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Dodsworth S, Guignard MS, Pérez-Escobar OA, Struebig M, Chase MW, Leitch AR. Repetitive DNA Restructuring Across Multiple Nicotiana Allopolyploidisation Events Shows a Lack of Strong Cytoplasmic Bias in Influencing Repeat Turnover. Genes (Basel) 2020; 11:E216. [PMID: 32092894 PMCID: PMC7074350 DOI: 10.3390/genes11020216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/19/2022] Open
Abstract
Allopolyploidy is acknowledged as an important force in plant evolution. Frequent allopolyploidy in Nicotiana across different timescales permits the evaluation of genome restructuring and repeat dynamics through time. Here we use a clustering approach on high-throughput sequence reads to identify the main classes of repetitive elements following three allotetraploid events, and how these are inherited from the closest extant relatives of the maternal and paternal subgenome donors. In all three cases, there was a lack of clear maternal, cytoplasmic bias in repeat evolution, i.e., lack of a predicted bias towards maternal subgenome-derived repeats, with roughly equal contributions from both parental subgenomes. Different overall repeat dynamics were found across timescales of <0.5 (N. rustica L.), 4 (N. repanda Willd.) and 6 (N. benthamiana Domin) Ma, with nearly additive, genome upsizing, and genome downsizing, respectively. Lower copy repeats were inherited in similar abundance to the parental subgenomes, whereas higher copy repeats contributed the most to genome size change in N. repanda and N. benthamiana. Genome downsizing post-polyploidisation may be a general long-term trend across angiosperms, but at more recent timescales there is species-specific variance as found in Nicotiana.
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Affiliation(s)
- Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, Luton LU1 3JU, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (M.S.G.); (M.S.)
| | - Maïté S. Guignard
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (M.S.G.); (M.S.)
- Royal Botanic Gardens, Kew, Richmond TW9 3AB, UK; (O.A.P.-E.); (M.W.C.)
| | | | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (M.S.G.); (M.S.)
| | - Mark W. Chase
- Royal Botanic Gardens, Kew, Richmond TW9 3AB, UK; (O.A.P.-E.); (M.W.C.)
- Department of Environment and Agriculture, Curtin University, Bentley 6102, Western Australia, Australia
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK; (M.S.G.); (M.S.)
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152
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The Origin of Land Plants Is Rooted in Two Bursts of Genomic Novelty. Curr Biol 2020; 30:530-536.e2. [DOI: 10.1016/j.cub.2019.11.090] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/15/2019] [Accepted: 11/29/2019] [Indexed: 12/22/2022]
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153
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Huang XC, German DA, Koch MA. Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events. ANNALS OF BOTANY 2020; 125:29-47. [PMID: 31314080 PMCID: PMC6948214 DOI: 10.1093/aob/mcz123] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/16/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution. METHODS We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed us to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of 48 individually analysed tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness. KEY RESULTS Brassicaceae diverged 29.9 million years ago (Mya) during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed, the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes. CONCLUSIONS The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant 'pump' for continuous and high species diversification.
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Affiliation(s)
- Xiao-Chen Huang
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Dmitry A German
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
- For correspondence. E-mail
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154
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De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evol Appl 2020; 13:210-227. [PMID: 31892953 PMCID: PMC6935586 DOI: 10.1111/eva.12839] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Affiliation(s)
| | - Anthony Piot
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
| | - Bobin Liu
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
- College of ForestryFujian Agricultural and Forestry UniversityFuzhouFujianChina
| | | | - Matthew Weiss
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
| | - Ilga Porth
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
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155
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Kirbis A, Waller M, Ricca M, Bont Z, Neubauer A, Goffinet B, Szövényi P. Transcriptional Landscapes of Divergent Sporophyte Development in Two Mosses, Physcomitrium (Physcomitrella) patens and Funaria hygrometrica. FRONTIERS IN PLANT SCIENCE 2020; 11:747. [PMID: 32587596 PMCID: PMC7299128 DOI: 10.3389/fpls.2020.00747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/11/2020] [Indexed: 05/03/2023]
Abstract
Understanding the molecular basis of morphological shifts is a fundamental question of evolutionary biology. New morphologies may arise through the birth/death of genes (gene gain/loss) or by reutilizing existing gene sets. Yet, the relative contribution of these two processes to radical morphological shifts is still poorly understood. Here, we use the model system of two mosses, Funaria hygrometrica and Physcomitrium (Physcomitrella) patens, to investigate the molecular mechanisms underlying contrasting sporophyte architectures. We used comparative analysis of time-series expression data for four stages of sporophyte development in both species to address this question in detail. We found that large-scale differences in sporophytic architecture are mainly governed by orthologous (i.e., shared) genes frequently experiencing temporal gene expression shifts between the two species. While the absolute number of species-specific genes expressed during sporophyte development is somewhat smaller, we observed a significant increase of their proportion in preferentially sporophyte expressed genes, suggesting a fundamental role in the sporophyte phase. However, further functional studies are necessary to determine their contribution to diverging sporophyte morphologies. Our results add to the growing set of studies suggesting that radical changes in morphology may rely on the heterochronic expression of conserved regulators.
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Affiliation(s)
- Alexander Kirbis
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Mariana Ricca
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Zoe Bont
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich and Zurich-Basel Plant Science Center, Zurich, Switzerland
- *Correspondence: Péter Szövényi,
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156
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Howard CC, Landis JB, Beaulieu JM, Cellinese N. Geophytism in monocots leads to higher rates of diversification. THE NEW PHYTOLOGIST 2020; 225:1023-1032. [PMID: 31469440 DOI: 10.1111/nph.16155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/21/2019] [Indexed: 05/27/2023]
Abstract
Geophytes, plants with buds on underground structures, are found throughout the plant tree of life. These below ground structures allow plants to inhabit highly seasonal and disturbance-prone environments across ecosystems. Past researchers have hypothesised that the bulbous, cormous and tuberous habits promote diversification, but this had yet to be tested. Using a comprehensive monocot data set of almost 13 000 taxa, we investigated the effects of the geophytic habit on diversification using both state-dependent and state-independent models. We found that geophytes exhibit increased rates of diversification relative to nongeophytes. State-dependent analyses recovered higher yet similar rates of diversification for bulbous, cormous and tuberous taxa compared with rhizomatous and nongeophytic taxa. However, the state-independent model returned no difference in rates among the different traits. Geophytism shows higher rates of diversification relative to nongeophytes but we found little support for the hypothesis that the evolution of the bulb, corm or tuber appears to provide a diversification increase relative to rhizomatous and nongeophytic taxa. Our broad-scale analysis highlights the overall evolutionary importance of the geophytic habit (i.e. belowground bud placement). However, our results also suggest that belowground morphological diversity alone cannot explain this rate increase. In order to further test the evolutionary significance of these underground structures, future studies should consider these in combination with other biotic and abiotic factors.
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Affiliation(s)
- Cody Coyotee Howard
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Jacob B Landis
- University of California, Riverside, Riverside, CA, 92521, USA
| | - Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72731, USA
| | - Nico Cellinese
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
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157
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Shan S, Soltis PS, Soltis DE, Yang B. Considerations in adapting CRISPR/Cas9 in nongenetic model plant systems. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11314. [PMID: 31993256 PMCID: PMC6976890 DOI: 10.1002/aps3.11314] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/26/2019] [Indexed: 05/03/2023]
Abstract
The past six years have seen the rapid growth of studies of CRISPR/Cas9 in plant genome editing, a method that enormously facilitates both basic research and practical applications. Most studies have focused on genetic model species, but plant species that are not genetic models may also be economically important or biologically significant, or both. However, developing the CRISPR/Cas9 system in a nongenetic model is challenging. Here, we summarize CRISPR/Cas9 applications in 45 plant genera across 24 families and provide a reference for practical application of CRISPR in nongenetic model plant systems. Suggestions for selecting plant species and target genes are given for proof-of-principle CRISPR studies, and the processes of vector construction are reviewed. We recommend using transient assays to identify a desired CRISPR/Cas9 system in a nongenetic model. We then review methods of plant transformation and describe approaches, using regenerated transgenic plants, for evaluating CRISPR editing results. Lastly, potential future applications of CRISPR in nongenetic model plant species are discussed. This review provides a road map for developing CRISPR in nongenetic models, an application that holds enormous potential in plant biology.
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Affiliation(s)
- Shengchen Shan
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida32611‐0180USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611‐7800USA
| | - Pamela S. Soltis
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida32611‐0180USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611‐7800USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611‐5585USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32610USA
| | - Douglas E. Soltis
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida32611‐0180USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611‐7800USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611‐5585USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32610USA
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611‐8525USA
| | - Bing Yang
- Division of Plant SciencesUniversity of MissouriColumbiaMissouri65211USA
- Donald Danforth Plant Science CenterSt. LouisMissouri63132USA
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158
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Marchant DB, Sessa EB, Wolf PG, Heo K, Barbazuk WB, Soltis PS, Soltis DE. The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly. Sci Rep 2019; 9:18181. [PMID: 31796775 PMCID: PMC6890710 DOI: 10.1038/s41598-019-53968-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 11/04/2019] [Indexed: 01/04/2023] Open
Abstract
Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.
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Affiliation(s)
- D Blaine Marchant
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Paul G Wolf
- Department of Biology, Utah State University, Logan, UT, 84322, USA
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Kweon Heo
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 24341, Korea
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
- The Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- The Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
- The Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
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159
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Soza VL, Lindsley D, Waalkes A, Ramage E, Patwardhan RP, Burton JN, Adey A, Kumar A, Qiu R, Shendure J, Hall B. The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae). Genome Biol Evol 2019; 11:3353-3371. [PMID: 31702783 PMCID: PMC6907397 DOI: 10.1093/gbe/evz245] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 02/06/2023] Open
Abstract
The genus Rhododendron (Ericaceae), which includes horticulturally important plants such as azaleas, is a highly diverse and widely distributed genus of >1,000 species. Here, we report the chromosome-scale de novo assembly and genome annotation of Rhododendron williamsianum as a basis for continued study of this large genus. We created multiple short fragment genomic libraries, which were assembled using ALLPATHS-LG. This was followed by contiguity preserving transposase sequencing (CPT-seq) and fragScaff scaffolding of a large fragment library, which improved the assembly by decreasing the number of scaffolds and increasing scaffold length. Chromosome-scale scaffolding was performed by proximity-guided assembly (LACHESIS) using chromatin conformation capture (Hi-C) data. Chromosome-scale scaffolding was further refined and linkage groups defined by restriction-site associated DNA (RAD) sequencing of the parents and progeny of a genetic cross. The resulting linkage map confirmed the LACHESIS clustering and ordering of scaffolds onto chromosomes and rectified large-scale inversions. Assessments of the R. williamsianum genome assembly and gene annotation estimate them to be 89% and 79% complete, respectively. Predicted coding sequences from genome annotation were used in syntenic analyses and for generating age distributions of synonymous substitutions/site between paralgous gene pairs, which identified whole-genome duplications (WGDs) in R. williamsianum. We then analyzed other publicly available Ericaceae genomes for shared WGDs. Based on our spatial and temporal analyses of paralogous gene pairs, we find evidence for two shared, ancient WGDs in Rhododendron and Vaccinium (cranberry/blueberry) members that predate the Ericaceae family and, in one case, the Ericales order.
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Affiliation(s)
- Valerie L Soza
- Department of Biology, University of Washington, Seattle, WA
| | - Dale Lindsley
- Department of Biology, University of Washington, Seattle, WA
- Retired
| | - Adam Waalkes
- Department of Biology, University of Washington, Seattle, WA
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | | | | | - Joshua N Burton
- Department of Genome Sciences, University of Washington, Seattle, WA
- Adaptive Biotechnologies, Seattle, WA
| | - Andrew Adey
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR
| | - Akash Kumar
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Pediatrics, Stanford University, Palo Alto, CA
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA
- Retired
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
- Brotman Baty Institute for Precision Medicine, Seattle, WA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA
| | - Benjamin Hall
- Department of Biology, University of Washington, Seattle, WA
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160
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Hornych O, Ekrt L, Riedel F, Koutecký P, Košnar J. Asymmetric hybridization in Central European populations of the Dryopteris carthusiana group. AMERICAN JOURNAL OF BOTANY 2019; 106:1477-1486. [PMID: 31634425 DOI: 10.1002/ajb2.1369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Hybridization is a key process in plant speciation. Despite its importance, there is no detailed study of hybridization rates in fern populations. A proper estimate of hybridization rates is needed to understand factors regulating hybridization. METHODS We studied hybridization in the European Dryopteris carthusiana group, represented by one diploid and two tetraploid species and their hybrids. We sampled ~100 individuals per population in 40 mixed populations of the D. carthusiana group across Europe. All plants were identified by measuring genome size (DAPI staining) using flow cytometry. To determine the maternal parentage of hybrids, we sequenced the chloroplast region trnL-trnF of all taxa involved. RESULTS We found hybrids in 85% of populations. Triploid D. ×ambroseae occurred in every population that included both parent species and is most abundant when the parent species are equally abundant. By contrast, tetraploid D. ×deweveri was rare (15 individuals total) and triploid D. ×sarvelae was absent. The parentage of hybrid taxa is asymmetric. Despite expectations from previous studies, tetraploid D. dilatata is the predominant male parent of its triploid hybrid. CONCLUSIONS This is a thorough investigation of hybridization rates in natural populations of ferns. Hybridization rates differ greatly even among closely related fern taxa. In contrast to angiosperms, our data suggest that hybridization rates are highest in balanced parent populations and support the notion that some ferns possess very weak barriers to hybridization. Our results from sequencing cpDNA challenge established notions about the correlation of ploidy level and mating tendencies.
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Affiliation(s)
- Ondřej Hornych
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Libor Ekrt
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Felix Riedel
- Botanischer Garten der Universität Potsdam, Maulbeerallee 3, Potsdam, D-14469, Germany
- Arboretum der Humboldt-Universität zu Berlin, Späthstrasse 80/81, Berlin, D-12437, Germany
| | - Petr Koutecký
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Jiří Košnar
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
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161
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Zenil-Ferguson R, Burleigh JG, Freyman WA, Igić B, Mayrose I, Goldberg EE. Interaction among ploidy, breeding system and lineage diversification. THE NEW PHYTOLOGIST 2019; 224:1252-1265. [PMID: 31617595 DOI: 10.1111/nph.16184] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/14/2019] [Indexed: 05/28/2023]
Abstract
If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs polyploid states) and breeding system (self-incompatible vs self-compatible states) are both thought to be drivers of differential diversification in angiosperms. We fit 29 diversification models to extensive trait and phylogenetic data in Solanaceae and investigate how speciation and extinction rate differences are associated with ploidy, breeding system, and the interaction between these traits. We show that diversification patterns in Solanaceae are better explained by breeding system and an additional unobserved factor, rather than by ploidy. We also find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization. Comparing multiple stochastic diversification models that include complex trait interactions alongside hidden states enhances our understanding of the macroevolutionary patterns in plant phylogenies.
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Affiliation(s)
| | - J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - William A Freyman
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Boris Igić
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
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162
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Clark JW, Puttick MN, Donoghue PCJ. Origin of horsetails and the role of whole-genome duplication in plant macroevolution. Proc Biol Sci 2019; 286:20191662. [PMID: 31662084 DOI: 10.1098/rspb.2019.1662] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Whole-genome duplication (WGD) has occurred commonly in land plant evolution and it is often invoked as a causal agent in diversification, phenotypic and developmental innovation, as well as conferring extinction resistance. The ancient and iconic lineage of Equisetum is no exception, where WGD has been inferred to have occurred prior to the Cretaceous-Palaeogene (K-Pg) boundary, coincident with WGD events in angiosperms. In the absence of high species diversity, WGD in Equisetum is interpreted to have facilitated the long-term survival of the lineage. However, this characterization remains uncertain as these analyses of the Equisetum WGD event have not accounted for fossil diversity. Here, we analyse additional available transcriptomes and summarize the fossil record. Our results confirm support for at least one WGD event shared among the majority of extant Equisetum species. Furthermore, we use improved dating methods to constrain the age of gene duplication in geological time and identify two successive Equisetum WGD events. The two WGD events occurred during the Carboniferous and Triassic, respectively, rather than in association with the K-Pg boundary. WGD events are believed to drive high rates of trait evolution and innovations, but analysed trends of morphological evolution across the historical diversity of Equisetum provide little evidence for further macroevolutionary consequences following WGD. WGD events cannot have conferred extinction resistance to the Equisetum lineage through the K-Pg boundary since the ploidy events occurred hundreds of millions of years before this mass extinction and we find evidence of extinction among fossil polyploid Equisetum lineages. Our findings precipitate the need for a review of the proposed roles of WGDs in biological innovation and extinction survival in angiosperm and non-angiosperm lineages alike.
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Affiliation(s)
- James W Clark
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, UK.,Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Mark N Puttick
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Philip C J Donoghue
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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163
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Baniaga AE, Marx HE, Arrigo N, Barker MS. Polyploid plants have faster rates of multivariate niche differentiation than their diploid relatives. Ecol Lett 2019; 23:68-78. [PMID: 31637845 DOI: 10.1111/ele.13402] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/01/2019] [Accepted: 09/16/2019] [Indexed: 01/02/2023]
Abstract
Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids. We found that polyploids are often more climatically differentiated from their diploid parents than the diploids are from each other. Consistent with this pattern, we estimated that polyploid species generally have higher rates of multivariate niche differentiation than their diploid relatives. In contrast to recent analyses, our results confirm that ecological niche differentiation is an important component of polyploid speciation and that niche differentiation is often significantly faster in polyploids.
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Affiliation(s)
- Anthony E Baniaga
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Hannah E Marx
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nils Arrigo
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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164
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Xue B, Guo X, Landis JB, Sun M, Tang CC, Soltis PS, Soltis DE, Saunders RMK. Accelerated diversification correlated with functional traits shapes extant diversity of the early divergent angiosperm family Annonaceae. Mol Phylogenet Evol 2019; 142:106659. [PMID: 31639525 DOI: 10.1016/j.ympev.2019.106659] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/04/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022]
Abstract
A major goal of phylogenetic systematics is to understand both the patterns of diversification and the processes by which these patterns are formed. Few studies have focused on the ancient, species-rich Magnoliales clade and its diversification pattern. Within Magnoliales, the pantropically distributed Annonaceae are by far the most genus-rich and species-rich family-level clade, with c. 110 genera and c. 2,400 species. We investigated the diversification patterns across Annonaceae and identified traits that show varied associations with diversification rates using a time-calibrated phylogeny of 835 species (34.6% sampling) and 11,211 aligned bases from eight regions of the plastid genome (rbcL, matK, ndhF, psbA-trnH, trnL-F, atpB-rbcL, trnS-G, and ycf1). Twelve rate shifts were identified using BAMM: in Annona, Artabotrys, Asimina, Drepananthus, Duguetia, Goniothalamus, Guatteria, Uvaria, Xylopia, the tribes Miliuseae and Malmeeae, and the Desmos-Dasymaschalon-Friesodielsia-Monanthotaxis clade. TurboMEDUSA and method-of-moments estimator analyses showed largely congruent results. A positive relationship between species richness and diversification rate is revealed using PGLS. Our results show that the high species richness in Annonaceae is likely the result of recent increased diversification rather than the steady accumulation of species via the 'museum model'. We further explore the possible role of selected traits (habit, pollinator trapping, floral sex expression, pollen dispersal unit, anther septation, and seed dispersal unit) in shaping diversification patterns, based on inferences of BiSSE, MuSSE, HiSSE, and FiSSE analyses. Our results suggest that the liana habit, the presence of circadian pollinator trapping, androdioecy, and the dispersal of seeds as single-seeded monocarp fragments are closely correlated with higher diversification rates; pollen aggregation and anther septation, in contrast, are associated with lower diversification rates.
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Affiliation(s)
- B Xue
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, China; Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China; Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, Guangdong, China
| | - X Guo
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China; Current address: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - J B Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - M Sun
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - C C Tang
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - P S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - D E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - R M K Saunders
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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165
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Abstract
Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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166
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Viruel J, Conejero M, Hidalgo O, Pokorny L, Powell RF, Forest F, Kantar MB, Soto Gomez M, Graham SW, Gravendeel B, Wilkin P, Leitch IJ. A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens. FRONTIERS IN PLANT SCIENCE 2019; 10:937. [PMID: 31396248 PMCID: PMC6667659 DOI: 10.3389/fpls.2019.00937] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 07/04/2019] [Indexed: 05/24/2023]
Abstract
Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam (Dioscorea) tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy (Dioscorea alata, D. communis, and D. sylvatica). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of Dioscorea. We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.
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Affiliation(s)
- Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Laboratori de Botànica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawai’i at Mânoa, Honolulu, HI, United States
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, Canada
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Endless Forms, Leiden, Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Science and Technology Faculty, University of Applied Sciences Leiden, Leiden, Netherlands
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
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167
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Reese JB, Williams JH. How does genome size affect the evolution of pollen tube growth rate, a haploid performance trait? AMERICAN JOURNAL OF BOTANY 2019; 106:1011-1020. [PMID: 31294836 DOI: 10.1002/ajb2.1326] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/17/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Male gametophytes of most seed plants deliver sperm to eggs via a pollen tube. Pollen tube growth rates (PTGRs) of angiosperms are exceptionally rapid, a pattern attributed to more effective haploid selection under stronger pollen competition. Paradoxically, whole genome duplication (WGD) has been common in angiosperms but rare in gymnosperms. Pollen tube polyploidy should initially accelerate PTGR because increased heterozygosity and gene dosage should increase metabolic rates. However, polyploidy should also independently increase tube cell size, causing more work which should decelerate growth. We asked how genome size changes have affected the evolution of seed plant PTGRs. METHODS We assembled a phylogenetic tree of 451 species with known PTGRs. We then used comparative phylogenetic methods to detect effects of neo-polyploidy (within-genus origins), DNA content, and WGD history on PTGR, and correlated evolution of PTGR and DNA content. RESULTS Gymnosperms had significantly higher DNA content and slower PTGR optima than angiosperms, and their PTGR and DNA content were negatively correlated. For angiosperms, 89% of model weight favored Ornstein-Uhlenbeck models with a faster PTGR optimum for neo-polyploids, whereas PTGR and DNA content were not correlated. For within-genus and intraspecific-cytotype pairs, PTGRs of neo-polyploids < paleo-polyploids. CONCLUSIONS Genome size increases should negatively affect PTGR when genetic consequences of WGDs are minimized, as found in intra-specific autopolyploids (low heterosis) and gymnosperms (few WGDs). But in angiosperms, the higher PTGR optimum of neo-polyploids and non-negative PTGR-DNA content correlation suggest that recurrent WGDs have caused substantial PTGR evolution in a non-haploid state.
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Affiliation(s)
- John B Reese
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996, U.S.A
| | - Joseph H Williams
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996, U.S.A
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168
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Walczyk AM, Hersch-Green EI. Impacts of soil nitrogen and phosphorus levels on cytotype performance of the circumboreal herb Chamerion angustifolium: implications for polyploid establishment. AMERICAN JOURNAL OF BOTANY 2019; 106:906-921. [PMID: 31283844 DOI: 10.1002/ajb2.1321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Although polyploidy commonly occurs in angiosperms, not all polyploidization events lead to successful lineages, and environmental conditions could influence cytotype dynamics and polyploid success. Low soil nitrogen and/or phosphorus concentrations often limit ecosystem primary productivity, and changes in these nutrients might differentially favor some cytotypes over others, thereby influencing polyploid establishment. METHODS We grew diploid, established tetraploid, and neotetraploid Chamerion angustifolium (fireweed) in a greenhouse under low and high soil nitrogen and phosphorus conditions and different competition treatments and measured plant performance (height, biomass, flower production, and root bud production) and insect damage responses. By comparing neotetraploids to established tetraploids, we were able to examine traits and responses that might directly arise from polyploidization before they are modified by natural selection and/or genetic drift. RESULTS We found that (1) neopolyploids were the least likely to survive and flower and experienced the most herbivore damage, regardless of nutrient conditions; (2) both neo- and established tetraploids had greater biomass and root bud production under nutrient-enriched conditions, whereas diploid biomass and root bud production was not significantly affected by nutrients; and (3) intra-cytotype competition more negatively affected diploids and established tetraploids than it did neotetraploids. CONCLUSIONS Following polyploidization, biomass and clonal growth might be more immediately affected by environmental nutrient availabilities than plant survival, flowering, and/or responses to herbivory, which could influence competitive dynamics. Specifically, polyploids might have competitive and colonizing advantages over diploids under nutrient-enriched conditions favoring their establishment, although establishment may also depend upon the density and occurrences of other related cytotypes in a population.
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Affiliation(s)
- Angela M Walczyk
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Erika I Hersch-Green
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA
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169
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Wang N, Yang Y, Moore MJ, Brockington SF, Walker JF, Brown JW, Liang B, Feng T, Edwards C, Mikenas J, Olivieri J, Hutchison V, Timoneda A, Stoughton T, Puente R, Majure LC, Eggli U, Smith SA. Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments. Mol Biol Evol 2019; 36:112-126. [PMID: 30371871 DOI: 10.1093/molbev/msy200] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we present detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and proposed a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche but did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and whereas these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.
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Affiliation(s)
- Ning Wang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, MN
| | - Michael J Moore
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Samuel F Brockington
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Joseph F Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Joseph W Brown
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Bin Liang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Tao Feng
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Caroline Edwards
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Jessica Mikenas
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Julia Olivieri
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Vera Hutchison
- Department of Biology, Oberlin College, Science Center K111, Oberlin, OH
| | - Alfonso Timoneda
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Tommy Stoughton
- Center for the Environment, MSC 63, Plymouth State University, Plymouth, NH
| | - Raúl Puente
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ
| | - Lucas C Majure
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ.,Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - Urs Eggli
- Sukkulenten-Sammlung Zürich, Zürich, Switzerland
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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170
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Hanušová K, Čertner M, Urfus T, Koutecký P, Košnar J, Rothfels CJ, Jarolímová V, Ptáček J, Ekrt L. Widespread co-occurrence of multiple ploidy levels in fragile ferns (Cystopteris fragilis complex; Cystopteridaceae) probably stems from similar ecology of cytotypes, their efficient dispersal and inter-ploidy hybridization. ANNALS OF BOTANY 2019; 123:845-855. [PMID: 30541055 PMCID: PMC6526313 DOI: 10.1093/aob/mcy219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 11/09/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Polyploidy has played an important role in the evolution of ferns. However, the dearth of data on cytotype diversity, cytotype distribution patterns and ecology in ferns is striking in comparison with angiosperms and prevents an assessment of whether cytotype coexistence and its mechanisms show similar patterns in both plant groups. Here, an attempt to fill this gap was made using the ploidy-variable and widely distributed Cystopteris fragilis complex. METHODS Flow cytometry was used to assess DNA ploidy level and monoploid genome size (Cx value) of 5518 C. fragilis individuals from 449 populations collected over most of the species' global distributional range, supplemented with data from 405 individuals representing other related species from the complex. Ecological preferences of C. fragilis tetraploids and hexaploids were compared using field-recorded parameters and database-extracted climate data. KEY RESULTS Altogether, five different ploidy levels (2x, 4x, 5x, 6x, 8x) were detected and three species exhibited intraspecific ploidy-level variation: C. fragilis, C. alpina and C. diaphana. Two predominant C. fragilis cytotypes, tetraploids and hexaploids, co-occur over most of Europe in a diffuse, mosaic-like pattern. Within this contact zone, 40 % of populations were mixed-ploidy and most also contained pentaploid hybrids. Environmental conditions had only a limited effect on the distribution of cytotypes. Differences were found in the Cx value of tetraploids and hexaploids: between-cytotype divergence was higher in uniform-ploidy than in mixed-ploidy populations. CONCLUSIONS High ploidy-level diversity and widespread cytotype coexistence in the C. fragilis complex match the well-documented patterns in some angiosperms. While ploidy coexistence in C. fragilis is not driven by environmental factors, it could be facilitated by the perennial life-form of the species, its reproductive modes and efficient wind dispersal of spores. Independent origins of hexaploids and/or inter-ploidy gene flow may be expected in mixed-ploidy populations according to Cx value comparisons.
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Affiliation(s)
- Kristýna Hanušová
- Department of Botany, Faculty of Science, Charles University, Benátská, Praha, Czech Republic
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Benátská, Praha, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek, Průhonice, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Benátská, Praha, Czech Republic
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
| | - Jiří Košnar
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Vlasta Jarolímová
- Institute of Botany, The Czech Academy of Sciences, Zámek, Průhonice, Czech Republic
| | - Jan Ptáček
- Department of Botany, Faculty of Science, Charles University, Benátská, Praha, Czech Republic
| | - Libor Ekrt
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
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171
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Czekanski-Moir JE, Rundell RJ. The Ecology of Nonecological Speciation and Nonadaptive Radiations. Trends Ecol Evol 2019; 34:400-415. [DOI: 10.1016/j.tree.2019.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 01/08/2023]
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172
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Barrett CF, McKain MR, Sinn BT, Ge XJ, Zhang Y, Antonelli A, Bacon CD. Ancient Polyploidy and Genome Evolution in Palms. Genome Biol Evol 2019; 11:1501-1511. [PMID: 31028709 PMCID: PMC6535811 DOI: 10.1093/gbe/evz092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2019] [Indexed: 12/23/2022] Open
Abstract
Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate palm genome dynamics using genomic and transcriptomic data in combination with a recent, densely sampled, phylogenetic tree. We find conclusive evidence of a paleopolyploid event shared by the ancestor of palms but not with the sister clade, Dasypogonales. We find evidence of incremental chromosome number change in the palms as opposed to one of recurrent polyploidy. We find strong phylogenetic signal in chromosome number, but no signal in genome size, and further no correlation between the two when correcting for phylogenetic relationships. Palms thus add to a growing number of diverse, ecologically successful clades with evidence of whole-genome duplication, sister to a species-poor clade with no evidence of such an event. Disentangling the causes of genome size variation in palms moves us closer to understanding the genomic conditions facilitating adaptive radiation and ecological dominance in an evolutionarily successful, emblematic tropical clade.
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Affiliation(s)
| | | | | | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Yuqu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Royal Botanical Gardens Kew, Richmond, United Kingdom
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
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173
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McCarthy EW, Landis JB, Kurti A, Lawhorn AJ, Chase MW, Knapp S, Le Comber SC, Leitch AR, Litt A. Early consequences of allopolyploidy alter floral evolution in Nicotiana (Solanaceae). BMC PLANT BIOLOGY 2019; 19:162. [PMID: 31029077 PMCID: PMC6486959 DOI: 10.1186/s12870-019-1771-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/10/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Polyploidy has played a major role in angiosperm evolution. Previous studies have examined polyploid phenotypes in comparison to their extant progenitors, but not in context of predicted progenitor phenotypes at allopolyploid origin. In addition, differences in the trends of polyploid versus diploid evolution have not been investigated. We use ancestral character-state reconstructions to estimate progenitor phenotype at allopolyploid origin to determine patterns of polyploid evolution leading to morphology of the extant species. We also compare trends in diploid versus allopolyploid evolution to determine if polyploidy modifies floral evolutionary patterns. RESULTS Predicting the ancestral phenotype of a nascent allopolyploid from reconstructions of diploid phenotypes at the time of polyploid formation generates different phenotype predictions than when extant diploid phenotypes are used, the outcome of which can alter conclusions about polyploid evolution; however, most analyses yield the same results. Using ancestral reconstructions of diploid floral phenotypes indicate that young polyploids evolve shorter, wider corolla tubes, but older polyploids and diploids do not show any detectable evolutionary trends. Lability of the traits examined (floral shape, corolla tube length, and corolla tube width) differs across young and older polyploids and diploids. Corolla length is more evolutionarily labile in older polyploids and diploids. Polyploids do not display unique suites of floral characters based on both morphological and color traits, but some suites of characters may be evolving together and seem to have arisen multiple times within Nicotiana, perhaps due to the influence of pollinators. CONCLUSIONS Young polyploids display different trends in floral evolution (shorter, wider corolla tubes, which may result in more generalist pollination) than older polyploids and diploids, suggesting that patterns of divergence are impacted by the early consequences of allopolyploidy, perhaps arising from genomic shock and/or subsequent genome stabilization associated with diploidization. Convergent evolution in floral morphology and color in Nicotiana can be consistent with pollinator preferences, suggesting that pollinators may have shaped floral evolution in Nicotiana.
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Affiliation(s)
- Elizabeth W. McCarthy
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
- Present address: Department of Biological Sciences, SUNY Cortland, Cortland, NY 13045 USA
| | - Jacob B. Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
| | - Amelda Kurti
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
| | - Amber J. Lawhorn
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
| | - Mark W. Chase
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102 Australia
| | | | - Steven C. Le Comber
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS UK
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS UK
| | - Amy Litt
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521 USA
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174
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Soltis PS, Folk RA, Soltis DE. Darwin review: angiosperm phylogeny and evolutionary radiations. Proc Biol Sci 2019; 286:20190099. [PMCID: PMC6452062 DOI: 10.1098/rspb.2019.0099] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/05/2019] [Indexed: 08/17/2023] Open
Abstract
Darwin's dual interests in evolution and plants formed the basis of evolutionary botany, a field that developed following his publications on both topics. Here, we review his many contributions to plant biology—from the evolutionary origins of angiosperms to plant reproduction, carnivory, and movement—and note that he expected one day there would be a ‘true’ genealogical tree for plants. This view fuelled the field of plant phylogenetics. With perhaps nearly 400 000 species, the angiosperms have diversified rapidly since their origin in the Early Cretaceous, often through what appear to be rapid radiations. We describe these evolutionary patterns, evaluate possible drivers of radiations, consider how new approaches to studies of diversification can contribute to our understanding of angiosperm diversity, and suggest new directions for further insight into plant evolution.
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Affiliation(s)
- Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Ryan A. Folk
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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175
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Farhat P, Hidalgo O, Robert T, Siljak-Yakovlev S, Leitch IJ, Adams RP, Bou Dagher-Kharrat M. Polyploidy in the Conifer Genus Juniperus: An Unexpectedly High Rate. FRONTIERS IN PLANT SCIENCE 2019; 10:676. [PMID: 31191584 PMCID: PMC6541006 DOI: 10.3389/fpls.2019.00676] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/06/2019] [Indexed: 05/02/2023]
Abstract
Recent research suggests that the frequency of polyploidy may have been underestimated in gymnosperms. One notable example is in the conifer genus Juniperus, where there are already a few reports of polyploids although data are still missing for most species. In this study, we evaluated the extent of polyploidy in Juniperus by conducting the first comprehensive screen across nearly all of the genus. Genome size data from fresh material, together with chromosome counts, were used to demonstrate that genome sizes estimated from dried material could be used as reliable proxies to uncover the extent of ploidy diversity across the genus. Our analysis revealed that 16 Juniperus taxa were polyploid, with tetraploids and one hexaploid being reported. Furthermore, by analyzing the genome size and chromosome data within a phylogenetic framework we provide the first evidence of possible lineage-specific polyploidizations within the genus. Genome downsizing following polyploidization is moderate, suggesting limited genome restructuring. This study highlights the importance of polyploidy in Juniperus, making it the first conifer genus and only the second genus in gymnosperms where polyploidy is frequent. In this sense, Juniperus represents an interesting model for investigating the genomic and ecological consequences of polyploidy in conifers.
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Affiliation(s)
- Perla Farhat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Beirut, Lebanon
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Oriane Hidalgo
- Royal Botanic Gardens Kew, Richmond, United Kingdom
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Unitat Associada CSIC, Barcelona, Spain
| | - Thierry Robert
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
- Biology Department, Sorbonne Université, Paris, France
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | | | - Robert P. Adams
- Biology Department, Baylor University, Waco, TX, United States
| | - Magda Bou Dagher-Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Beirut, Lebanon
- *Correspondence: Magda Bou Dagher-Kharrat
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176
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Alonso-Marcos H, Hülber K, Myllynen T, Rodríguez PP, Dobeš C. Pollen precedence in sexual Potentilla puberula and its role as a protective reproductive barrier against apomictic cytotypes. TAXON 2018; 67:1132-1142. [PMID: 30745710 PMCID: PMC6368848 DOI: 10.12705/676.9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 11/06/2018] [Indexed: 05/31/2023]
Abstract
Cross-pollination is a major factor determining the demographic dynamics of mixed-ploidy populations. Typically, rare cytotypes are suppressed due to reduced female fertility by losing gametes in heteroploid crosses (i.e., through minority cytotype exclusion). In species with reproductive differentiation into sexual and apomictic cytotypes, sexuals might be reproductively suppressed by apomicts (or transformed due to introgression of apomixis genes). Pollen precedence potentially acts as a post-pollination pre-fertilization barrier protecting sexuals against their apomictic counterparts. We estimated the role of pollen precedence as a barrier against cross-fertilization of tetraploid sexuals by penta- and heptaploid gametophytic apomicts in Potentilla puberula (Rosaceae) by means of controlled crosses, and inference of the paternity through DNA ploidy estimation of embryos. Individuals from five regions spanning an elevational and biogeographic gradient were used to account for the variation in the relative frequencies of reproductive modes across the study area. We tested (1) whether the application of heteroploid pollen (sexual × apomictic) causes a reduction of seed yield compared to homoploid crosses (sexual × sexual), and (2) if so, whether pollen precedence recovers the seed yield in simultaneous applications of pollen from sexuals and apomicts (mixed-ploidy). Seed yield was significantly lower in hetero- than in homoploid crosses. We found clear evidence for precedence of homoploid pollen, despite a 13% to 15% of embryos experienced a change in ploidy due to heteroploid fertilizations. Thus, our study indicates that pollen precedence operates as a barrier against intercytotype fertilization in P. puberula, promoting the integrity of the sexual cytotype and their co-existence with apomictic individuals.
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Affiliation(s)
- Henar Alonso-Marcos
- Department of Forest Genetics, Austrian Research Centre for Forests, Seckendorf-Gudent-Weg 8, 1131 Vienna, Austria
| | - Karl Hülber
- Department of Conservation Biology, Vegetation Ecology and Landscape Ecology, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Tuuli Myllynen
- Department of Conservation Biology, Vegetation Ecology and Landscape Ecology, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Patricia Pérez Rodríguez
- Department of Conservation Biology, Vegetation Ecology and Landscape Ecology, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Christoph Dobeš
- Department of Forest Genetics, Austrian Research Centre for Forests, Seckendorf-Gudent-Weg 8, 1131 Vienna, Austria
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177
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Blischak PD, Mabry ME, Conant GC, Pires JC. Integrating Networks, Phylogenomics, and Population Genomics for the Study of Polyploidy. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-121415-032302] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Duplication events are regarded as sources of evolutionary novelty, but our understanding of general trends for the long-term trajectory of additional genomic material is still lacking. Organisms with a history of whole genome duplication (WGD) offer a unique opportunity to study potential trends in the context of gene retention and/or loss, gene and network dosage, and changes in gene expression. In this review, we discuss the prevalence of polyploidy across the tree of life, followed by an overview of studies investigating genome evolution and gene expression. We then provide an overview of methods in network biology, phylogenomics, and population genomics that are critical for advancing our understanding of evolution post-WGD, highlighting the need for models that can accommodate polyploids. Finally, we close with a brief note on the importance of random processes in the evolution of polyploids with respect to neutral versus selective forces, ancestral polymorphisms, and the formation of autopolyploids versus allopolyploids.
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Affiliation(s)
- Paul D. Blischak
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Makenzie E. Mabry
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Gavin C. Conant
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
- Current affiliation: Bioinformatics Research Center, Program in Genetics and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - J. Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211-7310, USA
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178
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Yruela I, Contreras-Moreira B, Dunker AK, Niklas KJ. Evolution of Protein Ductility in Duplicated Genes of Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1216. [PMID: 30177944 PMCID: PMC6109787 DOI: 10.3389/fpls.2018.01216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Previous work has shown that ductile/intrinsically disordered proteins (IDPs) and residues (IDRs) are found in all unicellular and multicellular organisms, wherein they are essential for basic cellular functions and complement the function of rigid proteins. In addition, computational studies of diverse phylogenetic lineages have revealed: (1) that protein ductility increases in concert with organismic complexity, and (2) that distributions of IDPs and IDRs along the chromosomes of plant species are non-random and correlate with variations in the rates of the genetic recombination and chromosomal rearrangement. Here, we show that approximately 50% of aligned residues in paralogs across a spectrum of algae, bryophytes, monocots, and eudicots are IDRs and that a high proportion (ca. 60%) are in disordered segments greater than 30 residues. When three types of IDRs are distinguished (i.e., identical, similar and variable IDRs) we find that species with large numbers of chromosome and endoduplicated genes exhibit paralogous sequences with a higher frequency of identical IDRs, whereas species with small chromosomes numbers exhibit paralogous sequences with a higher frequency of similar and variable IDRs. These results are interpreted to indicate that genome duplication events influence the distribution of IDRs along protein sequences and likely favor the presence of identical IDRs (compared to similar IDRs or variable IDRs). We discuss the evolutionary implications of gene duplication events in the context of ductile/disordered residues and segments, their conservation, and their effects on functionality.
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Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology, Joint Unit to CSIC, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology, Joint Unit to CSIC, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
- Fundación Agencia Aragonesa para la Investigación y el Desarrollo (ARAID), Zaragoza, Spain
| | - A. Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Karl J. Niklas
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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179
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Soltis DE, Moore MJ, Sessa EB, Smith SA, Soltis PS. Using and navigating the plant tree of life. AMERICAN JOURNAL OF BOTANY 2018; 105:287-290. [PMID: 29702724 DOI: 10.1002/ajb2.1071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 02/07/2018] [Indexed: 05/24/2023]
Affiliation(s)
- Douglas E Soltis
- Florida Museum of Natural History, University of Florida, P. O. Box 117800, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, P. O. Box 118525, Gainesville, FL, 32611, USA
| | - Michael J Moore
- Department of Biology, Oberlin College, 119 Woodland Street, Oberlin, OH, 44074, USA
| | - Emily B Sessa
- Department of Biology, University of Florida, P. O. Box 118525, Gainesville, FL, 32611, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, MI, 48109, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, P. O. Box 117800, Gainesville, FL, 32611, USA
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