated to differences in genome size; the three different karyotype ranges mirrored the different sections of the genus. The smallest known plant genomes were not found in G. margaretae, as previously reported, but in G. tuberosa (1C ≈ 61 Mbp) and some strains of G. aurea (1C ≈ 64 Mbp). CONCLUSIONS Genlisea is an ideal candidate model organism for the understanding of genome reduction as the genus includes species with both relatively large (∼1700 Mbp) and ultrasmall (∼61 Mbp) genomes. This comparative, phylogeny-based analysis of genome sizes and karyotypes in Genlisea provides essential data for selection of suitable species for comparative whole-genome analyses, as well as for further studies on both the molecular and cytogenetic basis of genome reduction in plants.
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Affiliation(s)
- Andreas Fleischmann
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
| | - Todd P Michael
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | | | - Aretuza Sousa
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
| | - Wenqin Wang
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, A 1030 Vienna, Austria
| | - Johann Greilhuber
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, A 1030 Vienna, Austria
| | - Kai F Müller
- Institute for Evolution and Biodiversity, University of Muenster, Hüfferstrasse 1, D 48149 Münster, Germany
| | - Günther Heubl
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
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35
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Šmarda P, Bureš P, Horová L, Leitch IJ, Mucina L, Pacini E, Tichý L, Grulich V, Rotreklová O. Ecological and evolutionary significance of genomic GC content diversity in monocots. Proc Natl Acad Sci U S A 2014; 111:E4096-102. [PMID: 25225383 PMCID: PMC4191780 DOI: 10.1073/pnas.1321152111] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Genomic DNA base composition (GC content) is predicted to significantly affect genome functioning and species ecology. Although several hypotheses have been put forward to address the biological impact of GC content variation in microbial and vertebrate organisms, the biological significance of GC content diversity in plants remains unclear because of a lack of sufficiently robust genomic data. Using flow cytometry, we report genomic GC contents for 239 species representing 70 of 78 monocot families and compare them with genomic characters, a suite of life history traits and climatic niche data using phylogeny-based statistics. GC content of monocots varied between 33.6% and 48.9%, with several groups exceeding the GC content known for any other vascular plant group, highlighting their unusual genome architecture and organization. GC content showed a quadratic relationship with genome size, with the decreases in GC content in larger genomes possibly being a consequence of the higher biochemical costs of GC base synthesis. Dramatic decreases in GC content were observed in species with holocentric chromosomes, whereas increased GC content was documented in species able to grow in seasonally cold and/or dry climates, possibly indicating an advantage of GC-rich DNA during cell freezing and desiccation. We also show that genomic adaptations associated with changing GC content might have played a significant role in the evolution of the Earth's contemporary biota, such as the rise of grass-dominated biomes during the mid-Tertiary. One of the major selective advantages of GC-rich DNA is hypothesized to be facilitating more complex gene regulation.
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Affiliation(s)
- Petr Šmarda
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic;
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey TW93DS, United Kingdom
| | - Ladislav Mucina
- School of Plant Biology, University of Western Australia, Perth, WA 6009, Australia; Centre for Geographic Analysis, Department of Geography and Environmental Studies, Stellenbosch University, Stellenbosch 7600, South Africa; and
| | - Ettore Pacini
- Department of Life Sciences, Siena University, 53100 Siena, Italy
| | - Lubomír Tichý
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic
| | - Vít Grulich
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic
| | - Olga Rotreklová
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic
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