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Schöneberg Y, Audisio TL, Ben Hamadou A, Forman M, Král J, Kořínková T, Líznarová E, Mayer C, Prokopcová L, Krehenwinkel H, Prost S, Kennedy S. Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctorium (Cheiracanthiidae). Mol Ecol Resour 2024:e14038. [PMID: 39435585 DOI: 10.1111/1755-0998.14038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 09/26/2024] [Accepted: 10/04/2024] [Indexed: 10/23/2024]
Abstract
Spiders are a hyperdiverse taxon and among the most abundant predators in nearly all terrestrial habitats. Their success is often attributed to key developments in their evolution such as silk and venom production and major apomorphies such as a whole-genome duplication. Resolving deep relationships within the spider tree of life has been historically challenging, making it difficult to measure the relative importance of these novelties for spider evolution. Whole-genome data offer an essential resource in these efforts, but also for functional genomic studies. Here, we present de novo assemblies for three spider species: Ryuthela nishihirai (Liphistiidae), a representative of the ancient Mesothelae, the suborder that is sister to all other extant spiders; Uloborus plumipes (Uloboridae), a cribellate orbweaver whose phylogenetic placement is especially challenging; and Cheiracanthium punctorium (Cheiracanthiidae), which represents only the second family to be sequenced in the hyperdiverse Dionycha clade. These genomes fill critical gaps in the spider tree of life. Using these novel genomes along with 25 previously published ones, we examine the evolutionary history of spidroin gene and structural hox cluster diversity. Our assemblies provide critical genomic resources to facilitate deeper investigations into spider evolution. The near chromosome-level genome of the 'living fossil' R. nishihirai represents an especially important step forward, offering new insights into the origins of spider traits.
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Affiliation(s)
| | - Tracy Lynn Audisio
- Evolutionary Genomics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Alexander Ben Hamadou
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt am Main, Germany
| | - Martin Forman
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Jiří Král
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tereza Kořínková
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Eva Líznarová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Lenka Prokopcová
- Laboratory of Arachnid Cytogenetics, Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | | | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
- Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
| | - Susan Kennedy
- Department of Biogeography, Trier University, Trier, Germany
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Soto Gomez M, Brown MJM, Pironon S, Bureš P, Verde Arregoitia LD, Veselý P, Elliott TL, Zedek F, Pellicer J, Forest F, Nic Lughadha E, Leitch IJ. Genome size is positively correlated with extinction risk in herbaceous angiosperms. THE NEW PHYTOLOGIST 2024; 243:2470-2485. [PMID: 39080986 DOI: 10.1111/nph.19947] [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: 09/13/2023] [Accepted: 06/02/2024] [Indexed: 08/23/2024]
Abstract
Angiosperms with large genomes experience nuclear-, cellular-, and organism-level constraints that may limit their phenotypic plasticity and ecological niche, which could increase their risk of extinction. Therefore, we test the hypotheses that large-genomed species are more likely to be threatened with extinction than those with small genomes, and that the effect of genome size varies across three selected covariates: life form, endemism, and climatic zone. We collated genome size and extinction risk information for a representative sample of angiosperms comprising 3250 species, which we analyzed alongside life form, endemism, and climatic zone variables using a phylogenetic framework. Genome size is positively correlated with extinction risk, a pattern driven by a signal in herbaceous but not woody species, regardless of climate and endemism. The influence of genome size is stronger in endemic herbaceous species, but is relatively homogenous across different climates. Beyond its indirect link via endemism and climate, genome size is associated with extinction risk directly and significantly. Genome size may serve as a proxy for difficult-to-measure parameters associated with resilience and vulnerability in herbaceous angiosperms. Therefore, it merits further exploration as a useful biological attribute for understanding intrinsic extinction risk and augmenting plant conservation efforts.
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Affiliation(s)
| | | | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, CB3 0DL, UK
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Petr Bureš
- Faculty of Science, Department of Botany and Zoology, Masaryk University, Brno, 61137, Czech Republic
| | | | - Pavel Veselý
- Faculty of Science, Department of Botany and Zoology, Masaryk University, Brno, 61137, Czech Republic
| | - Tammy L Elliott
- Faculty of Science, Department of Botany and Zoology, Masaryk University, Brno, 61137, Czech Republic
- Department of Biological Sciences, University of Cape Town, Cape Town, 7700, South Africa
| | - František Zedek
- Faculty of Science, Department of Botany and Zoology, Masaryk University, Brno, 61137, Czech Republic
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Institut Botanic de Barcelona (IBB), CSIC-CMCNB, Barcelona, 08038, Spain
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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Kuhl H, Strassert JFH, Čertnerová D, Varga E, Kreuz E, Lamatsch DK, Wuertz S, Köhler J, Monaghan MT, Stöck M. The haplotype-resolved Prymnesium parvum (type B) microalga genome reveals the genetic basis of its fish-killing toxins. Curr Biol 2024; 34:3698-3706.e4. [PMID: 38986615 DOI: 10.1016/j.cub.2024.06.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/13/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024]
Abstract
The catastrophic loss of aquatic life in the Central European Oder River in 2022, caused by a toxic bloom of the haptophyte microalga Prymnesium parvum (in a wide sense, s.l.), underscores the need to improve our understanding of the genomic basis of the toxin. Previous morphological, phylogenetic, and genomic studies have revealed cryptic diversity within P. parvum s.l. and uncovered three clade-specific (types A, B, and C) prymnesin toxins. Here, we used state-of-the-art long-read sequencing and assembled the first haplotype-resolved diploid genome of a P. parvum type B from the strain responsible for the Oder disaster. Comparative analyses with type A genomes uncovered a genome-size expansion driven by repetitive elements in type B. We also found conserved synteny but divergent evolution in several polyketide synthase (PKS) genes, which are known to underlie toxin production in combination with environmental cues. We identified an approximately 20-kbp deletion in the largest PKS gene of type B that we link to differences in the chemical structure of types A and B prymnesins. Flow cytometry and electron microscopy analyses confirmed diploidy in the Oder River strain and revealed differences to closely related strains in both ploidy and morphology. Our results provide unprecedented resolution of strain diversity in P. parvum s.l. and a better understanding of the genomic basis of toxin variability in haptophytes. The reference-quality genome will enable us to better understand changes in microbial diversity in the face of increasing environmental pressures and provides a basis for strain-level monitoring of invasive Prymnesium in the future.
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Affiliation(s)
- Heiner Kuhl
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Jürgen F H Strassert
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Dora Čertnerová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic; Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Elisabeth Varga
- Department of Food Chemistry and Toxicology, University of Vienna, Vienna, Austria; Unit Food Hygiene and Technology, Centre for Food Science and Veterinary Public Health, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine, Vienna, Austria
| | - Eva Kreuz
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Dunja K Lamatsch
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Sven Wuertz
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Jan Köhler
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany.
| | - Matthias Stöck
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.
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Bureš P, Elliott TL, Veselý P, Šmarda P, Forest F, Leitch IJ, Nic Lughadha E, Soto Gomez M, Pironon S, Brown MJM, Šmerda J, Zedek F. The global distribution of angiosperm genome size is shaped by climate. THE NEW PHYTOLOGIST 2024; 242:744-759. [PMID: 38264772 DOI: 10.1111/nph.19544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.
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Affiliation(s)
- Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Tammy L Elliott
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
- Department of Biological Sciences, University of Cape Town, Cape Town, 7700, South Africa
| | - Pavel Veselý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | | | | | | | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, CB3 0DL, UK
| | | | - Jakub Šmerda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
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Choi B, Hwang Y, McAdam SAM, Jang TS. Comparative microscopic investigations of leaf epidermis in four Ajuga species from Korea. Microsc Res Tech 2024; 87:434-445. [PMID: 37909218 DOI: 10.1002/jemt.24450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/07/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023]
Abstract
The genus Ajuga is widely distributed in temperate to subtropical regions, and four species are currently recognized in Korea (A. decumbens, A. multiflora, A. nipponensis, and A. spectabilis), but epidermal anatomical differences across these species have never been described. A comparative study of the leaf micromorphological characteristics of Korean Ajuga species was performed using light microscopy (LM) and scanning electron microscopy (SEM) to elucidate their taxonomic usefulness and to assess leaf micromorphological diversity. Considerable diversity in epidermal and stomatal anatomy was observed across Korean Ajuga species. Species had both hypostomatic or amphistomatic leaves, with anomocytic, anisocytic, diactyic, or actinocytic stomatal complexes. Guard cell length across species ranged from 17.66 ± 0.57 μm to 32.50 ± 2.38 μm and correlated with genome size. Abnormal stomata were frequently observed in three species (A. decumbens, A. multiflora, and A. nipponensis) but not in A. spectabilis. Three types of glandular trichomes were found: peltate in all species, short-stalked in all species, and long-stalked glandular trichomes in A. multiflora. Among the investigated leaf micromophological characters, trichome type, epidermal cell shape, and stomatal morphology were all taxonomically informative traits at a species level. RESEARCH HIGHLIGHTS: A comprehensive micromorphological description of the leaf surface is provided for Korean Ajuga species using scanning electron microscopic (SEM) and light microscopic (LM) analyses. The diverse range of stomatal development and the occurrence of polymorphic stomatal types are documented for the first time in Korean Ajuga species. The great diversity in stomatal and trichome morphology in Korean Ajuga species are taxonomically useful traits for species identification.
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Affiliation(s)
- Bokyung Choi
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Yeojin Hwang
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Scott A M McAdam
- Department of Botany and Plant Pathology, Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Tae-Soo Jang
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
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6
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Záveská E, Šída O, Leong-Škorničková J, Chumová Z, Trávníček P, Newman MF, Poulsen AD, Böhmová A, Chudáčková H, Fér T. Testing the large genome constraint hypothesis in tropical rhizomatous herbs: life strategies, plant traits and habitat preferences in gingers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1223-1238. [PMID: 37991980 DOI: 10.1111/tpj.16559] [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: 02/08/2023] [Revised: 11/06/2023] [Accepted: 11/11/2023] [Indexed: 11/24/2023]
Abstract
Plant species with large genomes tend to be excluded from climatically more extreme environments with a shorter growing season. Species that occupy such environments are assumed to be under natural selection for more rapid growth and smaller genome size (GS). However, evidence for this is available only for temperate organisms. Here, we study the evolution of GS in two subfamilies of the tropical family Zingiberaceae to find out whether species with larger genomes are confined to environments where the vegetative season is longer. We tested our hypothesis on 337 ginger species from regions with contrasting climates by correlating their GS with an array of plant traits and environmental variables. We revealed 16-fold variation in GS which was tightly related to shoot seasonality. Negative correlations of GS with latitude, temperature and precipitation emerged in the subfamily Zingiberoidae, demonstrating that species with larger GS are excluded from areas with a shorter growing season. In the subfamily Alpinioideae, GS turned out to be correlated with the type of stem and light requirements and its members cope with seasonality mainly by adaptation to shady and moist habitats. The Ornstein-Uhlenbeck models suggested that evolution in regions with humid climates favoured larger GS than in drier regions. Our results indicate that climate seasonality exerts an upper constraint on GS not only in temperate regions but also in the tropics, unless species with large genomes find alternative ways to escape from that constraint.
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Affiliation(s)
- E Záveská
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - O Šída
- Department of Botany, National Museum in Prague, Prague, Czech Republic
| | - J Leong-Škorničková
- The Herbarium, Singapore Botanic Gardens, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Z Chumová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - P Trávníček
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - M F Newman
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - A D Poulsen
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - A Böhmová
- Department of Botany, National Museum in Prague, Prague, Czech Republic
- Department of Botany, Charles University, Prague, Czech Republic
| | - H Chudáčková
- Department of Botany, Charles University, Prague, Czech Republic
| | - T Fér
- Department of Botany, Charles University, Prague, Czech Republic
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7
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Liu Y, Liang N, Xian Q, Zhang W. GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2. BMC PLANT BIOLOGY 2023; 23:608. [PMID: 38036992 PMCID: PMC10691020 DOI: 10.1186/s12870-023-04634-9] [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: 04/21/2023] [Accepted: 11/26/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Despite GC variation constitutes a fundamental element of genome and species diversity, the precise mechanisms driving it remain unclear. The abundant sequence data available for the ITS2, a commonly employed phylogenetic marker in plants, offers an exceptional resource for exploring the GC variation across angiosperms. RESULTS A comprehensive selection of 8666 species, comprising 165 genera, 63 families, and 30 orders were used for the analyses. The alignment of ITS2 sequence-structures and partitioning of secondary structures into paired and unpaired regions were performed using 4SALE. Substitution rates and frequencies among GC base-pairs in the paired regions of ITS2 were calculated using RNA-specific models in the PHASE package. The results showed that the distribution of ITS2 GC contents on the angiosperm phylogeny was heterogeneous, but their increase was generally associated with ITS2 sequence homogenization, thereby supporting the occurrence of GC-biased gene conversion (gBGC) during the concerted evolution of ITS2. Additionally, the GC content in the paired regions of the ITS2 secondary structure was significantly higher than that of the unpaired regions, indicating the selection of GC for thermodynamic stability. Furthermore, the RNA substitution models demonstrated that base-pair transformations favored both the elevation and fixation of GC in the paired regions, providing further support for gBGC. CONCLUSIONS Our findings highlight the significance of secondary structure in GC investigation, which demonstrate that both gBGC and structure-based selection are influential factors driving angiosperm ITS2 GC content.
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Affiliation(s)
- Yubo Liu
- Marine College, Shandong University, Weihai, 264209, China
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Nan Liang
- Marine College, Shandong University, Weihai, 264209, China
- Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qing Xian
- Marine College, Shandong University, Weihai, 264209, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai, 264209, China.
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Bitomský M, Martínková J, Lubbe FC, Marešová I, Klimešová J. Genome size is strongly linked to carbohydrate storage and weakly linked to root sprouting ability in herbs. ANNALS OF BOTANY 2023; 132:1021-1032. [PMID: 37823724 PMCID: PMC10808013 DOI: 10.1093/aob/mcad158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/10/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND AND AIMS Several lines of evidence indicate that carbohydrate storage in plant below-ground organs might be positively related to genome size because both these plant properties represent resource sinks and can affect cell size, cell cycle time, water-use efficiency and plant growth. However, plants adapted to disturbance, such as root sprouters, could be an exception because their strategy would require higher carbohydrate reserves to fuel biomass production but small genomes to complete their cell cycles faster. METHODS We used data from a field survey to test the relationship between genome size and the probability of root sprouting ability in 172 Central European herbaceous species. Additionally, we conducted a pot experiment with 19 herbaceous species with different sprouting ability (nine congeneric pairs plus one species), and measured root non-structural carbohydrate concentrations and pools at the end of a growing season. KEY RESULTS In the Central European flora, the probability of root sprouting ability was lower in large-genome species but this pattern was weak. In the pot experiment, both total non-structural and water-soluble carbohydrates (mainly fructans) were positively and non-linearly related to genome size, regardless of sprouting strategy. The concentrations of mono- and disaccharides and all carbohydrate pools showed no link to genome size, and starch was absent in large-genome species. The link between genome size and carbohydrate storage was less apparent at a small phylogenetic scale because we only observed a higher carbohydrate concentration in species with larger genomes for four of the species pairs. CONCLUSIONS Root sprouters may have smaller genomes because of their frequent occurrence in dry and open habitats. Large-genome species with presumably large cells and vacuoles could accumulate more water-soluble carbohydrates at the end of the growing season to fuel their growth and perhaps protect vulnerable organs from freezing early in the next season.
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Affiliation(s)
- Martin Bitomský
- Institute of Botany of the Czech Academy of Sciences, Dukelská 135, 379 01 Třeboň, Czech Republic
| | - Jana Martínková
- Institute of Botany of the Czech Academy of Sciences, Dukelská 135, 379 01 Třeboň, Czech Republic
| | - F Curtis Lubbe
- Institute of Botany of the Czech Academy of Sciences, Dukelská 135, 379 01 Třeboň, Czech Republic
| | - Iveta Marešová
- Institute of Botany of the Czech Academy of Sciences, Dukelská 135, 379 01 Třeboň, Czech Republic
| | - Jitka Klimešová
- Institute of Botany of the Czech Academy of Sciences, Dukelská 135, 379 01 Třeboň, Czech Republic
- Department of Botany, Charles University, Benátská 2, 128 01 Prague, Czech Republic
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Gadagkar SR, Baeza JA, Buss K, Johnson N. De-novo whole genome assembly of the orange jewelweed, Impatiens capensis Meerb. (Balsaminaceae) using nanopore long-read sequencing. PeerJ 2023; 11:e16328. [PMID: 37901463 PMCID: PMC10601903 DOI: 10.7717/peerj.16328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 09/30/2023] [Indexed: 10/31/2023] Open
Abstract
The plant family Balsaminaceae comprises only two genera, and they are a study in contrasts. While Impatiens is an impressively prolific genus, with over 1,000 species and more being discovered each year, its sister genus, Hydrocera, has one solitary species, H. triflora. The two genera also differ in geographic distribution and habitat type (Impatiens species are widely distributed in much of the Old World and N. America, while H. triflora is confined to wetlands specific to S. India, Sri Lanka, and SE Asia). Other contrasting features include plant habit, habitat, floral architecture, mode of seed dispersal, and a host of other traits. The family Balsaminaceae is therefore an excellent model for studying speciation and character evolution as well as understanding the proximal and evolutionary forces that have driven the two genera to adopt such contrasting evolutionary paths. Various species of the Impatiens genus are also commercially important in the ornamental flower industry and as sources of phytochemicals that are of medicinal and other commercial value. As a preliminary step towards studying the genomic basis of the contrasting features of the two genera, we have sequenced and assembled, de novo, the genome of an iconic Impatiens species from N. America, namely I. capensis, and report our findings here.
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Affiliation(s)
- Sudhindra R. Gadagkar
- Biomedical Sciences Program, Midwestern University, Glendale, Arizona, United States of America
- College of Veterinary Medicine, Midwestern University, Glendale, Arizona, United States of America
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, Arizona, United States of America
| | - J. Antonio Baeza
- Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
- Smithsonian Marine Station at Fort Pierce, Fort Pierce, Florida, United States of America
| | - Kristina Buss
- Bioinformatics Core, Arizona State University, Tempe, Arizona, United States of America
| | - Nate Johnson
- Biomedical Sciences Program, Midwestern University, Glendale, Arizona, United States of America
- College of Veterinary Medicine, Midwestern University, Glendale, Arizona, United States of America
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, Arizona, United States of America
- Center for Biology and Society, Arizona State University, Tempe, Arizona, United States of America
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Kim H, Choi B, Lee C, Paik JH, Jang CG, Weiss-Schneeweiss H, Jang TS. Does the evolution of micromorphology accompany chromosomal changes on dysploid and polyploid levels in the Barnardia japonica complex (Hyacinthaceae)? BMC PLANT BIOLOGY 2023; 23:485. [PMID: 37817118 PMCID: PMC10565974 DOI: 10.1186/s12870-023-04456-9] [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: 05/10/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023]
Abstract
BACKGROUND Chromosome number and genome size changes via dysploidy and polyploidy accompany plant diversification and speciation. Such changes often impact also morphological characters. An excellent system to address the questions of how extensive and structured chromosomal changes within one species complex affect the phenotype is the monocot species complex of Barnardia japonica. This taxon contains two well established and distinct diploid cytotypes differing in base chromosome numbers (AA: x = 8, BB: x = 9) and their allopolyploid derivatives on several ploidy levels (from 3x to 6x). This extensive and structured genomic variation, however, is not mirrored by gross morphological differentiation. RESULTS The current study aims to analyze the correlations between the changes of chromosome numbers and genome sizes with palynological and leaf micromorphological characters in diploids and selected allopolyploids of the B. japonica complex. The chromosome numbers varied from 2n = 16 and 18 (2n = 25 with the presence of supernumerary B chromosomes), and from 2n = 26 to 51 in polyploids on four different ploidy levels (3x, 4x, 5x, and 6x). Despite additive chromosome numbers compared to diploid parental cytotypes, all polyploid cytotypes have experienced genome downsizing. Analyses of leaf micromorphological characters did not reveal any diagnostic traits that could be specifically assigned to individual cytotypes. The variation of pollen grain sizes correlated positively with ploidy levels. CONCLUSIONS This study clearly demonstrates that karyotype and genome size differentiation does not have to be correlated with morphological differentiation of cytotypes.
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Affiliation(s)
- Hyeonjin Kim
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Bokyung Choi
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Changyoung Lee
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jin-Hyub Paik
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Chang-Gee Jang
- Department of Biology Education, Kongju National University, Gongju, 32588, Republic of Korea
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, A-1030, Austria.
| | - Tae-Soo Jang
- Department of Biological Science, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea.
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11
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Gnanesh BN, Mondal R, G S A, H B M, Singh P, M R B, P S, Burji SM, T M, V S. Genome size, genetic diversity, and phenotypic variability imply the effect of genetic variation instead of ploidy on trait plasticity in the cross-pollinated tree species of mulberry. PLoS One 2023; 18:e0289766. [PMID: 37566619 PMCID: PMC10420377 DOI: 10.1371/journal.pone.0289766] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Elucidation of genome size (GS), genetic and phenotypic variation is the fundamental aspect of crop improvement programs. Mulberry is a cross-pollinated, highly heterozygous tree eudicot, and comprised of huge ploidy variation with great adaptability across the world. However, because of inadequate information on GS, ploidy-associated traits, as well as the correlation between genetic and phenotypic variation hinder the further improvement of mulberry. In this present research, a core set of 157 germplasm accessions belonging to eight accepted species of Morus including promising functional varieties were chosen to represent the genetic spectrum from the whole germplasm collection. To estimate the GS, accessions were subjected to flow cytometry (FCM) analysis and the result suggested that four different ploidies (2n = 2x, 3x, 4x, and 6x) with GS ranging from 0.72±0.005pg (S-30) to 2.89±0.015pg (M. serrata), accounting~4.01 fold difference. The predicted polyploidy was further confirmed with metaphase chromosome count. In addition, the genetic variation was estimated by selecting a representative morphologically, diverse population of 82 accessions comprised of all ploidy variations using simple sequence repeats (SSR). The estimated average Polymorphism Information Content (PIC) and expected heterozygosity showed high levels of genetic diversity. Additionally, three populations were identified by the model-based population structure (k = 3) with a moderate level of correlation between the populations and different species of mulberry, which imply the effect of genetic variation instead of ploidy on trait plasticity that could be a consequence of the high level of heterozygosity imposed by natural cross-pollination. Further, the correlation between ploidies, especially diploid and triploid with selected phenotypic traits was identified, however, consistency could not be defined with higher ploidy levels (>3x). Moreover, incite gained here can serve as a platform for future omics approaches to the improvement of mulberry traits.
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Affiliation(s)
- Belaghihalli N Gnanesh
- Molecular Biology Laboratory-1, Central Sericultural Research and Training Institute, Mysuru, Karnataka, India
| | - Raju Mondal
- Mulberry Tissue Culture Lab, Central Sericultural Germplasm Resources Centre, Hosur, Tamil Nadu, India
| | - Arunakumar G S
- Molecular Biology Laboratory-1, Central Sericultural Research and Training Institute, Mysuru, Karnataka, India
| | - Manojkumar H B
- Molecular Biology Laboratory-1, Central Sericultural Research and Training Institute, Mysuru, Karnataka, India
| | - Pradeep Singh
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Bhavya M R
- Molecular Biology Laboratory-1, Central Sericultural Research and Training Institute, Mysuru, Karnataka, India
| | - Sowbhagya P
- Molecular Biology Laboratory-1, Central Sericultural Research and Training Institute, Mysuru, Karnataka, India
| | - Shreyas M Burji
- Auxochromofours Solutions Pvt. Ltd., Bangalore, Karnataka, India
| | - Mogili T
- Molecular Biology Laboratory-1, Central Sericultural Research and Training Institute, Mysuru, Karnataka, India
| | - Sivaprasad V
- Molecular Biology Laboratory-1, Central Sericultural Research and Training Institute, Mysuru, Karnataka, India
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12
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Li S, Qi B, Peng X, Wang W, Wang W, Liu P, Liu B, Peng Z, Wang Q, Li Y. Genome size and GC content of myxomycetes. Eur J Protistol 2023; 90:125991. [PMID: 37331249 DOI: 10.1016/j.ejop.2023.125991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/20/2023]
Abstract
More than 1272 myxomycetes species have been described, accounting for more than half of all Amoebozoa species. However, the genome size of only three myxomycetes species has been reported. Therefore, we used flow cytometry to present an extensive survey and a phylogeny-based analysis of genome size and GC content evolution in 144 myxomycetes species. The genome size of myxomycetes ranged from 18.7 Mb to 470.3 Mb, and the GC content ranged from 38.7% to 70.1%. Bright-spored clade showed larger genome sizes and more intra-order genome size variations than the dark-spored clade. GC content and genome size were positively correlated in both bright-spored and dark-spored clades, and spore size was positively correlated with genome size and GC content in the bright-spored clade. We provided the first genome size data set in Myxomycetes, and our results will provide helpful information for future Myxomycetes studies, such as genome sequencing.
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Affiliation(s)
- Shu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Bao Qi
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Xueyan Peng
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Wei Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Wan Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Pu Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun, China.
| | - Qi Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
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13
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Bartish IV, Bonnefoi S, Aïnouche A, Bruelheide H, Bartish M, Prinzing A. Fewer chromosomes, more co-occurring species within plant lineages: A likely effect of local survival and colonization. AMERICAN JOURNAL OF BOTANY 2023; 110:e16139. [PMID: 36758168 DOI: 10.1002/ajb2.16139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 05/11/2023]
Abstract
PREMISE Plant lineages differ markedly in species richness globally, regionally, and locally. Differences in whole-genome characteristics (WGCs) such as monoploid chromosome number, genome size, and ploidy level may explain differences in global species richness through speciation or global extinction. However, it is unknown whether WGCs drive species richness within lineages also in a recent, postglacial regional flora or in local plant communities through local extinction or colonization and regional species turnover. METHODS We tested for relationships between WGCs and richness of angiosperm families across the Netherlands/Germany/Czechia as a region, and within 193,449 local vegetation plots. RESULTS Families that are species-rich across the region have lower ploidy levels and small monoploid chromosomes numbers or both (interaction terms), but the relationships disappear after accounting for continental and local richness of families. Families that are species-rich within occupied localities have small numbers of polyploidy and monoploid chromosome numbers or both, independent of their own regional richness and the local richness of all other locally co-occurring species in the plots. Relationships between WGCs and family species-richness persisted after accounting for niche characteristics and life histories. CONCLUSIONS Families that have few chromosomes, either monoploid or holoploid, succeed in maintaining many species in local communities and across a continent and, as indirect consequence of both, across a region. We suggest evolutionary mechanisms to explain how small chromosome numbers and ploidy levels might decrease rates of local extinction and increase rates of colonization. The genome of a macroevolutionary lineage may ultimately control whether its species can ecologically coexist.
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Affiliation(s)
- Igor V Bartish
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
- Department of Genetic Ecology, Institute of Botany, Academy of Sciences, CZ-25243 Pruhonice 1, Czech Republic
| | - Salomé Bonnefoi
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
| | - Abdelkader Aïnouche
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
| | - Helge Bruelheide
- Institute of Biology/Geobotany & Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany
| | - Mark Bartish
- Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - Andreas Prinzing
- Université de Rennes 1, CNRS Research Unit Ecosystèmes Biodiversité Evolution (ECOBIO), Campus de Beaulieu, 35042, Rennes, France
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14
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Elliott TL, Muasya AM, Bureš P. Complex patterns of ploidy in a holocentric plant clade (Schoenus, Cyperaceae) in the Cape biodiversity hotspot. ANNALS OF BOTANY 2023; 131:143-156. [PMID: 35226733 PMCID: PMC9904348 DOI: 10.1093/aob/mcac027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/27/2022] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS It is unclear how widespread polyploidy is throughout the largest holocentric plant family - the Cyperaceae. Because of the prevalence of chromosomal fusions and fissions, which affect chromosome number but not genome size, it can be impossible to distinguish if individual plants are polyploids in holocentric lineages based on chromosome count data alone. Furthermore, it is unclear how differences in genome size and ploidy levels relate to environmental correlates within holocentric lineages, such as the Cyperaceae. METHODS We focus our analyses on tribe Schoeneae, and more specifically the southern African clade of Schoenus. We examine broad-scale patterns of genome size evolution in tribe Schoeneae and focus more intensely on determining the prevalence of polyploidy across the southern African Schoenus by inferring ploidy level with the program ChromEvol, as well as interpreting chromosome number and genome size data. We further investigate whether there are relationships between genome size/ploidy level and environmental variables across the nutrient-poor and summer-arid Cape biodiversity hotspot. KEY RESULTS Our results show a large increase in genome size, but not chromosome number, within Schoenus compared to other species in tribe Schoeneae. Across Schoenus, there is a positive relationship between chromosome number and genome size, and our results suggest that polyploidy is a relatively common process throughout the southern African Schoenus. At the regional scale of the Cape, we show that polyploids are more often associated with drier locations that have more variation in precipitation between dry and wet months, but these results are sensitive to the classification of ploidy level. CONCLUSIONS Polyploidy is relatively common in the southern African Schoenus, where a positive relationship is observed between chromosome number and genome size. Thus, there may be a high incidence of polyploidy in holocentric plants, whose cell division properties differ from monocentrics.
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Affiliation(s)
| | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
| | - Petr Bureš
- Masaryk University, Faculty of Science, Department of Botany and Zoology, Kotlarska 2, Brno, Czech Republic
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15
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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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16
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Koprivý L, Fráková V, Kolarčik V, Mártonfiová L, Dudáš M, Mártonfi P. Genome size and endoreplication in two pairs of cytogenetically contrasting species of Pulmonaria (Boraginaceae) in Central Europe. AOB PLANTS 2022; 14:plac036. [PMID: 36128515 PMCID: PMC9476981 DOI: 10.1093/aobpla/plac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/16/2022] [Indexed: 06/13/2023]
Abstract
Genome size is species-specific feature and commonly constant in an organism. In various plants, DNA content in cell nucleus is commonly increased in process of endoreplication, cellular-specific multiplication of DNA content without mitosis. This leads to the endopolyploidy, the presence of multiplied chromosome sets in a subset of cells. The relationship of endopolyploidy to species-specific genome size is rarely analysed and is not fully understood. While negative correlation between genome size and endopolyploidy level is supposed, this is species- and lineage-specific. In the present study, we shed light on this topic, exploring both genome size and endoreplication-induced DNA content variation in two pairs of morphologically similar species of Pulmonaria, P. obscura-P. officinalis and P. mollis-P. murinii. We aim (i) to characterize genome size and chromosome numbers in these species using cytogenetic, root-tip squashing and flow cytometry (FCM) techniques; (ii) to investigate the degree of endopolyploidy in various plant organs, including the root, stem, leaf, calyx and corolla using FCM; and (iii) to comprehensively characterize and compare the level of endopolyploidy and DNA content in various organs of all four species in relation to species systematic relationships and genome size variation. We have confirmed the diploid-dysploid nature of chromosome complements, and divergent genome sizes for Pulmonaria species: P. murinii with 2n = 2x = 14, 2.31 pg/2C, P. obscura 2n = 2x = 14, 2.69 pg/2C, P. officinalis 2n = 2x = 16, 2.96 pg/2C and P. mollis 2n = 2x = 18, 3.18 pg/2C. Endopolyploidy varies between species and organs, and we have documented 4C-8C in all four organs and up to 32C (64C) endopolyploid nuclei in stems at least in some species. Two species with lower genome sizes tend to have higher endopolyploidy levels than their closest relatives. Endoreplication-generated tissue-specific mean DNA content is increased and more balanced among species in all four organs compared to genome size. Our results argue for the narrow relationship between genome size and endopolyploidy in the present plant group within the genus Pulmonaria, and endopolyploidization seems to play a compensatory developmental role in organs of related morphologically similar species.
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Affiliation(s)
- Lukáš Koprivý
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovak Republic
- Botanical Garden, Pavol Jozef Šafárik University, Mánesova 23, SK-043 52 Košice, Slovak Republic
| | - Viera Fráková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovak Republic
| | - Vladislav Kolarčik
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovak Republic
| | - Lenka Mártonfiová
- Botanical Garden, Pavol Jozef Šafárik University, Mánesova 23, SK-043 52 Košice, Slovak Republic
| | - Matej Dudáš
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovak Republic
| | - Pavol Mártonfi
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovak Republic
- Botanical Garden, Pavol Jozef Šafárik University, Mánesova 23, SK-043 52 Košice, Slovak Republic
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17
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Becker FW, Oberlander KC, Trávníček P, Dreyer LL. Inconsistent expression of the gigas effect in polyploid Oxalis. AMERICAN JOURNAL OF BOTANY 2022; 109:1607-1621. [PMID: 36193941 DOI: 10.1002/ajb2.16077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
PREMISE It is well-known that whole genome duplication (WGD) has played a significant role in the evolution of plants. The best-known phenotypic effect of WGD is the gigas effect, or the enlargement of polyploid plant traits. WGD is often linked with increased weediness, which could be a result of fitness advantages conferred by the gigas effect. As a result, the gigas effect could potentially explain polyploid persistence and abundance. We test whether a gigas effect is present in the polyploid-rich geophyte Oxalis, at both organ and cellular scales. METHODS We measured traits in conspecific diploid and polyploid accessions of 24 species across the genus. In addition, we measured the same and additional traits in 20 populations of the weedy and highly ploidy-variable species Oxalis purpurea L., including measures of clonality and selfing as a proxy for weediness. Ploidy level was determined using flow cytometry. RESULTS We found substantial variation and no consistent ploidy-related size difference, both between and within species, and across traits. Oxalis purpurea polyploids did, however, produce significantly more underground biomass and more bulbils than diploids, consistent with a potential role of WGD in the weediness of this species. CONCLUSIONS Our results suggest a more nuanced role for the gigas effect, at least in Oxalis. It may be temporary, short-lived, and inconsistently expressed and retained on evolutionary time scales, but in the short term can contribute to lineage success via increased vegetative reproduction.
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Affiliation(s)
- Frederik W Becker
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Kenneth C Oberlander
- H. G. W. J. Schweickerdt Herbarium, Department of Plant and Soil Sciences, Plant Sciences Complex, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Pavel Trávníček
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic, and Department of Botany, Charles University, Praha, Czech Republic
| | - Léanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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18
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Schley RJ, Pellicer J, Ge X, Barrett C, Bellot S, Guignard MS, Novák P, Suda J, Fraser D, Baker WJ, Dodsworth S, Macas J, Leitch AR, Leitch IJ. The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity. THE NEW PHYTOLOGIST 2022; 236:433-446. [PMID: 35717562 PMCID: PMC9796251 DOI: 10.1111/nph.18323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat 'communities' are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat 'community' composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat 'communities'.
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Affiliation(s)
- Rowan J. Schley
- University of ExeterLaver Building, North Park RoadExeterDevonEX4 4QEUK
- Royal Botanic GardensKewSurreyTW9 3ABUK
| | - Jaume Pellicer
- Royal Botanic GardensKewSurreyTW9 3ABUK
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia sn08038BarcelonaSpain
| | - Xue‐Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhou510650China
| | - Craig Barrett
- Department of BiologyWest Virginia UniversityMorgantownWV26506USA
| | | | | | - Petr Novák
- Biology Centre, Institute of Plant Molecular BiologyCzech Academy of Sciences370 05České BudějoviceCzech Republic
| | | | | | | | - Steven Dodsworth
- School of Biological SciencesUniversity of PortsmouthPortsmouthHampshirePO1 2DYUK
| | - Jiří Macas
- Biology Centre, Institute of Plant Molecular BiologyCzech Academy of Sciences370 05České BudějoviceCzech Republic
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Chumová Z, Belyayev A, Mandáková T, Zeisek V, Hodková E, Šemberová K, Euston-Brown D, Trávníček P. The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae). FRONTIERS IN PLANT SCIENCE 2022; 13:982852. [PMID: 36247607 PMCID: PMC9559566 DOI: 10.3389/fpls.2022.982852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Non-coding repetitive DNA (repeatome) is an active part of the nuclear genome, involved in its structure, evolution and function. It is dominated by transposable elements (TEs) and satellite DNA and is prone to the most rapid changes over time. The TEs activity presumably causes the global genome reorganization and may play an adaptive or regulatory role in response to environmental challenges. This assumption is applied here for the first time to plants from the Cape Floristic hotspot to determine whether changes in repetitive DNA are related to responses to a harsh, but extremely species-rich environment. The genus Pteronia (Asteraceae) serves as a suitable model group because it shows considerable variation in genome size at the diploid level and has high and nearly equal levels of endemism in the two main Cape biomes, Fynbos and Succulent Karoo. First, we constructed a phylogeny based on multiple low-copy genes that served as a phylogenetic framework for detecting quantitative and qualitative changes in the repeatome. Second, we performed a comparative analysis of the environments of two groups of Pteronia differing in their TEs bursts. Our results suggest that the environmental transition from the Succulent Karoo to the Fynbos is accompanied by TEs burst, which is likely also driving phylogenetic divergence. We thus hypothesize that analysis of rapidly evolving repeatome could serve as an important proxy for determining the molecular basis of lineage divergence in rapidly radiating groups.
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Affiliation(s)
- Zuzana Chumová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Alexander Belyayev
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Faculty of Science, Masaryk University, Brno, Czechia
| | - Vojtěch Zeisek
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Eva Hodková
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | - Kristýna Šemberová
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
| | | | - Pavel Trávníček
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czechia
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Flood PJ, Nowrousian M, Huettel B, Woehle C, Becker K, Wollenweber TE, Begerow D, Grefen C. Draft genome of the aardaker (Lathyrus tuberosus L.), a tuberous legume. BMC Genom Data 2022; 23:70. [PMID: 36057561 PMCID: PMC9441078 DOI: 10.1186/s12863-022-01083-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Lathyrus tuberosus is a nitrogen-fixing member of the Fabaceae which forms protein-rich tubers. To aid future domestication programs for this legume plant and facilitate evolutionary studies of tuber formation, we have generated a draft genome assembly based on Pacific Biosciences sequence reads. DATA DESCRIPTION Genomic DNA from L. tuberosus was sequenced with PacBio's HiFi sequencing chemistry generating 12.8 million sequence reads with an average read length of 14 kb (approximately 180 Gb of sequence data). The reads were assembled to give a draft genome of 6.8 Gb in 1353 contigs with an N50 contig length of 11.1 Mb. The GC content of the genome assembly was 38.3%. BUSCO analysis of the genome assembly indicated a genome completeness of at least 96%. The genome sequence will be a valuable resource, for example, in assessing genomic consequences of domestication efforts and developing marker sets for breeding programs. The L. tuberosus genome will also aid in the analysis of the evolutionary history of plants within the nitrogen-fixing Fabaceae family and in understanding the molecular basis of tuber evolution.
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Affiliation(s)
| | - Minou Nowrousian
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Bruno Huettel
- Max-Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Christian Woehle
- Max-Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Kerstin Becker
- Genomics & Transcriptomics Labor, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Tassilo Erik Wollenweber
- Genomics & Transcriptomics Labor, Biologisch-Medizinisches Forschungszentrum, and West German Genome Center, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Dominik Begerow
- Lehrstuhl für Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Christopher Grefen
- Lehrstuhl für Molekulare und Zelluläre Botanik, Ruhr-Universität Bochum, Universitätsstr. 150, 44801 Bochum, Germany
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21
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Temsch EM, Koutecký P, Urfus T, Šmarda P, Doležel J. Reference standards for flow cytometric estimation of absolute nuclear DNA content in plants. Cytometry A 2022; 101:710-724. [PMID: 34405937 PMCID: PMC9545105 DOI: 10.1002/cyto.a.24495] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 11/11/2022]
Abstract
The estimation of nuclear DNA content has been by far the most popular application of flow cytometry in plants. Because flow cytometry measures relative fluorescence intensities of nuclei stained by a DNA fluorochrome, ploidy determination, and estimation of the nuclear DNA content in absolute units both require comparison to a reference standard of known DNA content. This implies that the quality of the results obtained depends on the standard selection and use. Internal standardization, when the nuclei of an unknown sample and the reference standard are isolated, stained, and measured simultaneously, is mandatory for precise measurements. As DNA peaks representing G1 /G0 nuclei of the sample and standard appear on the same histogram of fluorescence intensity, the quotient of their position on the fluorescence intensity axis provides the quotient of DNA amounts. For the estimation of DNA amounts in absolute units, a number of well-established standards are now available to cover the range of known plant genome sizes. Since there are different standards in use, the standard and the genome size assigned to it has always to be reported. When none of the established standards fits, the introduction of a new standard species is needed. For this purpose, the regression line approach or simultaneous analysis of the candidate standard with several established standards should be prioritized. Moreover, the newly selected standard organism has to fulfill a number of requirements: it should be easy to identify and maintain, taxonomically unambiguous, globally available, with known genome size stability, lacking problematic metabolites, suitable for isolation of sufficient amounts of nuclei, and enabling measurements with low coefficients of variation of DNA peaks, hence suitable for the preparation of high quality samples.
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Affiliation(s)
- Eva M. Temsch
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Petr Koutecký
- Department of Botany, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of ScienceCharles UniversityPrague 2Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany of the Czech Academy of SciencesOlomoucCzech Republic
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Whole-Genome Sequencing and Comparative Genome Analysis of Fusarium solani-melongenae Causing Fusarium Root and Stem Rot in Sweetpotatoes. Microbiol Spectr 2022; 10:e0068322. [PMID: 35863027 PMCID: PMC9430127 DOI: 10.1128/spectrum.00683-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sweetpotato (Ipomoea batatas) is the eighth most important crop globally. However, the production and quality of sweetpotatoes are threatened by Fusarium diseases that are prevalent around the world. In this study, a Fusarium species that causes root and stem rot in sweetpotatoes was studied. The pathogenic fungus CRI 24-3 was isolated and sequenced using third- and next-generation sequencing techniques and a 49.6 Mb chromosome-level draft genome containing 15,374 putative coding genes were obtained. Molecular phylogenetic analysis showed that CRI 24-3 was an F. solani-melongenae strain within clade 3 of the F. solani species complex (FSSC). CRI 24-3 showed a relatively high number of virulence factors, such as carbohydrate-active enzymes (CAZymes), pathogen-host interaction (PHI) proteins, and terpene synthases (TSs), compared with the number of those identified in other sequenced FSSC members. Comparative genome analysis revealed considerable conservation and unique characteristics between CRI 24-3 and other FSSC species. In conclusion, the findings in the current study provide important genetic information about F. solani-melongenae and should be useful in the exploration of pathogenicity mechanisms and the development of Fusarium disease management strategies. IMPORTANCE Fusarium root and stem rot in sweetpotato are prevalent in the main sweetpotato-growing areas in China, and fungal isolation, morphological characteristics, and molecular phylogenetic analysis of the disease causal agent (F. solani-melongenae isolate CRI 24-3) were systematically studied. The genome sequence of F. solani-melongenae isolates CRI 24-3 was first reported, which should provide a basis for genome assembly of other closely related Fusarium species. Carbohydrate-active enzymes predicted in CRI 24-3 may be important to convert the substantial polysaccharides to sustainable and renewable energy. Moreover, other virulence factors facilitating Fusarium diseases, including effectors and toxic secondary metabolites, are ideal objects for pathogenicity mechanism research and molecular targets for fungicide development. The findings of comparative genome analysis of CRI 24-3 and 15 sequenced members of the F. solani species complex help promote an integral understanding of genomic features and evolutionary relationships in Fusarium.
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Comparative analysis of two Korean irises (Iris ruthenica and I. uniflora, Iridaceae) based on plastome sequencing and micromorphology. Sci Rep 2022; 12:9424. [PMID: 35676304 PMCID: PMC9177672 DOI: 10.1038/s41598-022-13528-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/06/2022] [Indexed: 11/12/2022] Open
Abstract
Iris ruthenica Ker Gawl. and I. uniflora Pall. ex Link, which are rare and endangered species in Korea, possess considerable horticultural and medicinal value among Korean irises. However, discrimination of the species is hindered by extensive morphological similarity. Thus, the aim of the present study was to identify discriminating features by comparing the species’ complete plastid genome (i.e., plastome) sequences and micromorphological features, including leaf margins, stomatal complex distribution (hypostomatic vs. amphistomatic leaves), anther stomata density, and tepal epidermal cell patterns. Plastome comparison revealed slightly divergent regions within intergenic spacer regions, and the most variable sequences, which were distributed in non-coding regions, could be used as molecular markers for the discrimination of I. ruthenica and I. uniflora. Phylogenetic analysis of the Iris species revealed that I. ruthenica and I. uniflora formed a well-supported clade. The comparison of plastomes and micromorphological features performed in this study provides useful information for elucidating taxonomic, phylogenetic, and evolutionary relationships in Iridaceae. Further studies, including those based on molecular cytogenetic approaches using species specific markers, will offer insights into species delimitation of the two closely related Iris species.
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Čertnerová D, Čertner M, Škaloud P. Alternating nuclear DNA content in chrysophytes provides evidence of their isomorphic haploid-diploid life cycle. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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25
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Genome-Wide Survey and Development of the First Microsatellite Markers Database ( AnCorDB) in Anemone coronaria L. Int J Mol Sci 2022; 23:ijms23063126. [PMID: 35328546 PMCID: PMC8949970 DOI: 10.3390/ijms23063126] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/31/2022] Open
Abstract
Anemone coronaria L. (2n = 2x = 16) is a perennial, allogamous, highly heterozygous plant marketed as a cut flower or in gardens. Due to its large genome size, limited efforts have been made in order to develop species-specific molecular markers. We obtained the first draft genome of the species by Illumina sequencing an androgenetic haploid plant of the commercial line “MISTRAL® Magenta”. The genome assembly was obtained by applying the MEGAHIT pipeline and consisted of 2 × 106 scaffolds. The SciRoKo SSR (Simple Sequence Repeats)-search module identified 401.822 perfect and 188.987 imperfect microsatellites motifs. Following, we developed a user-friendly “Anemone coronaria Microsatellite DataBase” (AnCorDB), which incorporates the Primer3 script, making it possible to design couples of primers for downstream application of the identified SSR markers. Eight genotypes belonging to eight cultivars were used to validate 62 SSRs and a subset of markers was applied for fingerprinting each cultivar, as well as to assess their intra-cultivar variability. The newly developed microsatellite markers will find application in Breeding Rights disputes, developing genetic maps, marker assisted breeding (MAS) strategies, as well as phylogenetic studies.
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Zhang ZS, Zeng QY, Liu YJ. Frequent ploidy changes in Salicaceae indicates widespread sharing of the salicoid whole genome duplication by the relatives of Populus L. and Salix L. BMC PLANT BIOLOGY 2021; 21:535. [PMID: 34773988 PMCID: PMC8590345 DOI: 10.1186/s12870-021-03313-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUNDS Populus and Salix belong to Salicaceae and are used as models to investigate woody plant physiology. The variation of karyotype and nuclear DNA content can partly reflect the evolutionary history of the whole genome, and can provide critical information for understanding, predicting, and potentially ameliorating the woody plant traits. Therefore, it is essential to study the chromosome number (CN) and genome size in detail to provide information for revealing the evolutionary process of Salicaceae. RESULTS In this study, we report the somatic CNs of seventeen species from eight genera in Salicaceae. Of these, CNs for twelve species and for five genera are reported for the first time. Among the three subfamilies of Salicaceae, the available data indicate CN in Samydoideae is n = 21, 22, 42. The only two genera, Dianyuea and Scyphostegia, in Scyphostegioideae respectively have n = 9 and 18. In Salicoideae, Populus, Salix and five genera closely related to them (Bennettiodendron, Idesia, Carrierea, Poliothyrsis, Itoa) are based on relatively high CNs from n = 19, 20, 21, 22 to n = 95 in Salix. However, the other genera of Salicoideae are mainly based on relatively low CNs of n = 9, 10, 11. The genome sizes of 35 taxa belonging to 14 genera of Salicaceae were estimated. Of these, the genome sizes of 12 genera and all taxa except Populus euphratica are first reported. Except for Dianyuea, Idesia and Bennettiodendron, all examined species have relatively small genome sizes of less than 1 pg, although polyploidization exists. CONCLUSIONS The variation of CN and genome size across Salicaceae indicates frequent ploidy changes and a widespread sharing of the salicoid whole genome duplication (WGD) by the relatives of Populus and Salix. The shrinkage of genome size after WGD indicates massive loss of genomic components. The phylogenetic asymmetry in clade of Populus, Salix, and their close relatives suggests that there is a lag-time for the subsequent radiations after the salicoid WGD event. Our results provide useful data for studying the evolutionary events of Salicaceae.
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Affiliation(s)
- Zhong-Shuai Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China
| | - Qing-Yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China
| | - Yan-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China.
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Hussain Z, Sun Y, Shah SH, Khan H, Ali S, Iqbal A, Zia MA, Ali SS. The dynamics of genome size and GC contents evolution in genus Nicotiana. BRAZ J BIOL 2021; 83:e245372. [PMID: 34669791 DOI: 10.1590/1519-6984.245372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 05/11/2021] [Indexed: 11/22/2022] Open
Abstract
Hybridization and Polyploidization are most common of the phenomenon observed in plants, especially in the genus Nicotiana leading to the duplication of genome. Although genomic changes associated with these events has been studied at various levels but the genome size and GC content variation is less understood because of absence of sufficient genomic data. In this study the flow cytometry technique was used to uncover the genome size and GC contents of 46 Nicotiana species and we compared the genomic changes associated with the hybridization events along evolutionary time scale. The genome size among Nicotiana species varied between 3.28 pg and 11.88 pg whereas GC contents varied between 37.22% and 51.25%. The tetraploid species in genus Nicotiana including section Polydiclae, Repandae, Nicotiana, Rustica and Sauveolentes revealed both up and downsizing in their genome sizes when compared to the sum of genomes of their ancestral species. The genome sizes of three homoploid hybrids were found near their ancestral species. Loss of large genome sequence was observed in the evolutionary more aged species (>10 Myr) as compared to the recently evolved one's (<0.2 Myr). The GC contents were found homogenous with a mean difference of 2.46% among the Nicotiana species. It is concluded that genome size change appeared in either direction whereas the GC contents were found more homogenous in genus Nicotiana.
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Affiliation(s)
- Z Hussain
- Chinese Academy of Agricultural Sciences, Qingdao, Shandong, China
- University of Swat, Centre for Biotechnology and Microbiology, Mingora, Swat, Khyber Pukhtunkhwa, Pakistan
| | - Y Sun
- Chinese Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - S H Shah
- Allama Iqbal Open University, Faculty of Sciences, Department of Agricultural Sciences, Islamabad, Pakistan
| | - H Khan
- Quid-e-Azam University, Department of Biotechnology, Islamabad, Pakistan
| | - S Ali
- University of Swat, Centre for Biotechnology and Microbiology, Mingora, Swat, Khyber Pukhtunkhwa, Pakistan
| | - A Iqbal
- University of Swat, Centre for Biotechnology and Microbiology, Mingora, Swat, Khyber Pukhtunkhwa, Pakistan
| | - M A Zia
- National Agricultural Research Centre - NARC, National Institute for Genomics and Advanced Biotechnology - NIGAB, Islamabad, Pakistan
| | - S S Ali
- University of Swat, Centre for Biotechnology and Microbiology, Mingora, Swat, Khyber Pukhtunkhwa, Pakistan
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Cytological Study of Cypripedium japonicum Thunb. (Orchidaceae Juss.): An Endangered Species from Korea. PLANTS 2021; 10:plants10101978. [PMID: 34685787 PMCID: PMC8540827 DOI: 10.3390/plants10101978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 01/07/2023]
Abstract
Changes in chromosome number and karyotype evolution are important to plant diversification, as they are both major drivers of speciation processes. Herein, chromosome number, karyotype, and genome size of the Korean lady's slipper orchid Cypripedium japonicum Thunb., an endangered species, were investigated in natural populations. Furthermore, all cytological data from this species are reported herein for the first time. The chromosome number of all investigated C. japonicum plants was diploid (2n = 2x = 22), with x = 11 as base chromosome number, whereby the species can now be clearly distinguished from the Japanese lady's slipper orchid. The karyotypes of all studied individuals were of similar length, symmetrical, and rather unimodal. Flow cytometry of the C. japonicum revealed that the genome size ranged from 28.38 to 30.14 pg/1C. Data on chromosome number and karyotypes were largely consistent with previous results indicating that Korean (x = 11) populations of C. japonicum are more closely related to Chinese populations (x = 11) compared to Japanese (x = 10) populations. These comprehensive cytological results will benefit the efforts to discriminate the geographically isolated and endangered Eastern Asian (China, Japan, and Korea) lady's slipper orchid species.
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Mossion V, Dauphin B, Grant J, Kessler M, Zemp N, Croll D. Transcriptome-wide SNPs for Botrychium lunaria ferns enable fine-grained analysis of ploidy and population structure. Mol Ecol Resour 2021; 22:254-271. [PMID: 34310066 PMCID: PMC9291227 DOI: 10.1111/1755-0998.13478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/02/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
Ferns are the second most diverse group of land plants after angiosperms. Extant species occupy a wide range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources and within‐species studies based on high‐resolution markers are entirely lacking. The genus Botrychium belongs to the family Ophioglossaceae, which includes species with very large genomes and chromosome numbers (e.g., Ophioglossum reticulatum 2n = 1520). The genus has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome for Botrychium lunaria (L.) Sw., a diploid species with an extremely large genome of about ~19.0–23.7 Gb. We assembled 25,677 high‐quality transcripts with an average length of 1,333 bp based on deep RNA‐sequencing of a single individual. We sequenced 11 additional transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,463 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kilobase. We found that all 12 transcriptomes were most likely from diploid individuals. The transcriptome‐wide markers provided unprecedented resolution of the population genetic structure, revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 92 taxa representing all fern orders to ascertain the placement of the genus Botrychium. High‐quality transcriptomic resources and SNP sets constitute powerful population genomic resources to investigate the ecology, and evolution of fern populations.
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Affiliation(s)
- Vinciane Mossion
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
| | - Benjamin Dauphin
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland.,Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Jason Grant
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zürich, Zurich, Switzerland
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, University of Neuchâtel, Neuchâtel, Switzerland
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Cacho NI, McIntyre PJ, Kliebenstein DJ, Strauss SY. Genome size evolution is associated with climate seasonality and glucosinolates, but not life history, soil nutrients or range size, across a clade of mustards. ANNALS OF BOTANY 2021; 127:887-902. [PMID: 33675229 PMCID: PMC8225284 DOI: 10.1093/aob/mcab028] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 02/21/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS We investigate patterns of evolution of genome size across a morphologically and ecologically diverse clade of Brassicaceae, in relation to ecological and life history traits. While numerous hypotheses have been put forward regarding autecological and environmental factors that could favour small vs. large genomes, a challenge in understanding genome size evolution in plants is that many hypothesized selective agents are intercorrelated. METHODS We contribute genome size estimates for 47 species of Streptanthus Nutt. and close relatives, and take advantage of many data collections for this group to assemble data on climate, life history, soil affinity and composition, geographic range and plant secondary chemistry to identify simultaneous correlates of variation in genome size in an evolutionary framework. We assess models of evolution across clades and use phylogenetically informed analyses as well as model selection and information criteria approaches to identify variables that can best explain genome size variation in this clade. KEY RESULTS We find differences in genome size and heterogeneity in its rate of evolution across subclades of Streptanthus and close relatives. We show that clade-wide genome size is positively associated with climate seasonality and glucosinolate compounds. Model selection and information criteria approaches identify a best model that includes temperature seasonality and fraction of aliphatic glucosinolates, suggesting a possible role for genome size in climatic adaptation or a role for biotic interactions in shaping the evolution of genome size. We find no evidence supporting hypotheses of life history, range size or soil nutrients as forces shaping genome size in this system. CONCLUSIONS Our findings suggest climate seasonality and biotic interactions as potential forces shaping the evolution of genome size and highlight the importance of evaluating multiple factors in the context of phylogeny to understand the effect of possible selective agents on genome size.
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Affiliation(s)
- N Ivalú Cacho
- Instituto de Biología, Universidad Nacional Autónoma de México. Circuito Exterior, Ciudad Universitaria, Mexico City, Mexico
- Center for Population Biology, University of California, One Shields Avenue, Davis, CA, USA
- Department of Evolution of Ecology, University of California, One Shields Avenue, Davis, CA, USA
| | - Patrick J McIntyre
- Center for Population Biology, University of California, One Shields Avenue, Davis, CA, USA
- NatureServe, Boulder, CO, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, USA
- DynaMo Centre of Excellence, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Sharon Y Strauss
- Center for Population Biology, University of California, One Shields Avenue, Davis, CA, USA
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Can Knowledge of Genetic Distances, Genome Sizes and Chromosome Numbers Support Breeding Programs in Hardy Geraniums? Genes (Basel) 2021; 12:genes12050730. [PMID: 34068148 PMCID: PMC8152959 DOI: 10.3390/genes12050730] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/23/2022] Open
Abstract
Breeding programs in ornamentals can be facilitated by integrating knowledge of phylogenetic relatedness of potential parents along with other genomic information. Using AFLP, genetic distances were determined for 59 Geranium genotypes, comprising 55 commercial cultivars of the three subgenera of a total collection of 61 Geranium genotypes. A subgroup of 45 genotypes, including intragroup and intergroup hybrids, were selected and further characterized for genome sizes and chromosome numbers. The variation in genome size ranged from 1.51 ± 0.01 pg/2C to 12.94 ± 0.07 pg/2C. The chromosome numbers ranged from 26 to 108–110 with some hybrids showing an aberrant number of chromosomes based on their parents’ constitution. All chromosome numbers of Geranium are an even number, which presumes that unreduced gametes occur in some cross combinations. Overall, parental difference in genome size and chromosome number were not limiting for cross compatibility. Good crossing compatibility was correlated to a Jaccard similarity coefficient as parameter for parental relatedness of about 0.5. Additionally, parent combinations with high differences in the DNA/chromosome value could not result in a successful cross. We expect that our results will enable breeding programs to overcome crossing barriers and support further breeding initiatives.
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Genome Size Diversity in Rare, Endangered, and Protected Orchids in Poland. Genes (Basel) 2021; 12:genes12040563. [PMID: 33924526 PMCID: PMC8070121 DOI: 10.3390/genes12040563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 01/25/2023] Open
Abstract
Orchidaceae is one of the largest and the most widespread plant families with many species threatened with extinction. However, only about 1.5% of orchids’ genome sizes have been known so far. The aim of this study was to estimate the genome size of 15 species and one infraspecific taxon of endangered and protected orchids growing wild in Poland to assess their variability and develop additional criterion useful in orchid species identification and characterization. Flow cytometric genome size estimation revealed that investigated orchid species possessed intermediate, large, and very large genomes. The smallest 2C DNA content possessed Liparis loeselii (14.15 pg), while the largest Cypripedium calceolus (82.10 pg). It was confirmed that the genome size is characteristic to the subfamily. Additionally, for four species Epipactis albensis, Ophrys insectifera, Orchis mascula, Orchis militaris and one infraspecific taxon, Epipactis purpurata f. chlorophylla the 2C DNA content has been estimated for the first time. Genome size estimation by flow cytometry proved to be a useful auxiliary method for quick orchid species identification and characterization.
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Glazier DS. Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem. BIOLOGY 2021; 10:270. [PMID: 33810583 PMCID: PMC8067107 DOI: 10.3390/biology10040270] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.
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Tribble CM, Martínez-Gómez J, Alzate-Guarín F, Rothfels CJ, Specht CD. Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation. Evol Dev 2021; 23:155-173. [PMID: 33465278 DOI: 10.1111/ede.12369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 11/27/2022]
Abstract
Many species from across the vascular plant tree-of-life have modified standard plant tissues into tubers, bulbs, corms, and other underground storage organs (USOs), unique innovations which allow these plants to retreat underground. Our ability to understand the developmental and evolutionary forces that shape these morphologies is limited by a lack of studies on certain USOs and plant clades. We take a comparative transcriptomics approach to characterizing the molecular mechanisms of tuberous root formation in Bomarea multiflora (Alstroemeriaceae) and compare these mechanisms to those identified in other USOs across diverse plant lineages; B. multiflora fills a key gap in our understanding of USO molecular development as the first monocot with tuberous roots to be the focus of this kind of research. We sequenced transcriptomes from the growing tip of four tissue types (aerial shoot, rhizome, fibrous root, and root tuber) of three individuals of B. multiflora. We identified differentially expressed isoforms between tuberous and non-tuberous roots and tested the expression of a priori candidate genes implicated in underground storage in other taxa. We identify 271 genes that are differentially expressed in root tubers versus non-tuberous roots, including genes implicated in cell wall modification, defense response, and starch biosynthesis. We also identify a phosphatidylethanolamine-binding protein, which has been implicated in tuberization signalling in other taxa and, through gene-tree analysis, place this copy in a phylogenetic context. These findings suggest that some similar molecular processes underlie the formation of USOs across flowering plants despite the long evolutionary distances among taxa and non-homologous morphologies (e.g., bulbs vs. tubers). (Plant development, tuberous roots, comparative transcriptomics, geophytes).
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Affiliation(s)
- Carrie M Tribble
- Department of Integrative Biology and, University Herbarium, University of California, Berkeley, California, USA
| | - Jesús Martínez-Gómez
- Department of Integrative Biology and, University Herbarium, University of California, Berkeley, California, USA.,School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, New York, USA
| | - Fernando Alzate-Guarín
- Grupo de Estudios Botánicos (GEOBOTA) and Herbario Universidad de Antioquia (HUA), Facultad de Ciencias Exactas y Naturales, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Carl J Rothfels
- Department of Integrative Biology and, University Herbarium, University of California, Berkeley, California, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, New York, USA
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Yu Y, Li HT, Wu YH, Li DZ. Correlation Analysis Reveals an Important Role of GC Content in Accumulation of Deletion Mutations in the Coding Region of Angiosperm Plastomes. J Mol Evol 2021; 89:73-80. [PMID: 33433638 DOI: 10.1007/s00239-020-09987-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/21/2020] [Indexed: 10/22/2022]
Abstract
Variation in GC content is assumed to correlate with various processes, including mutation biases, recombination, and environmental parameters. To date, most genomic studies exploring the evolution of GC content have focused on nuclear genomes, but relatively few have concentrated on organelle genomes. We explored the mechanisms maintaining the GC content in angiosperm plastomes, with a particular focus on the hypothesis of phylogenetic dependence and the correlation with deletion mutations. We measured three genetic traits, namely, GC content, A/T tracts, and G/C tracts, in the coding region of plastid genomes for 1382 angiosperm species representing 350 families and 64 orders, and tested the phylogenetic signal. Then, we performed correlation analyses and revealed the variation in evolutionary rate of selected traits using RRphylo. The plastid GC content in the coding region varied from 28.10% to 43.20% across angiosperms, with a few non-photosynthetic species showing highly reduced values, highlighting the significance of functional constraints. We found strong phylogenetic signal in A/T tracts, but weak ones in GC content and G/C tracts, indicating adaptive potential. GC content was positively and negatively correlated with G/C and A/T tracts, respectively, suggesting a trade-off between these two deletion events. GC content evolved at various rates across the phylogeny, with significant increases in monocots and Lamiids, and a decrease in Fabids, implying the effects of some other factors. We hypothesize that variation in plastid GC content might be a mixed strategy of species to optimize fitness in fluctuating climates, partly through influencing the trade-off between AT → GC and GC → AT mutations.
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Affiliation(s)
- Ying Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yu-Huan Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Jąkalski M, Minasiewicz J, Caius J, May M, Selosse MA, Delannoy E. The Genomic Impact of Mycoheterotrophy in Orchids. FRONTIERS IN PLANT SCIENCE 2021; 12:632033. [PMID: 34177974 PMCID: PMC8220222 DOI: 10.3389/fpls.2021.632033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 05/14/2021] [Indexed: 05/06/2023]
Abstract
Mycoheterotrophic plants have lost the ability to photosynthesize and obtain essential mineral and organic nutrients from associated soil fungi. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy to mycoheterotrophy has occurred independently in many major lineages of land plants, most frequently in Orchidaceae. Yet the molecular mechanisms underlying this shift are still poorly understood. A comparison of the transcriptomes of Epipogium aphyllum and Neottia nidus-avis, two completely mycoheterotrophic orchids, to other autotrophic and mycoheterotrophic orchids showed the unexpected retention of several genes associated with photosynthetic activities. In addition to these selected retentions, the analysis of their expression profiles showed that many orthologs had inverted underground/aboveground expression ratios compared to autotrophic species. Fatty acid and amino acid biosynthesis as well as primary cell wall metabolism were among the pathways most impacted by this expression reprogramming. Our study suggests that the shift in nutritional mode from autotrophy to mycoheterotrophy remodeled the architecture of the plant metabolism but was associated primarily with function losses rather than metabolic innovations.
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Affiliation(s)
- Marcin Jąkalski
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Julita Minasiewicz
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - José Caius
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Michał May
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Marc-André Selosse
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
- Sorbonne Université, CNRS, EPHE, Muséum National d’Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, Paris, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay, Orsay, France
- *Correspondence: Etienne Delannoy,
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Schnablová R, Huang L, Klimešová J, Šmarda P, Herben T. Inflorescence preformation prior to winter: a surprisingly widespread strategy that drives phenology of temperate perennial herbs. THE NEW PHYTOLOGIST 2021; 229:620-630. [PMID: 32805759 DOI: 10.1111/nph.16880] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
Organ preformation in overwintering buds of perennial plants has been known for almost two centuries. It is hypothesized to underlie fast growth and early flowering, but its frequency, phylogenetic distribution, and ecological relevance have never been systematically examined. We microscopically observed inflorescence preformation in overwintering buds (IPB) in the autumn. We studied a phylogenetically and ecologically representative set of 330 species of temperate perennial angiosperms and linked these observations with quantitative data on species' flowering phenology, genome size, and ecology. IPB was observed in 34% of species examined (in 14% species the stamens and/or pistils were already developed). IPB is fairly phylogenetically conserved and frequent in many genera (Alchemilla, Carex, Euphorbia, Geranium, Primula, Pulmonaria) or families (Ranunculaceae, Euphorbiaceae, Violaceae, Boraginaceae). It was found in species of any genome size, although it was almost universal in those with large genomes. Compared with non-IPB species, IPB species flowered 38 d earlier on average and were more common in shaded and undisturbed habitats. IPB is a surprisingly widespread adaptation for early growth in predictable (undisturbed) conditions. It contributes to temporal niche differentiation and has important consequences for understanding plant phenology, genome size evolution, and phylogenetic structure of plant communities.
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Affiliation(s)
- Renáta Schnablová
- Department of Population Ecology, Institute of Botany of the Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
| | - Lin Huang
- Department of Botany, Faculty of Science, Charles University, Praha 2, 128 43, Czech Republic
- Institute of Wetland Ecology & Clone Ecology, Taizhou University, Taizhou, 318000, China
| | - Jitka Klimešová
- Department of Functional Ecology, Institute of Botany of the Czech Academy of Sciences, Třeboň, 379 01, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Tomáš Herben
- Department of Population Ecology, Institute of Botany of the Czech Academy of Sciences, Průhonice, 252 43, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Praha 2, 128 43, Czech Republic
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Yoo MJ, Lee BY, Kim S, Lim CE. Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:645735. [PMID: 34305959 PMCID: PMC8296909 DOI: 10.3389/fpls.2021.645735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/16/2021] [Indexed: 05/14/2023]
Abstract
The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, NY, United States
| | - Byoung-Yoon Lee
- National Institute of Biological Resources, Incheon, South Korea
| | - Sangtae Kim
- Department of Biotechnology, Sungshin Women’s University, Seoul, South Korea
| | - Chae Eun Lim
- National Institute of Biological Resources, Incheon, South Korea
- *Correspondence: Chae Eun Lim,
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Duchoslav M, Jandová M, Kobrlová L, Šafářová L, Brus J, Vojtěchová K. Intricate Distribution Patterns of Six Cytotypes of Allium oleraceum at a Continental Scale: Niche Expansion and Innovation Followed by Niche Contraction With Increasing Ploidy Level. FRONTIERS IN PLANT SCIENCE 2020; 11:591137. [PMID: 33362819 PMCID: PMC7755979 DOI: 10.3389/fpls.2020.591137] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/06/2020] [Indexed: 05/23/2023]
Abstract
The establishment and success of polyploids are thought to often be facilitated by ecological niche differentiation from diploids. Unfortunately, most studies compared diploids and polyploids, ignoring variation in ploidy level in polyploids. To fill this gap, we performed a large-scale study of 11,163 samples from 1,283 populations of the polyploid perennial geophyte Allium oleraceum with reported mixed-ploidy populations, revealed distribution ranges of cytotypes, assessed their niches and explored the pattern of niche change with increasing ploidy level. Altogether, six ploidy levels (3x-8x) were identified. The most common were pentaploids (53.6%) followed by hexaploids (22.7%) and tetraploids (21.6%). Higher cytotype diversity was found at lower latitudes than at higher latitudes (>52° N), where only tetraploids and pentaploids occurred. We detected 17.4% of mixed-ploidy populations, usually as a combination of two, rarely of three, cytotypes. The majority of mixed-ploidy populations were found in zones of sympatry of the participating cytotypes, suggesting they have arisen through migration (secondary contact zone). Using coarse-grained variables (climate, soil), we found evidence of both niche expansion and innovation in tetraploids related to triploids, whereas higher ploidy levels showed almost zero niche expansion, but a trend of increased niche unfilling of tetraploids. Niche unfilling in higher ploidy levels was caused by a contraction of niche envelopes toward lower continentality of the climate and resulted in a gradual decrease of niche breadth and a gradual shift in niche optima. Field-recorded data indicated wide habitat breadth of tetraploids and pentaploids, but also a pattern of increasing synanthropy in higher ploidy levels. Wide niche breadth of tetra- and pentaploids might be related to their multiple origins from different environmental conditions, higher "age", and retained sexuality, which likely preserve their adaptive potential. In contrast, other cytotypes with narrower niches are mostly asexual, probably originating from a limited range of contrasting environments. Persistence of local ploidy mixtures could be enabled by the perenniality of A. oleraceum and its prevalence of vegetative reproduction, facilitating the establishment and decreasing exclusion of minority cytotype due to its reproductive costs. Vegetative reproduction might also significantly accelerate colonization of new areas, including recolonization of previously glaciated areas.
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Affiliation(s)
- Martin Duchoslav
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Michaela Jandová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
- Institute of Botany, Czech Academy of Sciences, Pruhonice, Czechia
| | - Lucie Kobrlová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Lenka Šafářová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Kateřina Vojtěchová
- Plant Biosystematics and Ecology RG, Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
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Samad NA, Hidalgo O, Saliba E, Siljak-Yakovlev S, Strange K, Leitch IJ, Dagher-Kharrat MB. Genome Size Evolution and Dynamics in Iris, with Special Focus on the Section Oncocyclus. PLANTS 2020; 9:plants9121687. [PMID: 33271865 PMCID: PMC7760388 DOI: 10.3390/plants9121687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/21/2020] [Accepted: 11/26/2020] [Indexed: 12/27/2022]
Abstract
Insights into genome size dynamics and its evolutionary impact remain limited by the lack of data for many plant groups. One of these is the genus Iris, of which only 53 out of c. 260 species have available genome sizes. In this study, we estimated the C-values for 41 species and subspecies of Iris mainly from the Eastern Mediterranean region. We constructed a phylogenetic framework to shed light on the distribution of genome sizes across subgenera and sections of Iris. Finally, we tested evolutionary models to explore the mode and tempo of genome size evolution during the radiation of section Oncocyclus. Iris as a whole displayed a great variety of C-values; however, they were unequally distributed across the subgenera and sections, suggesting that lineage-specific patterns of genome size diversification have taken place within the genus. The evolutionary model that best fitted our data was the speciational model, as changes in genome size appeared to be mainly associated with speciation events. These results suggest that genome size dynamics may have contributed to the radiation of Oncocyclus irises. In addition, our phylogenetic analysis provided evidence that supports the segregation of the Lebanese population currently attributed to Iris persica as a distinct species.
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Affiliation(s)
- Nour Abdel Samad
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Campus Sciences et Technologies, Université Saint-Joseph, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon; (N.A.S.); (E.S.)
- Ecologie Systématique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France;
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK; (K.S.); (I.J.L.)
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Spain
- Correspondence: (O.H.); (M.B.D.-K.)
| | - Elie Saliba
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Campus Sciences et Technologies, Université Saint-Joseph, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon; (N.A.S.); (E.S.)
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France;
| | - Kit Strange
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK; (K.S.); (I.J.L.)
| | - Ilia J. Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK; (K.S.); (I.J.L.)
| | - Magda Bou Dagher-Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Campus Sciences et Technologies, Université Saint-Joseph, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon; (N.A.S.); (E.S.)
- Correspondence: (O.H.); (M.B.D.-K.)
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Wesselingh RA. Winter is coming and the clock starts ticking. THE NEW PHYTOLOGIST 2020; 228:1458-1459. [PMID: 32890419 DOI: 10.1111/nph.16863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Renate A Wesselingh
- Biodiversity Research Centre, Earth & Life Institute, UCLouvain, Croix du Sud 4, Louvain-la-Neuve, B-1348, Belgium
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Čertnerová D, Škaloud P. Substantial intraspecific genome size variation in golden-brown algae and its phenotypic consequences. ANNALS OF BOTANY 2020; 126:1077-1087. [PMID: 32686820 PMCID: PMC7596369 DOI: 10.1093/aob/mcaa133] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS While nuclear DNA content variation and its phenotypic consequences have been well described for animals, vascular plants and macroalgae, much less about this topic is known regarding unicellular algae and protists in general. The dearth of data is especially pronounced when it comes to intraspecific genome size variation. This study attempts to investigate the extent of intraspecific variability in genome size and its adaptive consequences in a microalgal species. METHODS Propidium iodide flow cytometry was used to estimate the absolute genome size of 131 strains (isolates) of the golden-brown alga Synura petersenii (Chrysophyceae, Stramenopiles), identified by identical internal transcribed spacer (ITS) rDNA barcodes. Cell size, growth rate and genomic GC content were further assessed on a sub-set of strains. Geographic location of 67 sampling sites across the Northern hemisphere was used to extract climatic database data and to evaluate the ecogeographical distribution of genome size diversity. KEY RESULTS Genome size ranged continuously from 0.97 to 2.02 pg of DNA across the investigated strains. The genome size was positively associated with cell size and negatively associated with growth rate. Bioclim variables were not correlated with genome size variation. No clear trends in the geographical distribution of strains of a particular genome size were detected, and strains of different genome size occasionally coexisted at the same locality. Genomic GC content was significantly associated only with genome size via a quadratic relationship. CONCLUSIONS Genome size variability in S. petersenii was probably triggered by an evolutionary mechanism operating via gradual changes in genome size accompanied by changes in genomic GC content, such as, for example, proliferation of transposable elements. The variation was reflected in cell size and relative growth rate, possibly with adaptive consequences.
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Affiliation(s)
- Dora Čertnerová
- Department of Botany, Faculty of Science, Charles University, Benátská, Prague, Czech Republic
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, Benátská, Prague, Czech Republic
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44
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Molecular Study of Selected Taxonomically Critical Taxa of the Genus Iris L. from the Broader Alpine-Dinaric Area. PLANTS 2020; 9:plants9091229. [PMID: 32961899 PMCID: PMC7570032 DOI: 10.3390/plants9091229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 12/15/2022]
Abstract
Some wild, morphologically diverse taxa of the genus Iris in the broad Alpine-Dinaric area have never been explored molecularly, and/or have ambiguous systematic status. The main aims of our research were to perform a molecular study of critical Iris taxa from that area (especially a narrow endemic accepted species I. adriatica, for which we also analysed genome size) and to explore the contribution of eight microsatellites and highly variable chloroplast DNA (ndhJ, rpoC1) markers to the understanding of the Iris taxa taxonomy and phylogeny. Both the microsatellite-based UPGMA and plastid markers-based maximum likelihood analysis discriminated three main clusters in the set of 32 analysed samples, which correspond well to the lower taxonomic categories of the genus, and support separate status of ambiguous regional taxa (e.g., I. sibirica subsp. erirrhiza, I. x croatica and I. x rotschildii). The first molecular data on I. adriatica revealed its genome size (2C = 12.639 ± 0.202 pg) and indicated the existence of ecotypes. For future molecular characterisation of the genus we recommend the utilisation of microsatellite markers supplemented with a combination of plastid markers.
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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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Veselý P, Šmarda P, Bureš P, Stirton C, Muasya AM, Mucina L, Horová L, Veselá K, Šilerová A, Šmerda J, Knápek O. Environmental pressures on stomatal size may drive plant genome size evolution: evidence from a natural experiment with Cape geophytes. ANNALS OF BOTANY 2020; 126:323-330. [PMID: 32474609 PMCID: PMC7380457 DOI: 10.1093/aob/mcaa095] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/21/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS The idea that genome (size) evolution in eukaryotes could be driven by environmental factors is still vigorously debated. In extant plants, genome size correlates positively with stomatal size, leading to the idea that conditions enabling the existence of large stomata in fossil plants also supported growth of their genome size. We test this inductive assumption in drought-adapted, prostrate-leaved Cape (South Africa) geophytes where, compared with their upright-leaved geophytic ancestors, stomata develop in a favourably humid microclimate formed underneath their leaves. METHODS Stomatal parameters (leaf cuticle imprints) and genome size (flow cytometry) were measured in 16 closely related geophytic species pairs from seven plant families. In each pair, representing a different genus, we contrasted a prostrate-leaved species with its upright-leaved phylogenetic relative, the latter whose stomata are exposed to the ambient arid climate. KEY RESULTS Except for one, all prostrate-leaves species had larger stomata, and in 13 of 16 pairs they also had larger genomes than their upright-leaved relatives. Stomatal density and theoretical maximum conductance were less in prostrate-leaved species with small guard cells (<1 pL) but showed no systematic difference in species pairs with larger guard cells (>1 pL). Giant stomata were observed in the prostrate-leaved Satyrium bicorne (89-137 µm long), despite its relatively small genome (2C = 9 Gbp). CONCLUSIONS Our results imply that climate, through selection on stomatal size, might be able to drive genome size evolution in plants. The data support the idea that plants from 'greenhouse' geological periods with large stomata might have generally had larger genome sizes when compared with extant plants, though this might not have been solely due to higher atmospheric CO2 in these periods but could also have been due to humid conditions prevailing at fossil deposit sites.
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Affiliation(s)
- Pavel Veselý
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
- For correspondence. E-mail
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Charles Stirton
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Murdoch, Perth, Australia
- Department of Geography and Environmental Studies, Stellenbosch University, Matieland, Stellenbosch, South Africa
| | - Lucie Horová
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Kristýna Veselá
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Alexandra Šilerová
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Ondřej Knápek
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
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Howard CC, Landis JB, Beaulieu JM, Cellinese N. Geophytism in monocots leads to higher rates of diversification. THE NEW PHYTOLOGIST 2020; 225:1023-1032. [PMID: 31469440 DOI: 10.1111/nph.16155] [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: 05/24/2019] [Accepted: 08/21/2019] [Indexed: 05/27/2023]
Abstract
Geophytes, plants with buds on underground structures, are found throughout the plant tree of life. These below ground structures allow plants to inhabit highly seasonal and disturbance-prone environments across ecosystems. Past researchers have hypothesised that the bulbous, cormous and tuberous habits promote diversification, but this had yet to be tested. Using a comprehensive monocot data set of almost 13 000 taxa, we investigated the effects of the geophytic habit on diversification using both state-dependent and state-independent models. We found that geophytes exhibit increased rates of diversification relative to nongeophytes. State-dependent analyses recovered higher yet similar rates of diversification for bulbous, cormous and tuberous taxa compared with rhizomatous and nongeophytic taxa. However, the state-independent model returned no difference in rates among the different traits. Geophytism shows higher rates of diversification relative to nongeophytes but we found little support for the hypothesis that the evolution of the bulb, corm or tuber appears to provide a diversification increase relative to rhizomatous and nongeophytic taxa. Our broad-scale analysis highlights the overall evolutionary importance of the geophytic habit (i.e. belowground bud placement). However, our results also suggest that belowground morphological diversity alone cannot explain this rate increase. In order to further test the evolutionary significance of these underground structures, future studies should consider these in combination with other biotic and abiotic factors.
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Affiliation(s)
- Cody Coyotee Howard
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Jacob B Landis
- University of California, Riverside, Riverside, CA, 92521, USA
| | - Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72731, USA
| | - Nico Cellinese
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
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Han TS, Zheng QJ, Onstein RE, Rojas-Andrés BM, Hauenschild F, Muellner-Riehl AN, Xing YW. Polyploidy promotes species diversification of Allium through ecological shifts. THE NEW PHYTOLOGIST 2020; 225:571-583. [PMID: 31394010 DOI: 10.1111/nph.16098] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/01/2019] [Indexed: 05/14/2023]
Abstract
Despite the role of polyploidy in multiple evolutionary processes, its impact on plant diversification remains controversial. An increased polyploid frequency may facilitate speciation through shifts in ecology, morphology or both. Here we used Allium to evaluate: (1) the relationship between intraspecific polyploid frequency and species diversification rate; and (2) whether this process is associated with habitat and/or trait shifts. Using eight plastid and nuclear ribosomal markers, we built a phylogeny of 448 Allium species, representing 46% of the total. We quantified intraspecific ploidy diversity, heterogeneity in diversification rates and their relationship along the phylogeny using trait-dependent diversification models. Finally, we evaluated the association between polyploidisation and habitat or trait shifts. We detected high ploidy diversity in Allium and a polyploidy-related diversification rate shift with a probability of 95% in East Asia. Allium lineages with high polyploid frequencies had higher species diversification rates than those of diploids or lineages with lower polyploid frequencies. Shifts in speciation rates were strongly correlated with habitat shifts linked to particular soil conditions; 81.7% of edaphic variation could be explained by polyploidisation. Our study emphasises the role of intraspecific polyploid frequency combined with ecological drivers on Allium diversification, which may explain plant radiations more generally.
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Affiliation(s)
- Ting-Shen Han
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Quan-Jing Zheng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
| | - Blanca M Rojas-Andrés
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Frank Hauenschild
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Alexandra N Muellner-Riehl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Yao-Wu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
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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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Tyagi A, Sandhya, Sharma P, Saxena S, Sharma R, Amitha Mithra SV, Solanke AU, Singh NK, Sharma TR, Gaikwad K. The genome size of clusterbean (Cyamopsis tetragonoloba) is significantly smaller compared to its wild relatives as estimated by flow cytometry. Gene 2019; 707:205-211. [PMID: 30898697 DOI: 10.1016/j.gene.2019.02.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/04/2019] [Accepted: 02/28/2019] [Indexed: 02/06/2023]
Abstract
Clusterbean (C. tetragonoloba) is an important, leguminous vegetable and industrial crop with vast genetic diversity but meager genetic, cytological and genomic information. In the present study, an optimized procedure of flow cytometry was used to estimate the genome size of three clusterbean species, represented by C. tetragonoloba (cv. RGC-936) and two wild relatives (C. serreta and C. senegalensis). For accurate estimation of genomic content, singlet G0/G1 populations of multiple tissues such as leaves, hypocotyl, and matured seeds were determined and used along with three different plant species viz. Pisum sativum (as primary), Oryza sativa, and Glycine max (secondary), as external and internal reference standards. Seed tissue of the test sample and G. max provided the best estimate of nuclear DNA content in comparison to other sample tissues and reference standards. The genome size of C. tetragonoloba was detemined at 580.9±0.02Mbp (1C), while that of C. serreta and C. senegalensis was estimated at 979.6±0.02Mbp (1C) and 943.4±0.03Mbp (1C), respectively. Thus, the wild relatives harbor, nearly double the genome content of the cultivated cluster bean. Findings of this study will enrich genomic database of the legume family and can serve as the starting point for clusterbean evolutionary and genomics studies.
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Affiliation(s)
- Anshika Tyagi
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Sandhya
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Priya Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Swati Saxena
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ramavtar Sharma
- ICAR-Central Arid Zone Research Institute (CAZRI), Jodhpur, India
| | - S V Amitha Mithra
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | | | | | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Kishor Gaikwad
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
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