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Ren J, Cui Z, Wang Y, Ning Q, Gao Y. Transcriptomic insights into the potential impacts of flavonoids and nodule-specific cysteine-rich peptides on nitrogen fixation in Vicia villosa and Vicia sativa. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108936. [PMID: 39018775 DOI: 10.1016/j.plaphy.2024.108936] [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: 06/16/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
Vicia villosa (VV) and Vicia sativa (VS) are legume forages highly valued for their excellent nitrogen fixation. However, no research has addressed the mechanisms underlying their differences in nitrogen fixation. This study employed physiological, cytological, and comparative transcriptomic approaches to elucidate the disparities in nitrogen fixation between them. Our results showed that the total amount of nitrogen fixed was 60.45% greater in VV than in VS, and the comprehensive nitrogen response performance was 94.19% greater, while the nitrogen fixation efficiency was the same. The infection zone and differentiated bacteroid proportion in mature VV root nodules were 33.76% and 19.35% greater, respectively, than those in VS. The size of the VV genome was 15.16% larger than that of the VS genome, consistent with its greater biomass. A significant enrichment of the flavonoid biosynthetic pathway was found only for VV-specific genes, among which chalcone-flavonone isomerase, caffeoyl-CoA-O-methyltransferase and stilbene synthase were extremely highly expressed. The VV-specific genes also exhibited significant enrichment in symbiotic nodulation; genes related to nodule-specific cysteine-rich peptides (NCRs) comprised 61.11% of the highly expressed genes. qRT‒PCR demonstrated that greater enrichment and expression of the dominant NCR (Unigene0004451) were associated with greater nodule bacteroid differentiation and greater nitrogen fixation in VV. Our findings suggest that the greater total nitrogen fixation of VV was attributed to its larger biomass, leading to a greater nitrogen demand and enhanced fixation physiology. This process is likely achieved by the synergistic effects of high bacteroid differentiation along with high expression of flavonoid and NCR genes.
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Affiliation(s)
- Jian Ren
- Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Institute of Grassland Science, Northeast Normal University, Changchun, 130024, China; Xinjiang Agricultural University, Key Laboratory of Grassland Resources and Ecology of Western Arid Desert Area of the Ministry of Education, College of Grassland Science, Urumqi, 830052, China
| | - Zhengguo Cui
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, 130033, China
| | - Yueqiang Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences/National Engineering Research Center for Soybean, Changchun, 130033, China
| | - Qiushi Ning
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yingzhi Gao
- Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Institute of Grassland Science, Northeast Normal University, Changchun, 130024, China; Xinjiang Agricultural University, Key Laboratory of Grassland Resources and Ecology of Western Arid Desert Area of the Ministry of Education, College of Grassland Science, Urumqi, 830052, China.
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2
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Hrabovský M, Kubalová S, Mičieta K, Ščevková J. Environmental impacts on intraspecific variation in Ambrosia artemisiifolia genome size in Slovakia, Central Europe. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33960-33974. [PMID: 38693457 PMCID: PMC11136817 DOI: 10.1007/s11356-024-33410-x] [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: 06/08/2023] [Accepted: 04/16/2024] [Indexed: 05/03/2024]
Abstract
The quantity of DNA in angiosperms exhibits variation attributed to many external influences, such as environmental factors, geographical features, or stress factors, which exert constant selection pressure on organisms. Since invasive species possess adaptive capabilities to acclimate to novel environmental conditions, ragweed (Ambrosia artemisiifolia L.) was chosen as a subject for investigating their influence on genome size variation. Slovakia has diverse climatic conditions, suitable for testing the hypothesis that air temperature and precipitation, the main limiting factors of ragweed occurrence, would also have an impact on its genome size. Our results using flow cytometry confirmed this hypothesis and also found a significant association with geographical features such as latitude, altitude, and longitude. We can conclude that plants growing in colder environments farther from oceanic influences exhibit smaller DNA amounts, while optimal growth conditions result in a greater variability in genome size, reflecting the diminished effect of selection pressure.
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Affiliation(s)
- Michal Hrabovský
- Department of Botany, Faculty of Natural Sciences, Comenius University, Révová 39, 811 02, Bratislava, Slovakia.
| | - Silvia Kubalová
- Department of Botany, Faculty of Natural Sciences, Comenius University, Révová 39, 811 02, Bratislava, Slovakia
| | - Karol Mičieta
- Department of Botany, Faculty of Natural Sciences, Comenius University, Révová 39, 811 02, Bratislava, Slovakia
| | - Jana Ščevková
- Department of Botany, Faculty of Natural Sciences, Comenius University, Révová 39, 811 02, Bratislava, Slovakia
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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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4
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Cang FA, Welles SR, Wong J, Ziaee M, Dlugosch KM. Genome size variation and evolution during invasive range expansion in an introduced plant. Evol Appl 2024; 17:e13624. [PMID: 38283607 PMCID: PMC10810172 DOI: 10.1111/eva.13624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 01/30/2024] Open
Abstract
Plants demonstrate exceptional variation in genome size across species, and their genome sizes can also vary dramatically across individuals and populations within species. This aspect of genetic variation can have consequences for traits and fitness, but few studies attributed genome size differentiation to ecological and evolutionary processes. Biological invasions present particularly useful natural laboratories to infer selective agents that might drive genome size shifts across environments and population histories. Here, we test hypotheses for the evolutionary causes of genome size variation across 14 invading populations of yellow starthistle, Centaurea solstitialis, in California, United States. We use a survey of genome sizes and trait variation to ask: (1) Is variation in genome size associated with developmental trait variation? (2) Are genome sizes smaller toward the leading edge of the expansion, consistent with selection for "colonizer" traits? Or alternatively, does genome size increase toward the leading edge of the expansion, consistent with predicted consequences of founder effects and drift? (3) Finally, are genome sizes smaller at higher elevations, consistent with selection for shorter development times? We found that 2C DNA content varied 1.21-fold among all samples, and was associated with flowering time variation, such that plants with larger genomes reproduced later, with lower lifetime capitula production. Genome sizes increased toward the leading edge of the invasion, but tended to decrease at higher elevations, consistent with genetic drift during range expansion but potentially strong selection for smaller genomes and faster development time at higher elevations. These results demonstrate how genome size variation can contribute to traits directly tied to reproductive success, and how selection and drift can shape that variation. We highlight the influence of genome size on dynamics underlying a rapid range expansion in a highly problematic invasive plant.
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Affiliation(s)
- F. Alice Cang
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
| | - Shana R. Welles
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
- Utah Valley UniversityOremUtahUSA
| | - Jenny Wong
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
| | - Maia Ziaee
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
- Mills CollegeOaklandCaliforniaUSA
| | - Katrina M. Dlugosch
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
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5
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Ptáček J, Ekrt L, Hornych O, Urfus T. Interploidy gene flow via a 'pentaploid bridge' and ploidy reduction in Cystopteris fragilis fern complex (Cystopteridaceae: Polypodiales). PLANT REPRODUCTION 2023; 36:321-331. [PMID: 37532893 DOI: 10.1007/s00497-023-00476-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/15/2023] [Indexed: 08/04/2023]
Abstract
KEY MESSAGE Our results indicate the existence of interploidy gene flow in Cystopteris fragilis, resulting in sexual triploid and diploid gametophytes from pentaploid parents. Similar evolutionary dynamics might operate in other fern complexes and need further investigation. Polyploidization and hybridization are a key evolutionary processes in ferns. Here, we outline an interploidy gene flow pathway operating in the polyploid Cystopteris fragilis complex. The conditions necessary for the existence of this pathway were tested. A total of 365 C. fragilis individuals were collected covering representatives of all three predominant ploidy levels (tetraploid, pentaploid, and hexaploid), cultivated, had their ploidy level estimated by flow cytometry, and their spores collected. The spores, as well as gametophytes and sporophytes established from them, were analysed by flow cytometry. Spore abortion rate was also estimated. In tetraploids, we observed the formation of unreduced (tetraploid) spores (ca 2%). Collected pentaploid individuals indicate ongoing hybridization between ploidy levels. Pentaploids formed up to 52% viable spores, ca 79% of them reduced, i.e. diploid and triploid. Reduced spores formed viable gametophytes, and, in the case of triploids, filial hexaploid sporophytes, showing evidence of sexual reproduction. Some tetraploid sporophytes reproduce apomictically (based on uniform ploidy of their metagenesis up to filial sporophytes). Triploid and diploid gametophytes from pentaploid parents are able to mate among themselves, or with "normal" reduced gametophytes from the sexual tetraploid sporophytes (the dominant ploidy level in the sporophytes in this populations), to produce tetraploid, pentaploid, and hexaploid sporophytes, allowing for geneflow from the pentaploids to both the tetraploid and hexaploid populations. Similar evolutionary dynamics might operate in other fern complexes and need further investigation.
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Affiliation(s)
- Jan Ptáček
- Department of Botany, Faculty of Science, Charles University, Benátská 2, , 128 00, Praha, Czech Republic
| | - Libor Ekrt
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Ondřej Hornych
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Benátská 2, , 128 00, Praha, Czech Republic.
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Shao L, Peng Y, Liu H, Zhao R, Jiang L, Li Y, Han P, Jiang Y, Wei C, Han X, Huang J. Applied phosphorus is maintained in labile and moderately occluded fractions in a typical meadow steppe with the addition of multiple nutrients. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118807. [PMID: 37591093 DOI: 10.1016/j.jenvman.2023.118807] [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: 04/15/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/19/2023]
Abstract
Phosphorus (P) is a limiting nutrient second only to nitrogen (N) in the drylands of the world. Most previous studies have focused on N transformation processes in grassland ecosystems, particularly under artificial fertilization with N and atmospheric N deposition. However, P cycling processes under natural conditions and when P is applied as an inorganic P fertilizer have been understudied. Therefore, it is essential to examine the fate of applied P in grassland ecosystems that have experienced long-term grazing and, under certain circumstances, continuous hay harvest. We conducted a 3-year field experiment with the addition of multiple nutrient elements in a typical meadow steppe to investigate the fate of the applied P in various fractions of P pools in the top soil. We found that the addition of multiple nutrients significantly increased P concentrations in the labile inorganic P (Lab-Pi) and moderately occluded inorganic P (Mod-Pi) fractions but not in the recalcitrant inorganic P (Rec-Pi) fraction. An increase in the concentration of total inorganic P was found only when P and N were applied together. However, the addition of other nutrients did not change P concentrations in any fraction of the mineral soil. The addition of P and N significantly increased the total amount of P taken up by the aboveground plants but had no effect on the levels of organic and microbial P in the soil. Together, our results indicate that the P applied in this grassland ecosystem is taken up by plants, leaving most of the unutilized P as Lab-Pi and Mod-Pi rather than being immobilized in Rec-Pi or by microbial biomass. This implies that the grassland ecosystem that we studied has a relatively low P adsorption capacity, and the application of inorganic P to replenish soil P deficiency in degraded grasslands due to long-term grazing of livestock or continuous harvest of forage in the region could be a practical management strategy to maintain soil P fertility.
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Affiliation(s)
- Lingyu Shao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Erguna Forest-Steppe Ecotone Ecosystem Research Station, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Yang Peng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heyong Liu
- School of Life Sciences, Hebei University, Baoding, 071002, China
| | - Ruonan Zhao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liangchao Jiang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Han
- Erguna Forest-Steppe Ecotone Ecosystem Research Station, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Yong Jiang
- School of Life Sciences, Hebei University, Baoding, 071002, China
| | - Cunzheng Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingguo Han
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhui Huang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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Bhadra S, Leitch IJ, Onstein RE. From genome size to trait evolution during angiosperm radiation. Trends Genet 2023; 39:728-735. [PMID: 37582671 DOI: 10.1016/j.tig.2023.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023]
Abstract
Angiosperm diversity arises from trait flexibility and repeated evolutionary radiations, but the role of genomic characters in these radiations remains unclear. In this opinion article, we discuss how genome size can influence angiosperm diversification via its intricate link with cell size, tissue packing, and physiological processes which, in turn, influence the macroevolution of functional traits. We propose that integrating genome size, functional traits, and phylogenetic data across a wide range of lineages allows us to test whether genome size decrease consistently leads to increased trait flexibility, while genome size increase constrains trait evolution. Combining theories from molecular biology, functional ecology and macroevolution, we provide a framework to better understand the role of genome size in trait evolution, evolutionary radiations, and the global distribution of angiosperms.
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Affiliation(s)
- Sreetama Bhadra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, D-04103, Leipzig, Germany; Leipzig University, Ritterstraße 26, 04109 Leipzig, Germany.
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, D-04103, Leipzig, Germany; Leipzig University, Ritterstraße 26, 04109 Leipzig, Germany; Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
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8
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Walczyk AM, Hersch-Green EI. Genome-material costs and functional trade-offs in the autopolyploid Solidago gigantea (giant goldenrod) series. AMERICAN JOURNAL OF BOTANY 2023; 110:e16218. [PMID: 37551707 DOI: 10.1002/ajb2.16218] [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: 03/23/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 08/09/2023]
Abstract
PREMISE Increased genome-material costs of N and P atoms inherent to organisms with larger genomes have been proposed to limit growth under nutrient scarcities and to promote growth under nutrient enrichments. Such responsiveness may reflect a nutrient-dependent diploid versus polyploid advantage that could have vast ecological and evolutionary implications, but direct evidence that material costs increase with ploidy level and/or influence cytotype-dependent growth, metabolic, and/or resource-use trade-offs is limited. METHODS We grew diploid, autotetraploid, and autohexaploid Solidago gigantea plants with one of four ambient or enriched N:P ratios and measured traits related to material costs, primary and secondary metabolism, and resource-use. RESULTS Relative to diploids, polyploids invested more N and P into cells, and tetraploids grew more with N enrichments, suggesting that material costs increase with ploidy level. Polyploids also generally exhibited strategies that could minimize material-cost constraints over both long (reduced monoploid genome size) and short (more extreme transcriptome downsizing, reduced photosynthesis rates and terpene concentrations, enhanced N-use efficiencies) evolutionary time periods. Furthermore, polyploids had lower transpiration rates but higher water-use efficiencies than diploids, both of which were more pronounced under nutrient-limiting conditions. CONCLUSIONS N and P material costs increase with ploidy level, but material-cost constraints might be lessened by resource allocation/investment mechanisms that can also alter ecological dynamics and selection. Our results enhance mechanistic understanding of how global increases in nutrients might provide a release from material-cost constraints in polyploids that could impact ploidy (or genome-size)-specific performances, cytogeographic patterning, and multispecies community structuring.
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Affiliation(s)
- Angela M Walczyk
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
- Biology Department, Gustavus Adolphus College, 800 West College Avenue, St. Peter, MN, 56082, USA
| | - Erika I Hersch-Green
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
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Pyšek P, Lučanová M, Dawson W, Essl F, Kreft H, Leitch IJ, Lenzner B, Meyerson LA, Pergl J, van Kleunen M, Weigelt P, Winter M, Guo WY. Small genome size and variation in ploidy levels support the naturalization of vascular plants but constrain their invasive spread. THE NEW PHYTOLOGIST 2023; 239:2389-2403. [PMID: 37438886 DOI: 10.1111/nph.19135] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/17/2023] [Indexed: 07/14/2023]
Abstract
Karyological characteristics are among the traits underpinning the invasion success of vascular plants. Using 11 049 species, we tested the effects of genome size and ploidy levels on plant naturalization (species forming self-sustaining populations where they are not native) and invasion (naturalized species spreading rapidly and having environmental impact). The probability that a species naturalized anywhere in the world decreased with increasing monoploid genome size (DNA content of a single chromosome set). Naturalized or invasive species with intermediate monoploid genomes were reported from many regions, but those with either small or large genomes occurred in fewer regions. By contrast, large holoploid genome sizes (DNA content of the unreplicated gametic nucleus) constrained naturalization but favoured invasion. We suggest that a small genome is an advantage during naturalization, being linked to traits favouring adaptation to local conditions, but for invasive spread, traits associated with a large holoploid genome, where the impact of polyploidy may act, facilitate long-distance dispersal and competition with other species.
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Affiliation(s)
- Petr Pyšek
- Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, CZ-128 44, Czech Republic
| | - Magdalena Lučanová
- Department of Evolutionary Biology of Plants, Institute of Botany, Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-370 05, Czech Republic
| | - Wayne Dawson
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Franz Essl
- Division of Bioinvasions, Global Change & Macroecology, Department of Botany and Biodiversity Research, University of Vienna, Wien, 1030, Austria
| | - Holger Kreft
- Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, Göttingen, 37077, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Goettingen, Büsgenweg 1, Göttingen, D-37077, Germany
- Campus-Institute Data Science, Goldschmidtstraße 1, Göttingen, 37077, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Bernd Lenzner
- Division of Bioinvasions, Global Change & Macroecology, Department of Botany and Biodiversity Research, University of Vienna, Wien, 1030, Austria
| | - Laura A Meyerson
- University of Rhode Island, Natural Resources Science, 9 East Alumni Avenue, Kingston, 02881, RI, USA
| | - Jan Pergl
- Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
| | - Mark van Kleunen
- Ecology, Department of Biology, University of Konstanz, Universitätsstrasse 10, Constance, D-78464, Germany
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, China
| | - Patrick Weigelt
- Biodiversity, Macroecology & Biogeography, University of Göttingen, Büsgenweg 1, Göttingen, 37077, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Goettingen, Büsgenweg 1, Göttingen, D-37077, Germany
- Campus-Institute Data Science, Goldschmidtstraße 1, Göttingen, 37077, Germany
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig, 04103, Germany
| | - Wen-Yong Guo
- Research Centre for Global Change and Complex Ecosystems, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
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10
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Wolfe TM, Balao F, Trucchi E, Bachmann G, Gu W, Baar J, Hedrén M, Weckwerth W, Leitch AR, Paun O. Recurrent allopolyploidizations diversify ecophysiological traits in marsh orchids (Dactylorhiza majalis s.l.). Mol Ecol 2023; 32:4777-4790. [PMID: 37452724 PMCID: PMC10947288 DOI: 10.1111/mec.17070] [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: 01/03/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Whole-genome duplication has shaped the evolution of angiosperms and other organisms, and is important for many crops. Structural reorganization of chromosomes and repatterning of gene expression are frequently observed in allopolyploids, with physiological and ecological consequences. Recurrent origins from different parental populations are widespread among polyploids, resulting in an array of lineages that provide excellent models to uncover mechanisms of adaptation to divergent environments in early phases of polyploid evolution. We integrate here transcriptomic and ecophysiological comparative studies to show that sibling allopolyploid marsh orchid species (Dactylorhiza, Orchidaceae) occur in different habitats (low nutrient fens vs. meadows with mesic soils) and are characterized by a complex suite of intertwined, pronounced ecophysiological differences between them. We uncover distinct features in leaf elemental chemistry, light-harvesting, photoprotection, nutrient transport and stomata activity of the two sibling allopolyploids, which appear to match their specific ecologies, in particular soil chemistry differences at their native sites. We argue that the phenotypic divergence between the sibling allopolyploids has a clear genetic basis, generating ecological barriers that maintain distinct, independent lineages, despite pervasive interspecific gene flow. This suggests that recurrent origins of polyploids bring about a long-term potential to trigger and maintain functional and ecological diversity in marsh orchids and other groups.
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Affiliation(s)
- Thomas M. Wolfe
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Vienna Graduate School of Population GeneticsViennaAustria
- Department of Forest and Soil SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Francisco Balao
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Departamento de Biologia Vegetal y EcologiaUniversity of SevilleSevillaSpain
| | - Emiliano Trucchi
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
- Marche Polytechnic UniversityAnconaItaly
| | - Gert Bachmann
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS)University of ViennaViennaAustria
| | - Wenjia Gu
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Juliane Baar
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | | | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS)University of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | - Andrew R. Leitch
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
| | - Ovidiu Paun
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
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11
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Roxo G, Brilhante M, Moura M, de Sequeira MM, Silva L, Costa JC, Vasconcelos R, Talhinhas P, Romeiras MM. Genome size variation within Crithmum maritimum: Clues on the colonization of insular environments. Ecol Evol 2023; 13:e10009. [PMID: 37091572 PMCID: PMC10116024 DOI: 10.1002/ece3.10009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Angiosperms present an astonishing diversity of genome sizes that can vary intra- or interspecifically. The remarkable new cytogenomic data shed some light on our understanding of evolution, but few studies were performed with insular and mainland populations to test possible correlations with dispersal, speciation, and adaptations to insular environments. Here, patterns of cytogenomic diversity were assessed among geographic samples (ca. 114) of Crithmum maritimum (Apiaceae), collected across the Azores and Madeira archipelagos, as well as in adjacent continental areas of Portugal. Using flow cytometry, the results indicated a significant intraspecific genome size variation, spanning from reduced sizes in the insular populations to larger ones in the mainland populations. Moreover, there was a tendency for an increase in genome size along the mainland populations, associated with lower temperatures, higher precipitation, and lower precipitation seasonality. However, this gradient might be the result of historic phylogeographical events associated with previous dispersal and extinction of local populations. Overall, our findings provided evidence that smaller genome sizes might play a critical role in the colonization of islands, corroborating other studies that argue that organisms with smaller genomes use fewer resources, having a selective advantage under insular environments. Although further studies are needed to improve our understanding of the mechanisms underlying genome size evolution on islands, conservation strategies must be promoted to protect the rich cytogenomic diversity found among C. maritimum populations, which occur in coastal areas that are particularly threatened by human activity, pollution, invasive species, and climate changes.
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Affiliation(s)
- Guilherme Roxo
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
- CIBIO‐Azores, Departamento de BiologiaUniversidade dos AçoresPonta DelgadaPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | - Miguel Brilhante
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
| | - Mónica Moura
- CIBIO‐Azores, Departamento de BiologiaUniversidade dos AçoresPonta DelgadaPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | | | - Luís Silva
- CIBIO‐Azores, Departamento de BiologiaUniversidade dos AçoresPonta DelgadaPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | - José Carlos Costa
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
| | - Raquel Vasconcelos
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de VairãoVairãoPortugal
| | - Pedro Talhinhas
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
| | - Maria M. Romeiras
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA)Universidade de Lisboa, Tapada da AjudaLisbonPortugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de CiênciasUniversidade de LisboaLisbonPortugal
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12
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Zhang HY, Lü XT, Wei CZ, Powell JR, Wang XB, Xing DL, Xu ZW, Li HL, Han XG. β-diversity in temperate grasslands is driven by stronger environmental filtering of plant species with large genomes. Ecology 2023; 104:e3941. [PMID: 36469035 DOI: 10.1002/ecy.3941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022]
Abstract
Elucidating mechanisms underlying community assembly and biodiversity patterns is central to ecology and evolution. Genome size (GS) has long been hypothesized to potentially affect species' capacity to tolerate environmental stress and might therefore help drive community assembly. However, its role in driving β-diversity (i.e., spatial variability in species composition) remains unclear. We measured GS for 161 plant species and community composition across 52 sites spanning a 3200-km transect in the temperate grasslands of China. By correlating the turnover of species composition with environmental dissimilarity, we found that resource filtering (i.e., environmental dissimilarity that includes precipitation, and soil nitrogen and phosphorus concentrations) affected β-diversity patterns of large-GS species more than small-GS species. By contrast, geographical distance explained more variation of β-diversity for small-GS than for large-GS species. In a 10-year experiment manipulating levels of water, nitrogen, and phosphorus, adding resources increased plant biomass in species with large GS, suggesting that large-GS species are more sensitive to the changes in resource availability. These findings highlight the role of GS in driving community assembly and predicting species responses to global change.
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Affiliation(s)
- Hai-Yang Zhang
- College of Life Sciences, Hebei University, Baoding, China.,Erguna Forest-Steppe Ecotone Research Station, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Xiao-Tao Lü
- Erguna Forest-Steppe Ecotone Research Station, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Cun-Zheng Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Xiao-Bo Wang
- Erguna Forest-Steppe Ecotone Research Station, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.,Center for Grassland Microbiome, State Key Laboratory of Grassland Agroecosystems, and College of Pastoral, Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Ding-Liang Xing
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Zhu-Wen Xu
- Department of Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Huan-Long Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xing-Guo Han
- Erguna Forest-Steppe Ecotone Research Station, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.,State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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13
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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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14
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Wang G, Zhou N, Chen Q, Yang Y, Yang Y, Duan Y. Gradual genome size evolution and polyploidy in Allium from the Qinghai-Tibetan Plateau. ANNALS OF BOTANY 2023; 131:109-122. [PMID: 34932785 PMCID: PMC9904346 DOI: 10.1093/aob/mcab155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/20/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Genome size is an important plant trait, with substantial interspecies variation. The mechanisms and selective pressures underlying genome size evolution are important topics in evolutionary biology. There is considerable diversity in Allium from the Qinghai-Tibetan Plateau, where genome size variation and related evolutionary mechanisms are poorly understood. METHODS We reconstructed the Allium phylogeny using DNA sequences from 71 species. We also estimated genome sizes of 62 species, and determined chromosome numbers in 65 species. We examined the phylogenetic signal associated with genome size variation, and tested how well the data fit different evolutionary models. Correlations between genome size variations and seed mass, altitude and 19 bioclimatic factors were determined. KEY RESULTS Allium genome sizes differed substantially between species and within diploids, triploids, tetraploids, hexaploids and octaploids. Size per monoploid genome (1Cx) tended to decrease with increasing ploidy levels. Allium polyploids tended to grow at a higher altitude than diploids. The phylogenetic tree was divided into three evolutionary branches. The genomes in Clade I were mostly close to the ancestral genome (18.781 pg) while those in Clades II and III tended to expand and contract, respectively. A weak phylogenetic signal was detected for Allium genome size. Furthermore, significant positive correlations were detected between genome size and seed mass, as well as between genome size and altitude. However, genome size was not correlated with 19 bioclimatic variables. CONCLUSIONS Allium genome size shows gradual evolution, followed by subsequent adaptive radiation. The three well-supported Allium clades are consistent with previous studies. The evolutionary patterns in different Allium clades revealed genome contraction, expansion and relative stasis. The Allium species in Clade II may follow adaptive radiation. The genome contraction in Clade III may be due to DNA loss after polyploidization. Allium genome size might be influenced by selective pressure due to the conditions on the Qinghai-Tibetan Plateau (low temperature, high UV irradiation and abundant phosphate in the soil).
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Affiliation(s)
| | | | - Qian Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming 650201, China
| | - Ya Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming 650201, China
| | - Yongping Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming 650201, China
| | - Yuanwen Duan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming 650201, China
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15
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Bafort Q, Wu T, Natran A, De Clerck O, Van de Peer Y. The immediate effects of polyploidization of Spirodela polyrhiza change in a strain-specific way along environmental gradients. Evol Lett 2023; 7:37-47. [PMID: 37065435 PMCID: PMC10091501 DOI: 10.1093/evlett/qrac003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/15/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023] Open
Abstract
Abstract
The immediate effects of plant polyploidization are well characterized and it is generally accepted that these morphological, physiological, developmental, and phenological changes contribute to polyploid establishment. Studies on the environmental dependence of the immediate effects of whole-genome duplication (WGD) are, however, scarce but suggest that these immediate effects are altered by stressful conditions. As polyploid establishment seems to be associated with environmental disturbance, the relationship between ploidy-induced phenotypical changes and environmental conditions is highly relevant. Here, we use a common garden experiment on the greater duckweed Spirodela polyrhiza to test whether the immediate effects of WGD can facilitate the establishment of tetraploid duckweed along gradients of two environmental stressors. Because successful polyploid establishment often depends on recurrent polyploidization events, we include four genetically diverse strains and assess whether these immediate effects are strain-specific. We find evidence that WGD can indeed confer a fitness advantage under stressful conditions and that the environment affects ploidy-induced changes in fitness and trait reaction norms in a strain-specific way.
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Affiliation(s)
- Quinten Bafort
- Department of Biology, Ghent University , Ghent , Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
| | - Tian Wu
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
| | - Annelore Natran
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
| | | | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB-UGent Center for Plant Systems Biology , Ghent , Belgium
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University , Nanjing , China
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria , Pretoria , South Africa
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16
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Duan T, Sicard A, Glémin S, Lascoux M. Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole-genome duplication. THE NEW PHYTOLOGIST 2023; 237:339-353. [PMID: 36254103 PMCID: PMC10099941 DOI: 10.1111/nph.18542] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Polyploidization, the process leading to the increase in chromosome sets, is a major evolutionary transition in plants. Whole-genome duplication (WGD) within the same species gives rise to autopolyploids, whereas allopolyploids result from a compound process with two distinct components: WGD and interspecific hybridization. To dissect the instant effects of WGD and hybridization on gene expression and phenotype, we created a series of synthetic hybrid and polyploid Capsella plants, including diploid hybrids, autotetraploids of both parental species, and two kinds of resynthesized allotetraploids with different orders of WGD and hybridization. Hybridization played a major role in shaping the relative expression pattern of the neo-allopolyploids, whereas WGD had almost no immediate effect on relative gene expression pattern but, nonetheless, still affected phenotypes. No transposable element-mediated genomic shock scenario was observed in either neo-hybrids or neo-polyploids. Finally, WGD and hybridization interacted and the distorting effects of WGD were less strong in hybrids. Whole-genome duplication may even improve hybrid fertility. In summary, while the initial relative gene expression pattern in neo-allotetraploids was almost entirely determined by hybridization, WGD only had trivial effects on relative expression patterns, both processes interacted and had a strong impact on physical attributes and meiotic behaviors.
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Affiliation(s)
- Tianlin Duan
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
| | - Adrien Sicard
- Department of Plant BiologySwedish University of Agricultural Sciences750 07UppsalaSweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
- UMR CNRS 6553 ECOBIOCampus Beaulieu, bât 14a, p.118, CS 7420535042RennesFrance
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
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17
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Henniges MC, Johnston E, Pellicer J, Hidalgo O, Bennett MD, Leitch IJ. The Plant DNA C-Values Database: A One-Stop Shop for Plant Genome Size Data. Methods Mol Biol 2023; 2703:111-122. [PMID: 37646941 DOI: 10.1007/978-1-0716-3389-2_9] [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] [Indexed: 09/01/2023]
Abstract
Genome size is a plant character with far-reaching implications, ranging from impacts on the financial and computing feasibility of sequencing and assembling genomes all the way to influencing the very ecology and evolution of species. The increasing recognition of the role of genome size in plant science has led to a rising demand for comprehensive and easily accessible sources of genome size data. The Plant DNA C-values database has established itself as a trusted and widely used central hub for users needing to access available plant genome size data, complemented with related cytogenetic (ploidy level) and karyological (chromosome number) information where available. Since its inception in 2001, the database has undergone six major updates to incorporate newly available genome size information, leading to the most recent release (Release 7.1), which comprises data for 12,273 species across all the major land plant and some algal lineages. Here we describe how to use the database efficiently, making use of its different query and filtering settings.
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Affiliation(s)
- Marie C Henniges
- Royal Botanic Gardens, Kew, Richmond, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, UK
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, UK
- Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona), Barcelona, Spain
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18
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Phylogenomics and genome size evolution in Amomum s. s. (Zingiberaceae): Comparison of traditional and modern sequencing methods. Mol Phylogenet Evol 2023; 178:107666. [PMID: 36384185 DOI: 10.1016/j.ympev.2022.107666] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND AIMS A targeted enrichment NGS approach was used to construct the phylogeny of Amomum Roxb. (Zingiberaceae). Phylogenies based on hundreds of nuclear genes, the whole plastome and the rDNA cistron were compared with an ITS-based phylogeny. Trends in genome size (GS) evolution were examined, chromosomes were counted and the geographical distribution of phylogenetic lineages was evaluated. METHODS In total, 92 accessions of 54 species were analysed. ITS was obtained for 79 accessions, 37 accessions were processed with Hyb-Seq and sequences from 449 nuclear genes, the whole cpDNA, and the rDNA cistron were analysed using concatenation, coalescence and supertree approaches. The evolution of absolute GS was analysed in a phylogenetic and geographical context. The chromosome numbers of 12 accessions were counted. KEY RESULTS Four groups were recognised in all datasets though their mutual relationships differ among datasets. While group A (A. subulatum and A. petaloideum) is basal to the remaining groups in the nuclear gene phylogeny, in the cpDNA topology it is sister to group B (A. repoeense and related species) and, in the ITS topology, it is sister to group D (the Elettariopsis lineage). The former Elettariopsis makes a monophyletic group. There is an increasing trend in GS during evolution. The largest GS values were found in group D in two tetraploid taxa, A. cinnamomeum and A. aff. biphyllum (both 2n = 96 chromosomes). The rest varied in GS (2C = 3.54-8.78 pg) with a constant chromosome number 2n = 48. There is a weak connection between phylogeny, GS and geography in Amomum. CONCLUSIONS Amomum consists of four groups, and the former Elettariopsis is monophyletic. Species in this group have the largest GS. Two polyploids were found and GS greatly varied in the rest of Amomum.
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19
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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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20
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Pincheira‐Donoso D, Harvey LP, Johnson JV, Hudson D, Finn C, Goodyear LEB, Guirguis J, Hyland EM, Hodgson DJ. Genome size does not influence extinction risk in the world's amphibians. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Lilly P. Harvey
- School of Science and Technology Nottingham Trent University Nottingham UK
| | - Jack V. Johnson
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Dave Hudson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences University of Exeter Penryn UK
| | - Catherine Finn
- School of Biological Sciences Queen's University Belfast Belfast UK
| | | | - Jacinta Guirguis
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Edel M. Hyland
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Dave J. Hodgson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences University of Exeter Penryn UK
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21
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Feng X, Chen H, Xiao B, Wu Q, Zhang J, Zhang N, Li P, Wang L, Yin J, Sui Z. Ploidy Identification by Flow Cytometry and Application of the Method to Characterize Seasonal Ploidy Variation of Wild Populations of the Red Alga Gracilariopsis lemaneiformis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:1073-1083. [PMID: 36198873 DOI: 10.1007/s10126-022-10167-3] [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: 03/15/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Gracilariopsis lemaneiformis (Gp. lemaneiformis) is an economically important alga. At present, there is no way to quickly and easily determine its ploidy and life cycle dynamics in wild populations, which affects the process of genetic breeding. In this study, we developed and verified a ploidy identification method using flow cytometry and then used it to explore the seasonal fluctuation of the ploidy ratio and the environmental factors that influence it in wild populations of this species. Of the three methods we tested for nucleus extraction, quick chopping was the best because of its high extraction efficiency, low debris background, obvious subcellular scatter plot, and clear typical histogram. Samples from the tip of the alga were more suitable for preparing the nuclear suspension than samples from the base. Generalized linear model analysis based on diagnosis of multicollinearity revealed a negative correlation between temperature and ploidy ratio. Among the environmental factors tested, temperature had the greatest influence on the ploidy ratio, whereas precipitation and sunshine duration had no effect on the ploidy ratio fluctuation. Our study will be useful for material collection and studies of utilization and life cycle dynamics. Moreover, understanding of ploidy dynamics may provide a theoretical basis for improving variety and breeding of Gp. lemaneiformis in the future.
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Affiliation(s)
- Xiaoqing Feng
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Haihong Chen
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Baoheng Xiao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Qiong Wu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Jingyu Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Ni Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Pingping Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Lu Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Jingru Yin
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
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22
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Peng Y, Yang J, Leitch IJ, Guignard MS, Seabloom EW, Cao D, Zhao F, Li H, Han X, Jiang Y, Leitch AR, Wei C. Plant genome size modulates grassland community responses to multi-nutrient additions. THE NEW PHYTOLOGIST 2022; 236:2091-2102. [PMID: 36110049 DOI: 10.1111/nph.18496] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
Grassland ecosystems cover c. 40% of global land area and contain c. 40% of soil organic carbon. Understanding the effects of adding nutrients to grasslands is essential because they provide much of our food, support diverse ecosystem services and harbor rich biodiversity. Using the meadow steppe (grassland) study site of Inner Mongolia, we manipulated seven key nutrients and a cocktail of micronutrients to examine their effects on grassland biomass productivity and diversity. The results, explained in structural equation models, link two previously disparate hypotheses in grassland ecology: (1) the light asymmetry competition hypothesis and (2) the genome size-nutrient interaction hypothesis. We show that aboveground net primary productivity increases predominantly from species with large genome sizes with the addition of nitrogen, and nitrogen plus phosphorus. This drives an asymmetric competition for light, causing a decline in species richness mainly in species with small genome sizes. This dynamic is likely to be caused by the nutrient demands of the nucleus and/or the scaling effects of nuclear size on cell size which impact water use efficiency. The model will help inform the best management approaches to reverse the rapid and unprecedented degradation of grasslands globally.
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Affiliation(s)
- Yang Peng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Erguna Forest-Steppe Ecotone Ecosystem Research Station, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Jianxia Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Maïté S Guignard
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
- School of Biological and Behavioral Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN, 55108, USA
| | - Dong Cao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangyuan Zhao
- National Hulunber Grassland Ecosystem Observation and Research Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Huanlong Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingguo Han
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Jiang
- School of Life Sciences, Hebei University, Baoding, 071002, China
| | - Andrew R Leitch
- School of Biological and Behavioral Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Cunzheng Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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23
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Li S, Feng Z, Yuan X, Wang M, Agathokleous E. Elevated ozone inhibits isoprene emission of a diploid and a triploid genotype of Populus tomentosa by different mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6449-6462. [PMID: 35767843 DOI: 10.1093/jxb/erac288] [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: 02/18/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Ozone (O3) pollution affects plant growth and isoprene (ISO) emission. However, the response mechanism of isoprene emission rate (ISOrate) to elevated O3 (EO3) remains poorly understood. ISOrate was investigated in two genotypes (diploid and triploid) of Chinese white poplar (Populus tomentosa Carr.) exposed to EO3 in an open top chamber system. The triploid genotype had higher photosynthetic rate (A) and stomatal conductance (gs) than the diploid one. EO3 significantly decreased A, gs, and ISOrate of middle and lower leaves in both genotypes. In the diploid genotype, the reduction of ISOrate was caused by a systematic decrease related to ISO synthesis capacity, as indicated by decreased contents of the isoprene precursor dimethylallyl diphosphate and decreased isoprene synthase protein and activity. On the other hand, the negative effect of O3 on ISOrate of the triploid genotype did not result from inhibited ISO synthesis capacity, but from increased ISO oxidative loss within the leaf. Our findings will be useful for breeding poplar genotypes with high yield and lower ISOrate, depending on local atmospheric volatile organic compound/NOx ratio, to cope with both the rising O3 concentrations and increasing biomass demand. They can also inform the incorporation of O3 effects into process-based models of isoprene emission.
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Affiliation(s)
- Shuangjiang Li
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, China
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, China
| | - Zhaozhong Feng
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, China
| | - Xiangyang Yuan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Miaomiao Wang
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing, China
| | - Evgenios Agathokleous
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, China
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24
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Walczyk AM, Hersch-Green EI. Do water and soil nutrient scarcities differentially impact the performance of diploid and tetraploid Solidago gigantea (Giant Goldenrod, Asteraceae)? PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:1031-1042. [PMID: 35727918 DOI: 10.1111/plb.13448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Plants require water and nutrients for survival, although the effects of their availabilities on plant fitness differ amongst species. Genome size variation, within and across species, is suspected to influence plant water and nutrient requirements, but little is known about how variations in these resources concurrently affect plant fitness based on genome size. We examined how genome size variation between autopolyploid cytotypes influences plant morphological and physiological traits, and whether cytotype-specific trait responses differ based on water and/or nutrient availability. Diploid and autotetraploid Solidago gigantea (Giant Goldenrod) were grown in a greenhouse under four soil water:N+P treatments (L:L, L:H, H:L, H:H), and stomata characteristics (size, density), growth (above- and belowground biomass, R/S), and physiological (Anet , E, WUE) responses were measured. Resource availabilities and cytotype identity influenced some plant responses but their effects were independent of each other. Plants grown in high-water and nutrient treatments were larger, plants grown in low-water or high-nutrient treatments had higher WUE but lower E, and Anet and E rates decreased as plants aged. Autotetraploids also had larger and fewer stomata, higher biomass and larger Anet than diploids. Nutrient and water availability could influence intra- and interspecific competitive outcomes. Although S. gigantea cytotypes were not differentially affected by resource treatments, genome size may influence cytogeographic range patterning and population establishment likelihood. For instance, the larger size of autotetraploid S. gigantea might render them more competitive for resources and niche space than diploids.
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Affiliation(s)
- A M Walczyk
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - E I Hersch-Green
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
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25
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Moraes AP, Engel TBJ, Forni-Martins ER, de Barros F, Felix LP, Cabral JS. Are chromosome number and genome size associated with habit and environmental niche variables? Insights from the Neotropical orchids. ANNALS OF BOTANY 2022; 130:11-25. [PMID: 35143612 PMCID: PMC9295925 DOI: 10.1093/aob/mcac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS The entangled relationship of chromosome number and genome size with species distribution has been the subject of study for almost a century, but remains an open question due to previous ecological and phylogenetic knowledge constraints. To better address this subject, we used the clade Maxillariinae, a widely distributed and karyotypically known orchid group, as a model system to infer such relationships in a robust methodological framework. METHODS Based on the literature and new data, we gathered the chromosome number and genome size for 93 and 64 species, respectively. We built a phylogenetic hypothesis and assessed the best macroevolutionary model for both genomic traits. Additionally, we collected together ecological data (preferences for bioclimatic variables, elevation and habit) used as explanatory variables in multivariate phylogenetic models explaining genomic traits. Finally, the impact of polyploidy was estimated by running the analyses with and without polyploids in the sample. KEY RESULTS The association between genomic and ecological data varied depending on whether polyploids were considered or not. Without polyploids, chromosome number failed to present consistent associations with ecological variables. With polyploids, there was a tendency to waive epiphytism and colonize new habitats outside humid forests. The genome size showed association with ecological variables: without polyploids, genome increase was associated with flexible habits, with higher elevation and with drier summers; with polyploids, genome size increase was associated with colonizing drier environments. CONCLUSIONS The chromosome number and genome size variations, essential but neglected traits in the ecological niche, are shaped in the Maxillariinae by both neutral and adaptive evolution. Both genomic traits are partially correlated to bioclimatic variables and elevation, even when controlling for phylogenetic constraints. While polyploidy was associated with shifts in the environmental niche, the genome size emerges as a central trait in orchid evolution by the association between small genome size and epiphytism, a key innovation to Neotropical orchid diversification.
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Affiliation(s)
| | - Thaissa Brogliato Junqueira Engel
- Universidade de Campinas – UNICAMP, Instituto de Biologia, Departamento de Biologia Vegetal, Programa de Pós Graduação em Biologia Vegetal, Campinas, 13083-970, São Paulo, Brazil
| | - Eliana R Forni-Martins
- Universidade de Campinas – UNICAMP, Instituto de Biologia, Departamento de Biologia Vegetal, Programa de Pós Graduação em Biologia Vegetal, Campinas, 13083-970, São Paulo, Brazil
| | - Fábio de Barros
- Instituto de Botânica, Núcleo de Pesquisa Orquidário do Estado, São Paulo, 04045-972, São Paulo, Brazil
| | - Leonardo P Felix
- Universidade Federal da Paraíba – UFPB, Campus II, Departamento de Ciências Biológicas, Areia, 58397-000, Paraíba, Brazil
| | - Juliano Sarmento Cabral
- University of Würzburg, Ecosystem Modeling, Center for Computational and Theoretical Biology (CCTB), Klara-Oppenheimer-Weg 32, D-97074, Würzburg, Germany
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26
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Costa L, Marques A, Buddenhagen C, Thomas WW, Huettel B, Schubert V, Dodsworth S, Houben A, Souza G, Pedrosa-Harand A. Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA. ANNALS OF BOTANY 2021; 128:835-848. [PMID: 34050647 PMCID: PMC8577205 DOI: 10.1093/aob/mcab063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/26/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS With the advance of high-throughput sequencing, reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information, particularly from coding regions. As the off-target reads from such sequencing are expected to be similar to genome skimming (GS), we assessed the quality of repeat characterization in plant genomes using these data. METHODS Repeat composition obtained from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa. In addition, a FISH probe was designed based on the most abundant satellite found in the TCS dataset of Rhynchospora cephalotes. Finally, repeat-based phylogenies of the five Rhynchospora species were constructed based on the GS and TCS datasets and the topologies were compared with a gene-alignment-based phylogenetic tree. KEY RESULTS All the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01 % in the GS data. Rank correlations between GS and TCS repeat abundances were moderately high (r = 0.58-0.85), increasing after filtering out the targeted loci from the raw TCS reads (r = 0.66-0.92). Repeat data obtained by TCS were also reliable in developing a cytogenetic probe of a new variant of the holocentromeric satellite Tyba. Repeat-based phylogenies from TCS data were congruent with those obtained from GS data and the gene-alignment tree. CONCLUSIONS Our results show that off-target TCS reads can be recycled to identify repeats for cyto- and phylogenomic investigations. Given the growing availability of TCS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity.
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Affiliation(s)
- Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
| | - André Marques
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife-PE, Brazil
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27
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Kuo L, Tang SK, Kao T, Ebihara A, Fawcett S, Hsiao M, Shinohara W, Dauphin B. A dormant resource for genome size estimation in ferns: C-value inference of the Ophioglossaceae using herbarium specimen spores. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11452. [PMID: 34938613 PMCID: PMC8664048 DOI: 10.1002/aps3.11452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
PREMISE The great variation of genome size (C-value) across land plants is linked to various adaptative features. Flow cytometry (FCM), the standard approach to estimating C-values, relies mostly on fresh materials, performing poorly when used with herbarium materials. No fern C-value reports have been derived from herbarium specimens; however, the herbarium spores of some ferns remain highly viable for decades and are thus promising for further investigation. To explore this possibility, we evaluated herbarium spore collections of Ophioglossaceae ferns using FCM. METHODS Flow cytometry was conducted on 24 spore samples, representing eight of the 12 genera of the Ophioglossaceae, using specimens ranging in age from 2.6 to 111 years obtained from five herbaria. RESULTS Regardless of the genus or the source herbarium, high-quality C-value data were generated from 17 samples, with the oldest being 26 years old. Estimates of the C-values from sporophytic tissues of known ploidy did not reveal any evidence of apomixis for the species surveyed here. We also detected a pronounced genome downsizing in Sceptridium polyploids. DISCUSSION The recent success of FCM for C-value estimation using spores provides a much more convenient method of utilizing "dry" refrigerated materials. We demonstrate here that herbarium spores of some ferns are also promising for this use, even for older specimens.
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Affiliation(s)
- Li‐Yaung Kuo
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Sheng Kai Tang
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Tzu‐Tong Kao
- Department of BiologyDuke UniversityDurhamNorth CarolinaUSA
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei CityTaiwan
| | - Atsushi Ebihara
- Department of BotanyNational Museum of Nature and Science, TsukubaIbarakiJapan
| | - Susan Fawcett
- University and Jepson Herbaria, University of California, BerkeleyCaliforniaUSA
| | - Min‐Chien Hsiao
- Institute of Ecology and Evolutionary BiologyNational Taiwan UniversityTaipei CityTaiwan
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28
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Wang M, Li G, Feng Z, Liu Y, Xu Y, Uscola M. Uptake of nitrogen forms by diploid and triploid white poplar depends on seasonal carbon use strategy and elevated summer ozone. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7180-7190. [PMID: 34228101 DOI: 10.1093/jxb/erab317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
The ability of plants to acquire soil nitrogen (N) sources is plastic in response to abiotic and biotic factors. However, information about how plant preferences among N forms changes in response to internal plant N demand through growth phases, or to environmental stress such as ozone (O3), is scarce. Diploid and triploid Chinese white poplar were used to investigate N form preferences at two key developmental periods (spring, summer) and in response to summer O3 (ambient, 60 ppb above ambient). We used stable isotopes to quantify NH4+, NO3- and glycine N-uptake rates. Carbon acquisition was recorded simultaneously. Both ploidy levels differed in growth, N form preferences, and N and C use strategies. Diploid white poplars grew faster in spring but slower in summer compared with triploids. Diploid white poplars also showed plasticity among N form preferences through the season, with no preferences in spring, and NO3- preferred in summer, while triploids showed an overall preference for NO3-. Carbon acquisition and NO3- uptake were inhibited in both ploidy levels of poplar at elevated O3, which also reduced diploid total N uptake. However, triploid white poplars alleviated N uptake reduction, switching to similar preferences among N forms. We conclude that N form preferences by white poplar are driven by internal C and N use in response to nutrient demands, and external factors such as O3.
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Affiliation(s)
- Miaomiao Wang
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing 100083, China
- National Innovation Alliance of Valuable Deciduous Tree Industry, Beijing Forestry University, Beijing 100083, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China
| | - Guolei Li
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing 100083, China
- National Innovation Alliance of Valuable Deciduous Tree Industry, Beijing Forestry University, Beijing 100083, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China
| | - Zhaozhong Feng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Agrometeorology of Jiangsu Province, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yong Liu
- Research Center of Deciduous Oaks, Beijing Forestry University, Beijing 100083, China
- National Innovation Alliance of Valuable Deciduous Tree Industry, Beijing Forestry University, Beijing 100083, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, Beijing 100083, China
| | - Yansen Xu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mercedes Uscola
- Forest Ecology and Restoration Group, Departamento de Ciencias de la Vida, U.D. Ecología, Universidad de Alcalá, Apdo. 20, E-28805, Alcalá de Henares, Madrid, Spain
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29
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Faizullah L, Morton JA, Hersch-Green EI, Walczyk AM, Leitch AR, Leitch IJ. Exploring environmental selection on genome size in angiosperms. TRENDS IN PLANT SCIENCE 2021; 26:1039-1049. [PMID: 34219022 DOI: 10.1016/j.tplants.2021.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 05/22/2023]
Abstract
Angiosperms show a remarkable range in genome size (GS), yet most species have small genomes, despite the frequency of polyploidy and repeat amplification in the ancestries of most lineages. It has been suggested that larger genomes incur costs that have driven selection for GS reduction, although the nature of these costs and how they might impact selection remain unclear. We explore potential costs of increased GS encompassing impacts on minimum cell size with consequences for photosynthesis and water-use efficiency and effects of greater nitrogen and phosphorus demands of the nucleus leading to more severe trade-offs with photosynthesis. We suggest that nutrient-, water-, and/or CO2-stressed conditions might favour species with smaller genomes, with implications for species' ecological and evolutionary dynamics.
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Affiliation(s)
- Lubna Faizullah
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK
| | - Joseph A Morton
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK
| | - Erika I Hersch-Green
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Angela M Walczyk
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK.
| | - Ilia J Leitch
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
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30
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Becher H, Powell RF, Brown MR, Metherell C, Pellicer J, Leitch IJ, Twyford AD. The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights. ANNALS OF BOTANY 2021; 128:639-651. [PMID: 34318876 PMCID: PMC8422891 DOI: 10.1093/aob/mcab102] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species. METHODS We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples. KEY RESULTS We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small. CONCLUSIONS We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.
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Affiliation(s)
- Hannes Becher
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Max R Brown
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Wellcome Trust Genome Campus, Hinxton, Saffron Walden, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, Harpenden, Hertfordshire, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | | | - Alex D Twyford
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
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Raven JA. Nucleic acid requirement of plants from low phosphorus habitats. A Commentary on: Foliar nutrient-allocation patterns in Banksia attenuata and Banksia sessilis differing in growth rate and adaptation to low-phosphorus habitats. ANNALS OF BOTANY 2021; 128:iv-vi. [PMID: 34296255 PMCID: PMC8414594 DOI: 10.1093/aob/mcab084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This article comments on: Zhongming Han, Jianmin Shi, Jiayin Pang, Li Yan, Patrick M. Finnegan and Hans Lambers. Foliar nutrient allocation patterns in Banksia attenuata and Banksia sessilis differing in growth rate and adaptation to low-phosphorus habitats, Annals of Botany, Volume 128, Issue 4, 03 September 2021, Pages 419–430, https://doi.org/10.1093/aob/mcab013
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Affiliation(s)
- John A Raven
- Division of Plant Science, University of Dundee at the James Hutton Institute, Invergowrie, Dundee, UK
- Climate Change Cluster, University of Technology, Sydney, Ultimo, NSW, Australia
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- Corresponding author details: John A. Raven,
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Liddell LG, Lee WG, Dale EE, Meudt HM, Matzke NJ. Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae). Biol Lett 2021; 17:20210297. [PMID: 34464540 PMCID: PMC8437022 DOI: 10.1098/rsbl.2021.0297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
The role of whole-genome duplication (WGD) in facilitating shifts into novel biomes remains unknown. Focusing on two diverse woody plant groups in New Zealand, Coprosma (Rubiaceae) and Veronica (Plantaginaceae), we investigate how biome occupancy varies with ploidy level, and test the hypothesis that WGD increases the rate of biome shifting. Ploidy levels and biome occupancy (forest, open and alpine) were determined for indigenous species in both clades. The distribution of low-ploidy (Coprosma: 2x, Veronica: 6x) versus high-ploidy (Coprosma: 4-10x, Veronica: 12-18x) species across biomes was tested statistically. Estimation of the phylogenetic history of biome occupancy and WGD was performed using time-calibrated phylogenies and the R package BioGeoBEARS. Trait-dependent dispersal models were implemented to determine support for an increased rate of biome shifting among high-ploidy lineages. We find support for a greater than random portion of high-ploidy species occupying multiple biomes. We also find strong support for high-ploidy lineages showing a three- to eightfold increase in the rate of biome shifts. These results suggest that WGD promotes ecological expansion into new biomes.
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Affiliation(s)
- Luke G. Liddell
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - William G. Lee
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Ecosystems and Conservation, Manaaki Whenua - Landcare Research Dunedin, Dunedin 9054, New Zealand
| | - Esther E. Dale
- Ecosystems and Conservation, Manaaki Whenua - Landcare Research Dunedin, Dunedin 9054, New Zealand
- Department of Botany, University of Otago, Dunedin 9054, New Zealand
| | - Heidi M. Meudt
- Museum of New Zealand Te Papa Tongarewa, Wellington 6011, New Zealand
| | - Nicholas J. Matzke
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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Wang X, Morton JA, Pellicer J, Leitch IJ, Leitch AR. Genome downsizing after polyploidy: mechanisms, rates and selection pressures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1003-1015. [PMID: 34077584 DOI: 10.1111/tpj.15363] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 05/20/2023]
Abstract
An analysis of over 10 000 plant genome sizes (GSs) indicates that most species have smaller genomes than expected given the incidence of polyploidy in their ancestries, suggesting selection for genome downsizing. However, comparing ancestral GS with the incidence of ancestral polyploidy suggests that the rate of DNA loss following polyploidy is likely to have been very low (4-70 Mb/million years, 4-482 bp/generation). This poses a problem. How might such small DNA losses be visible to selection, overcome the power of genetic drift and drive genome downsizing? Here we explore that problem, focussing on the role that double-strand break (DSB) repair pathways (non-homologous end joining and homologous recombination) may have played. We also explore two hypotheses that could explain how selection might favour genome downsizing following polyploidy: to reduce (i) nitrogen (N) and phosphate (P) costs associated with nucleic acid synthesis in the nucleus and the transcriptome and (ii) the impact of scaling effects of GS on cell size, which influences CO2 uptake and water loss. We explore the hypothesis that losses of DNA must be fastest in early polyploid generations. Alternatively, if DNA loss is a more continuous process over evolutionary time, then we propose it is a byproduct of selection elsewhere, such as limiting the damaging activity of repetitive DNA. If so, then the impact of GS on photosynthesis, water use efficiency and/or nutrient costs at the nucleus level may be emergent properties, which have advantages, but not ones that could have been selected for over generational timescales.
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Affiliation(s)
- Xiaotong Wang
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Joseph A Morton
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia sn, Barcelona, 08038, Spain
| | | | - Andrew R Leitch
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
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Lyko P, Wicke S. Genomic reconfiguration in parasitic plants involves considerable gene losses alongside global genome size inflation and gene births. PLANT PHYSIOLOGY 2021; 186:1412-1423. [PMID: 33909907 PMCID: PMC8260112 DOI: 10.1093/plphys/kiab192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/13/2021] [Indexed: 05/02/2023]
Abstract
Parasitic plant genomes and transcriptomes reveal numerous genetic innovations, the functional-evolutionary relevance and roles of which open unprecedented research avenues.
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Affiliation(s)
- Peter Lyko
- Institute for Biology, Humboldt-University of Berlin, Germany
| | - Susann Wicke
- Institute for Biology, Humboldt-University of Berlin, Germany
- Author for communication:
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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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Catarino S, Brilhante M, Essoh AP, Charrua AB, Rangel J, Roxo G, Varela E, Moldão M, Ribeiro-Barros A, Bandeira S, Moura M, Talhinhas P, Romeiras MM. Exploring physicochemical and cytogenomic diversity of African cowpea and common bean. Sci Rep 2021; 11:12838. [PMID: 34145302 PMCID: PMC8213759 DOI: 10.1038/s41598-021-91929-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/26/2021] [Indexed: 11/09/2022] Open
Abstract
In sub-Saharan Africa, grain legumes (pulses) are essential food sources and play an important role in sustainable agriculture. Among the major pulse crops, the native cowpea (Vigna unguiculata) and introduced common bean (Phaseolus vulgaris) stand out. This paper has two main goals. First, we provide a comprehensive view of the available genetic resources of these genera in Africa, including data on germplasm collections and mapping biodiversity-rich areas. Second, we investigate patterns of physicochemical and cytogenomic variation across Africa to explore the geographical structuring of variation between native and introduced beans. Our results revealed that 73 Vigna and 5 Phaseolus species occur in tropical regions of Africa, with 8 countries accounting for more than 20 native species. Conversely, germplasm collections are poorly represented when compared to the worldwide collections. Regarding the nuclear DNA content, on average, V. unguiculata presents significantly higher values than P. vulgaris. Also, V. unguiculata is enriched in B, Mg, S, and Zn, while P. vulgaris has more Fe, Ca, and Cu. Overall, our study suggests that the physicochemical and cytogenomic diversity of native Vigna species is higher than previously thought, representing valuable food resources to reduce food insecurity and hunger, particularly of people living in African developing countries.
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Affiliation(s)
- Sílvia Catarino
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
- Forest Research Center (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Miguel Brilhante
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Anyse Pereira Essoh
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
- Research Centre in Biodiversity and Genetic Resources (CIBIO), InBIO Associate Laboratory, Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal
- Nova School of Business and Economics, Universidade Nova de Lisboa, Campus de Carcavelos, Rua da Holanda, n.1, Carcavelos, 2775-405, Cascais, Portugal
| | - Alberto B Charrua
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
- Nova School of Business and Economics, Universidade Nova de Lisboa, Campus de Carcavelos, Rua da Holanda, n.1, Carcavelos, 2775-405, Cascais, Portugal
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Licungo University, P.O. Box 2025, 2100, Beira, Mozambique
| | - Josefa Rangel
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
- Centro de Botânica, Universidade Agostinho Neto, Luanda, Angola
| | - Guilherme Roxo
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Eromise Varela
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Margarida Moldão
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Ana Ribeiro-Barros
- Forest Research Center (CEF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Salomão Bandeira
- Department of Biological Sciences, Eduardo Mondlane University, PO Box 257, 1100, Maputo, Mozambique
| | - Mónica Moura
- Research Centre in Biodiversity and Genetic Resources (CIBIO), InBIO Associate Laboratory, Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal
| | - Pedro Talhinhas
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal
| | - Maria M Romeiras
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Tapada da Ajuda, 1340-017, Lisbon, Portugal.
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
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The Application of Flow Cytometry for Estimating Genome Size, Ploidy Level Endopolyploidy, and Reproductive Modes in Plants. Methods Mol Biol 2021; 2222:325-361. [PMID: 33301101 DOI: 10.1007/978-1-0716-0997-2_17] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Over the years, the amount of DNA in a nucleus (genome size) has been estimated using a variety of methods, but increasingly, flow cytometry (FCM) has become the method of choice. The popularity of this technique lies in the ease of sample preparation and in the large number of particles (i.e., nuclei) that can be analyzed in a very short period of time. This chapter presents a step-by-step guide to estimating the nuclear DNA content of plant nuclei using FCM. Attempting to serve as a tool for daily laboratory practice, we list, in detail, the equipment required, specific reagents and buffers needed, as well as the most frequently used protocols to carry out nuclei isolation. In addition, solutions to the most common problems that users may encounter when working with plant material and troubleshooting advice are provided. Finally, information about the correct terminology to use and the importance of obtaining chromosome counts to avoid cytological misinterpretations of the FCM data are discussed.
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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: 2] [Impact Index Per Article: 0.5] [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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Becher H, Brown MR, Powell G, Metherell C, Riddiford NJ, Twyford AD. Maintenance of Species Differences in Closely Related Tetraploid Parasitic Euphrasia (Orobanchaceae) on an Isolated Island. PLANT COMMUNICATIONS 2020; 1:100105. [PMID: 33367265 PMCID: PMC7748025 DOI: 10.1016/j.xplc.2020.100105] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/24/2020] [Accepted: 08/27/2020] [Indexed: 05/02/2023]
Abstract
Polyploidy is pervasive in angiosperm evolution and plays important roles in adaptation and speciation. However, polyploid groups are understudied due to complex sequence homology, challenging genome assembly, and taxonomic complexity. Here, we study adaptive divergence in taxonomically complex eyebrights (Euphrasia), where recent divergence, phenotypic plasticity, and hybridization blur species boundaries. We focus on three closely related tetraploid species with contrasting ecological preferences that are sympatric on Fair Isle, a small isolated island in the British Isles. Using a common garden experiment, we show a genetic component to the morphological differences present between these species. Using whole-genome sequencing and a novel k-mer approach we call "Tetmer", we demonstrate that the species are of allopolyploid origin, with a sub-genome divergence of approximately 5%. Using ∼2 million SNPs, we show sub-genome homology across species, with a very low sequence divergence characteristic of recent speciation. This genetic variation is broadly structured by species, with clear divergence of Fair Isle heathland Euphrasia micrantha, while grassland Euphrasia arctica and coastal Euphrasia foulaensis are more closely related. Overall, we show that tetraploid Euphrasia is a system of allopolyploids of postglacial species divergence, where adaptation to novel environments may be conferred by old variants rearranged into new genetic lineages.
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Affiliation(s)
- Hannes Becher
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
- Corresponding author
| | - Max R. Brown
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Gavin Powell
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, 4 High Firs Crescent, Harpenden, Hertfordshire AL5 1NA, UK
| | | | - Alex D. Twyford
- University of Edinburgh, School of Biological Sciences, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
- Corresponding author
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Escudero M, Wendel JF. The grand sweep of chromosomal evolution in angiosperms. THE NEW PHYTOLOGIST 2020; 228:805-808. [PMID: 32772369 DOI: 10.1111/nph.16802] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Reina Mercedes s/n, Seville, ES-41012, Spain
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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Siljak-Yakovlev S, Lamy F, Takvorian N, Valentin N, Gouesbet V, Hennion F, Robert T. Genome size and chromosome number of ten plant species from Kerguelen Islands. Polar Biol 2020. [DOI: 10.1007/s00300-020-02755-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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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Meyerson LA, Pyšek P, Lučanová M, Wigginton S, Tran C, Cronin JT. Plant genome size influences stress tolerance of invasive and native plants via plasticity. Ecosphere 2020. [DOI: 10.1002/ecs2.3145] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Laura A. Meyerson
- Department of Natural Resources Science The University of Rhode Island Kingston Rhode Island 02881 USA
| | - Petr Pyšek
- Department of Invasion Ecology Institute of Botany Czech Academy of Sciences CZ‐252 43 Průhonice Czech Republic
- Department of Ecology Faculty of Science Charles University Viničná 7 CZ‐128 44 Prague Czech Republic
| | - Magdalena Lučanová
- Department of Evolutionary Biology of Plants Institute of Botany Czech Academy of Sciences CZ‐252 43 Průhonice Czech Republic
- Department of Botany Faculty of Science University of South Bohemia CZ‐370 05 České Budějovice Czech Republic
| | - Sara Wigginton
- Department of Natural Resources Science The University of Rhode Island Kingston Rhode Island 02881 USA
| | - Cao‐Tri Tran
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803 USA
| | - James T. Cronin
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803 USA
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Pellicer J, Leitch IJ. The Plant DNA C-values database (release 7.1): an updated online repository of plant genome size data for comparative studies. THE NEW PHYTOLOGIST 2020; 226:301-305. [PMID: 31608445 DOI: 10.1111/nph.16261] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/08/2019] [Indexed: 05/07/2023]
Affiliation(s)
- Jaume Pellicer
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
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Naciri Y, Linder HP. The genetics of evolutionary radiations. Biol Rev Camb Philos Soc 2020; 95:1055-1072. [PMID: 32233014 DOI: 10.1111/brv.12598] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 02/06/2023]
Abstract
With the realization that much of the biological diversity on Earth has been generated by discrete evolutionary radiations, there has been a rapid increase in research into the biotic (key innovations) and abiotic (key environments) circumstances in which such radiations took place. Here we focus on the potential importance of population genetic structure and trait genetic architecture in explaining radiations. We propose a verbal model describing the stages of an evolutionary radiation: first invading a suitable adaptive zone and expanding both spatially and ecologically through this zone; secondly, diverging genetically into numerous distinct populations; and, finally, speciating. There are numerous examples of the first stage; the difficulty, however, is explaining how genetic diversification can take place from the establishment of a, presumably, genetically depauperate population in a new adaptive zone. We explore the potential roles of epigenetics and transposable elements (TEs), of neutral process such as genetic drift in combination with trait genetic architecture, of gene flow limitation through isolation by distance (IBD), isolation by ecology and isolation by colonization, the possible role of intra-specific competition, and that of admixture and hybridization in increasing the genetic diversity of the founding populations. We show that many of the predictions of this model are corroborated. Most radiations occur in complex adaptive zones, which facilitate the establishment of many small populations exposed to genetic drift and divergent selection. We also show that many radiations (especially those resulting from long-distance dispersal) were established by polyploid lineages, and that many radiating lineages have small genome sizes. However, there are several other predictions which are not (yet) possible to test: that epigenetics has played a role in radiations, that radiations occur more frequently in clades with small gene flow distances, or that the ancestors of radiations had large fundamental niches. At least some of these may be testable in the future as more genome and epigenome data become available. The implication of this model is that many radiations may be hard polytomies because the genetic divergence leading to speciation happens within a very short time, and that the divergence history may be further obscured by hybridization. Furthermore, it suggests that only lineages with the appropriate genetic architecture will be able to radiate, and that such a radiation will happen in a meta-population environment. Understanding the genetic architecture of a lineage may be an essential part of accounting for why some lineages radiate, and some do not.
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Affiliation(s)
- Yamama Naciri
- Plant Systematics and Biodiversity Laboratory, Department of Botany and Plant biology of the University of Geneva, 1 Chemin de l'Impératrice, CH-1292, Chambésy, Geneva, Switzerland
| | - H Peter Linder
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
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Decanter L, Colling G, Elvinger N, Heiðmarsson S, Matthies D. Ecological niche differences between two polyploid cytotypes of Saxifraga rosacea. AMERICAN JOURNAL OF BOTANY 2020; 107:423-435. [PMID: 32067225 PMCID: PMC7216898 DOI: 10.1002/ajb2.1431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/04/2019] [Indexed: 05/30/2023]
Abstract
PREMISE Different cytotypes of a species may differ in their morphology, phenology, physiology, and their tolerance of extreme environments. We studied the ecological niches of two subspecies of Saxifraga rosacea with different ploidy levels: the hexaploid Central European endemic subspecies sponhemica and the more widely distributed octoploid subspecies rosacea. METHODS For both cytotypes, we recorded local environmental conditions and mean plant trait values in populations across their areas of distribution, analyzed their distributions by niche modeling, studied their performance at two transplant sites with contrasting conditions, and experimentally tested their cold resistance. RESULTS Mean annual temperature was higher in hexaploid than in octoploid populations and experiments indicated that frost tolerance of the hexaploid is lower than that of the octoploid. Reproduction of octoploids from Central Europe was higher than that of hexaploids at a transplant site in subarctic Iceland, whereas the opposite was true in temperate Luxembourg, indicating adaptation of the octoploids to colder conditions. Temperature variables were also most important in niche models predicting the distribution of the two cytotypes. Genetic differences in survival among populations were larger for the octoploids than for the hexaploids in both field gardens, suggesting that greater genetic variability may contribute to the octoploid's larger distributional range. CONCLUSIONS Our results support the hypotheses that different cytotypes may have different niches leading to spatial segregation, and that higher ploidy levels can result in a broader ecological niche and greater tolerance of more extreme conditions.
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Affiliation(s)
- Lucile Decanter
- Fondation Faune‐Flore c/o Musée national d'histoire naturelle25 rue MünsterL‐2160LuxembourgLuxembourg
- Population Biology and EvolutionMusée national d'histoire naturelle25 rue MunsterL‐2160LuxembourgLuxembourg
- Unit of Plant EcologyDepartment of BiologyUniversity of MarburgKarl‐von‐Frisch‐Straße 8D‐35043MarburgGermany
| | - Guy Colling
- Population Biology and EvolutionMusée national d'histoire naturelle25 rue MunsterL‐2160LuxembourgLuxembourg
| | - Nora Elvinger
- Population Biology and EvolutionMusée national d'histoire naturelle25 rue MunsterL‐2160LuxembourgLuxembourg
| | - Starri Heiðmarsson
- The Icelandic Institute of Natural HistoryBorgir vid Nordurslod600AkureyriIceland
| | - Diethart Matthies
- Unit of Plant EcologyDepartment of BiologyUniversity of MarburgKarl‐von‐Frisch‐Straße 8D‐35043MarburgGermany
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Paule J, Heller S, Maciel JR, Monteiro RF, Leme EMC, Zizka G. Early Diverging and Core Bromelioideae (Bromeliaceae) Reveal Contrasting Patterns of Genome Size Evolution and Polyploidy. FRONTIERS IN PLANT SCIENCE 2020; 11:1295. [PMID: 33013949 PMCID: PMC7509451 DOI: 10.3389/fpls.2020.01295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/07/2020] [Indexed: 05/13/2023]
Abstract
The subfamily Bromelioideae is one of the most diverse groups among the neotropical Bromeliaceae. Previously, key innovations have been identified which account for the extraordinary radiation and species richness of this subfamily, especially in the so-called core Bromelioideae. However, in order to extend our understanding of the evolutionary mechanisms, the genomic mechanisms (e.g. polyploidy, dysploidy) that potentially underlie this accelerated speciation also need to be tested. Here, using PI and DAPI staining and flow cytometry we estimated genome size and GC content of 231 plants covering 30 genera and 165 species and combined it with published data. The evolutionary and ecological significance of all three genomic characters was tested within a previously generated dated phylogenetic framework using ancestral state reconstructions, comparative phylogenetic methods, and multiple regressions with climatic variables. The absolute genome size (2C) of Bromelioideae varied between 0.59 and 4.11 pg, and the GC content ranged between 36.73 and 41.43%. The monoploid genome sizes (Cx) differed significantly between core and early diverging lineages. The occurrence of dysploidy and polyploidy was, with few exceptions, limited to the phylogenetically isolated early diverging tank-less lineages. For Cx and GC content Ornstein-Uhlenbeck models outperformed the Brownian motion models suggesting adaptive potential linked to the temperature conditions. 2C-values revealed different rates of evolution in core and early diverging lineages also related to climatic conditions. Our results suggest that polyploidy is not associated with higher net diversification and fast radiation in core bromelioids. On the other hand, although coupled with higher extinction rates, dysploidy, polyploidy, and resulting genomic reorganizations might have played a role in the survival of the early diverging bromelioids in hot and arid environments.
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Affiliation(s)
- Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
- *Correspondence: Juraj Paule,
| | - Sascha Heller
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | | | - Raquel F. Monteiro
- Department of Botany, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elton M. C. Leme
- Marie Selby Botanical Gardens, Sarasota, FL, United States
- Rio de Janeiro Botanical Garden, Rio de Janeiro, Brazil
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
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49
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Yu JP, Liu W, Mai CL, Liao WB. Genome size variation is associated with life‐history traits in birds. J Zool (1987) 2019. [DOI: 10.1111/jzo.12755] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. P. Yu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City China West Normal University Nanchong China
- Institute of Eco‐adaptation in Amphibians and Reptiles China West Normal University Nanchong China
| | - W. Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City China West Normal University Nanchong China
- Institute of Eco‐adaptation in Amphibians and Reptiles China West Normal University Nanchong China
| | - C. L. Mai
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City China West Normal University Nanchong China
- Institute of Eco‐adaptation in Amphibians and Reptiles China West Normal University Nanchong China
| | - W. B. Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City China West Normal University Nanchong China
- Institute of Eco‐adaptation in Amphibians and Reptiles China West Normal University Nanchong China
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Yin Y, Li B, Mou K, Khan MT, Kaushik AC, Wei D, Zhang YJ. Stoichioproteomics reveal oxygen usage bias, key proteins and pathways in glioma. BMC Med Genomics 2019; 12:125. [PMID: 31464612 PMCID: PMC6716898 DOI: 10.1186/s12920-019-0571-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/12/2019] [Indexed: 02/08/2023] Open
Abstract
Background The five-year survival rate and therapeutic effect of malignant glioma is low. Identification of key/associated proteins and pathways in glioma is necessary for developing effective diagnosis and targeted therapy of glioma. In addition, Glioma involves hypoxia-specific microenvironment, whether hypoxia restriction influences the stoichioproteomic characteristics of expressed proteins is unknown. Methods In this study, we analyzed the most comprehensive immunohistochemical data from 12 human glioma samples and 4 normal cell types of cerebral cortex, identified differentially expressed proteins (DEPs), and researched the oxygen contents of DEPs, highly and lowly expressed proteins. Further we located key genes on human genome to determine their locations and enriched them for key functional pathways. Results Our results showed that although no difference was detected on whole proteome, the average oxygen content of highly expressed proteins is 6.65% higher than that of lowly expressed proteins in glioma. A total of 1480 differentially expressed proteins were identified in glioma, including 226 up regulated proteins and 1254 down regulated proteins. The average oxygen content of up regulated proteins is 2.56% higher than that of down regulated proteins in glioma. The localization of differentially expressed genes on human genome showed that most genes were on chromosome 1 and least on Y. The up regulated proteins were significantly enriched in pathways including cell cycle, pathways in cancer, oocyte meiosis, DNA replication etc. Functional dissection of the up regulated proteins with high oxygen contents showed that 51.28% of the proteins were involved in cell cycle and cyclins. Conclusions Element signature of oxygen limitation could not be detected in glioma, just as what happened in plants and microbes. Unsaved use of oxygen by the highly expressed proteins and DEPs were adapted to the fast division of glioma cells. This study can help to reveal the molecular mechanism of glioma, and provide a new approach for studies of cancer-related biomacromolecules. In addition, this study lays a foundation for application of stoichioproteomics in precision medicine. Electronic supplementary material The online version of this article (10.1186/s12920-019-0571-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yongqin Yin
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, University City, Chongqing, 401331, People's Republic of China
| | - Bo Li
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, University City, Chongqing, 401331, People's Republic of China
| | - Kejie Mou
- Department of Neurosurgery, Bishan Hospital, Bishan, Chongqing, 402760, China
| | - Muhammad T Khan
- Shanghai Jiao Tong University, Shanghai, China.,Capital University of Science & Technology, Islamabad, Pakistan
| | | | - Dongqing Wei
- Shanghai Jiao Tong University, Shanghai, China. .,Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong, 518055, China.
| | - Yu-Juan Zhang
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, University City, Chongqing, 401331, People's Republic of China.
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