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Barba‐Montoya J, dos Reis M, Schneider H, Donoghue PCJ, Yang Z. Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution. THE NEW PHYTOLOGIST 2018; 218:819-834. [PMID: 29399804 PMCID: PMC6055841 DOI: 10.1111/nph.15011] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 12/20/2017] [Indexed: 05/02/2023]
Abstract
Through the lens of the fossil record, angiosperm diversification precipitated a Cretaceous Terrestrial Revolution (KTR) in which pollinators, herbivores and predators underwent explosive co-diversification. Molecular dating studies imply that early angiosperm evolution is not documented in the fossil record. This mismatch remains controversial. We used a Bayesian molecular dating method to analyse a dataset of 83 genes from 644 taxa and 52 fossil calibrations to explore the effect of different interpretations of the fossil record, molecular clock models, data partitioning, among other factors, on angiosperm divergence time estimation. Controlling for different sources of uncertainty indicates that the timescale of angiosperm diversification is much less certain than previous molecular dating studies have suggested. Discord between molecular clock and purely fossil-based interpretations of angiosperm diversification may be a consequence of false precision on both sides. We reject a post-Jurassic origin of angiosperms, supporting the notion of a cryptic early history of angiosperms, but this history may be as much as 121 Myr, or as little as 23 Myr. These conclusions remain compatible with palaeobotanical evidence and a more general KTR in which major groups of angiosperms diverged later within the Cretaceous, alongside the diversification of pollinators, herbivores and their predators.
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Affiliation(s)
- Jose Barba‐Montoya
- Department of Genetics, Evolution and EnvironmentUniversity College LondonDarwin BuildingGower StreetLondonWC1E 6BTUK
| | - Mario dos Reis
- School of Biological and Chemical SciencesQueen Mary University of LondonMile End RoadLondonE1 4NSUK
| | - Harald Schneider
- Center of Integrative ConservationXishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglunYunnanChina
- Department of BotanyNatural History MuseumCromwell RoadLondonSW7 5BDUK
| | - Philip C. J. Donoghue
- School of Earth SciencesUniversity of BristolLife Sciences BuildingTyndall AvenueBristolBS8 1TQUK
| | - Ziheng Yang
- Department of Genetics, Evolution and EnvironmentUniversity College LondonDarwin BuildingGower StreetLondonWC1E 6BTUK
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Sgorbati S, D'Antraccoli M, Citterio S, Gentili R, Peruzzi L. Was Charles Darwin right in his explanation of the ‘abominable mystery’? ITALIAN BOTANIST 2018. [DOI: 10.3897/ib.5.24699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The site and time of origin of angiosperms are still debated. The co-occurrence of many of the early branching lineages of flowering plants in a region somewhere between Australia and the SW Pacific islands suggests a possible Gondwanan origin of angiosperms. The recent recognition of Zealandia, a 94% submerged continent in the east of Australia, could explain the discrepancy between molecular clocks and fossil records about the age of angiosperms, supporting the old Darwinian hypothesis of a “lost continent” to explain the “abominable mystery” regarding the origin and rapid radiation of flowering plants.
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Sgorbati S, D'Antraccoli M, Citterio S, Gentili R, Peruzzi L. Was Charles Darwin right in his explanation of the ‘abominable mystery’? ITALIAN BOTANIST 2018. [DOI: 10.3897/italianbotanist.5.24699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The site and time of origin of angiosperms are still debated. The co-occurrence of many of the early branching lineages of flowering plants in a region somewhere between Australia and the SW Pacific islands suggests a possible Gondwanan origin of angiosperms. The recent recognition of Zealandia, a 94% submerged continent in the east of Australia, could explain the discrepancy between molecular clocks and fossil records about the age of angiosperms, supporting the old Darwinian hypothesis of a “lost continent” to explain the “abominable mystery” regarding the origin and rapid radiation of flowering plants.
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54
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Jiao Y. Double the Genome, Double the Fun: Genome Duplications in Angiosperms. MOLECULAR PLANT 2018; 11:357-358. [PMID: 29476919 DOI: 10.1016/j.molp.2018.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 02/14/2018] [Accepted: 02/18/2018] [Indexed: 05/14/2023]
Affiliation(s)
- Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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55
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Katz O. Extending the scope of Darwin's 'abominable mystery': integrative approaches to understanding angiosperm origins and species richness. ANNALS OF BOTANY 2018; 121:1-8. [PMID: 29040393 PMCID: PMC5786222 DOI: 10.1093/aob/mcx109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/09/2017] [Indexed: 05/04/2023]
Abstract
Background and aims Angiosperms are the most species-rich group of land plants, but their origins and fast and intense diversification still require an explanation. Scope Extending research scopes can broaden theoretical frameworks and lines of evidence that can lead to solving this 'abominable mystery'. Solutions lie in understanding evolutionary trends across taxa and throughout the Phanerozoic, and integration between hypotheses and ideas that are derived from multiple disciplines. Key Findings Descriptions of evolutionary chronologies should integrate between molecular phylogenies, descriptive palaeontology and palaeoecology. New molecular chronologies open new avenues of research of possible Palaeozoic angiosperm ancestors and how they evolved during as many as 200Myr until the emergence of true angiosperms. The idea that 'biodiversity creates biodiversity' requires evidence from past and present ecologies, with changes in herbivory and resource availability throughout the Phanerozoic appearing to be particularly promising. Conclusions Promoting our understanding of angiosperm origins and diversification in particular, and the evolution of biodiversity in general, requires more profound understanding of the ecological past through integrating taxonomic, temporal and ecological scopes.
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Affiliation(s)
- Ofir Katz
- Department of Geography and Environmental Development, Ben-Gurion University of the Negev, Be’er-Sheva, Israel
- The Dead Sea and Arava Science Center, Mt Massada, Tamar Regional Council, Israel
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56
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Vargas P, Fernández-Mazuecos M, Heleno R. Phylogenetic evidence for a Miocene origin of Mediterranean lineages: species diversity, reproductive traits and geographical isolation. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20 Suppl 1:157-165. [PMID: 28892240 DOI: 10.1111/plb.12626] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/30/2017] [Indexed: 05/27/2023]
Abstract
A review of 27 angiosperm clades (26 genera) of species-rich and species-poor plant groups of the Mediterranean floristic region was performed with phylogenetic and biological trait data. The emergent pattern is that a majority of Mediterranean plant clades split from their sister groups between the Miocene (23-5 Ma) and the Oligocene (34-23 Ma), far earlier than the onset of the Mediterranean climate (ca. 3.2 Ma). In addition, 12 of 14 clades of the species-poor group have stem ages inferred for each clade in the Miocene or older, and six of 13 clades within the species-rich group show divergence of each stem clade within the Oligocene and/or Miocene. High levels of species diversity are related to an ancient (Paleocene-Miocene) origin and also to recent origin (Pliocene-Pleistocene) followed by active speciation and even explosive radiations: some species and lineages diversified over a short period (Aquilegia, Cistus, Dianthus, Linaria sect. Supinae, Reseda). In the species-rich group, key reproductive characters were found to be significantly more important for species recognition than key vegetative characters in eight clades, but no difference was found in four clades, and vegetative characters were predominant in one clade (Saxifraga). Geographical differentiation is proposed as predominant over divergence driven by pollination ecology. We hypothesise an evolutionary process in which lineages adapted to pre-Mediterranean (pre-Pliocene) conditions in relatively small, xeric areas became strongly competitive and expanded as the Mediterranean climate became dominant (Pliocene-Quaternary) across the Mediterranean Basin.
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Affiliation(s)
- P Vargas
- Real Jardín Botánico de Madrid (RJB-CSIC), Madrid, Spain
| | | | - R Heleno
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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57
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Baluška F, Mancuso S. Plant Cognition and Behavior: From Environmental Awareness to Synaptic Circuits Navigating Root Apices. MEMORY AND LEARNING IN PLANTS 2018. [DOI: 10.1007/978-3-319-75596-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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58
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Ruiz-Martín J, Santos-Gally R, Escudero M, Midgley JJ, Pérez-Barrales R, Arroyo J. Style polymorphism in Linum (Linaceae): a case of Mediterranean parallel evolution? PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20 Suppl 1:100-111. [PMID: 29164751 DOI: 10.1111/plb.12670] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 11/16/2017] [Indexed: 06/07/2023]
Abstract
Heterostyly is a sex polymorphism that has challenged evolutionary biologists ever since Darwin. One of the lineages where heterostyly and related stylar conditions appear more frequently is Linum (Linaceae). This group is particularly suitable for testing competing hypotheses about ancestral and transitional stages on the evolutionary building up of heterostyly. We generated a phylogeny of Linum based on extensive sampling and plastid and nuclear DNA sequences, and used it to trace the evolution of character states of style polymorphism. We also revised available data on pollination, breeding systems, and polyploidy to analyse their associations. Our results supported former phylogenetic hypotheses: the paraphyly of Linum and the non-monophyly of current taxonomic sections. Heterostyly was common in the genus, but appeared concentrated in the Mediterranean Basin and the South African Cape. Ancestral character state reconstruction failed to determine a unique state as the most probable condition for style polymorphism in the genus. In contrast, approach herkogamy was resolved as ancestral state in some clades, giving support to recent hypotheses. Some traits putatively related to heterostyly, such as life history and polyploidy, did show marginal or non-significant phylogenetic correlation, respectively. Although pollinator data are limited, we suggest that beeflies are associated with specific cases of heterostyly. The consistent association between style polymorphism and heteromorphic incompatibility points to ecological factors as drivers of the multiple evolution of style polymorphism in Linum. Albeit based on limited evidence, we hypothesised that specialised pollinators and lack of mating opportunities drive evolution of style polymorphism and loss of the polymorphism, respectively.
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Affiliation(s)
- J Ruiz-Martín
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - R Santos-Gally
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - M Escudero
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - J J Midgley
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - R Pérez-Barrales
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - J Arroyo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
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Chanderbali AS, Berger BA, Howarth DG, Soltis DE, Soltis PS. Evolution of floral diversity: genomics, genes and gamma. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0509. [PMID: 27994132 DOI: 10.1098/rstb.2015.0509] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 11/12/2022] Open
Abstract
A salient feature of flowering plant diversification is the emergence of a novel suite of floral features coinciding with the origin of the most species-rich lineage, Pentapetalae. Advances in phylogenetics, developmental genetics and genomics, including new analyses presented here, are helping to reconstruct the specific evolutionary steps involved in the evolution of this clade. The enormous floral diversity among Pentapetalae appears to be built on a highly conserved ground plan of five-parted (pentamerous) flowers with whorled phyllotaxis. By contrast, lability in the number and arrangement of component parts of the flower characterize the early-diverging eudicot lineages subtending Pentapetalae. The diversification of Pentapetalae also coincides closely with ancient hexaploidy, referred to as the gamma whole-genome triplication, for which the phylogenetic timing, mechanistic details and molecular evolutionary consequences are as yet not fully resolved. Transcription factors regulating floral development often persist in duplicate or triplicate in gamma-derived genomes, and both individual genes and whole transcriptional programmes exhibit a shift from broadly overlapping to tightly defined expression domains in Pentapetalae flowers. Investigations of these changes associated with the origin of Pentapetalae can lead to a more comprehensive understanding of what is arguably one of the most important evolutionary diversification events within terrestrial plants.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Andre S Chanderbali
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.,Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Brent A Berger
- Department of Biological Sciences, St John's University, Queens, NY 11439, USA
| | - Dianella G Howarth
- Department of Biological Sciences, St John's University, Queens, NY 11439, USA
| | - Douglas 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
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA .,Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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60
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Theißen G, Melzer R, Rümpler F. MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution. Development 2017; 143:3259-71. [PMID: 27624831 DOI: 10.1242/dev.134080] [Citation(s) in RCA: 247] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The floral quartet model of floral organ specification poses that different tetramers of MIKC-type MADS-domain transcription factors control gene expression and hence the identity of floral organs during development. Here, we provide a brief history of the floral quartet model and review several lines of recent evidence that support the model. We also describe how the model has been used in contemporary developmental and evolutionary biology to shed light on enigmatic topics such as the origin of land and flowering plants. Finally, we suggest a novel hypothesis describing how floral quartet-like complexes may interact with chromatin during target gene activation and repression.
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Affiliation(s)
- Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Florian Rümpler
- Department of Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
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61
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Roy R, Schmitt AJ, Thomas JB, Carter CJ. Review: Nectar biology: From molecules to ecosystems. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 262:148-164. [PMID: 28716410 DOI: 10.1016/j.plantsci.2017.04.012] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 05/06/2023]
Abstract
Plants attract mutualistic animals by offering a reward of nectar. Specifically, floral nectar (FN) is produced to attract pollinators, whereas extrafloral nectar (EFN) mediates indirect defenses through the attraction of mutualist predatory insects to limit herbivory. Nearly 90% of all plant species, including 75% of domesticated crops, benefit from animal-mediated pollination, which is largely facilitated by FN. Moreover, EFN represents one of the few defense mechanisms for which stable effects on plant health and fitness have been demonstrated in multiple systems, and thus plays a crucial role in the resistance phenotype of plants producing it. In spite of its central role in plant-animal interactions, the molecular events involved in the development of both floral and extrafloral nectaries (the glands that produce nectar), as well as the synthesis and secretion of the nectar itself, have been poorly understood until recently. This review will cover major recent developments in the understanding of (1) nectar chemistry and its role in plant-mutualist interactions, (2) the structure and development of nectaries, (3) nectar production, and (4) its regulation by phytohormones.
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Affiliation(s)
- Rahul Roy
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Anthony J Schmitt
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jason B Thomas
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Clay J Carter
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA.
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63
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Freeling M. Picking up the Ball at the K/Pg Boundary: The Distribution of Ancient Polyploidies in the Plant Phylogenetic Tree as a Spandrel of Asexuality with Occasional Sex. THE PLANT CELL 2017; 29:202-206. [PMID: 28213362 PMCID: PMC5354197 DOI: 10.1105/tpc.16.00836] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/05/2017] [Accepted: 02/15/2017] [Indexed: 05/23/2023]
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64
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Chen F, Liu X, Yu C, Chen Y, Tang H, Zhang L. Water lilies as emerging models for Darwin's abominable mystery. HORTICULTURE RESEARCH 2017; 4:17051. [PMID: 28979789 PMCID: PMC5626932 DOI: 10.1038/hortres.2017.51] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 06/30/2017] [Accepted: 07/26/2017] [Indexed: 05/02/2023]
Abstract
Water lilies are not only highly favored aquatic ornamental plants with cultural and economic importance but they also occupy a critical evolutionary space that is crucial for understanding the origin and early evolutionary trajectory of flowering plants. The birth and rapid radiation of flowering plants has interested many scientists and was considered 'an abominable mystery' by Charles Darwin. In searching for the angiosperm evolutionary origin and its underlying mechanisms, the genome of Amborella has shed some light on the molecular features of one of the basal angiosperm lineages; however, little is known regarding the genetics and genomics of another basal angiosperm lineage, namely, the water lily. In this study, we reviewed current molecular research and note that water lily research has entered the genomic era. We propose that the genome of the water lily is critical for studying the contentious relationship of basal angiosperms and Darwin's 'abominable mystery'. Four pantropical water lilies, especially the recently sequenced Nymphaea colorata, have characteristics such as small size, rapid growth rate and numerous seeds and can act as the best model for understanding the origin of angiosperms. The water lily genome is also valuable for revealing the genetics of ornamental traits and will largely accelerate the molecular breeding of water lilies.
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Affiliation(s)
- Fei Chen
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xing Liu
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuiwei Yu
- Zhejiang Humanities Landscape Co., LTD, Hangzhou 310030, China
| | - Yuchu Chen
- Zhejiang Humanities Landscape Co., LTD, Hangzhou 310030, China
| | - Haibao Tang
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
- )
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65
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Liu YY, Yang KZ, Wei XX, Wang XQ. Revisiting the phosphatidylethanolamine-binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in gymnosperms and sheds new light on functional evolution. THE NEW PHYTOLOGIST 2016; 212:730-744. [PMID: 27375201 DOI: 10.1111/nph.14066] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/16/2016] [Indexed: 05/19/2023]
Abstract
Angiosperms and gymnosperms are two major groups of extant seed plants. It has been suggested that gymnosperms lack FLOWERING LOCUS T (FT), a key integrator at the core of flowering pathways in angiosperms. Taking advantage of newly released gymnosperm genomes, we revisited the evolutionary history of the plant phosphatidylethanolamine-binding protein (PEBP) gene family through phylogenetic reconstruction. Expression patterns in three gymnosperm taxa and heterologous expression in Arabidopsis were studied to investigate the functions of gymnosperm FT-like and TERMINAL FLOWER 1 (TFL1)-like genes. Phylogenetic reconstruction suggests that an ancient gene duplication predating the divergence of seed plants gave rise to the FT and TFL1 genes. Expression patterns indicate that gymnosperm TFL1-like genes play a role in the reproductive development process, while GymFT1 and GymFT2, the FT-like genes resulting from a duplication event in the common ancestor of gymnosperms, function in both growth rhythm and sexual development pathways. When expressed in Arabidopsis, both spruce FT-like and TFL1-like genes repressed flowering. Our study demonstrates that gymnosperms do have FT-like and TFL1-like genes. Frequent gene and genome duplications contributed significantly to the expansion of the plant PEBP gene family. The expression patterns of gymnosperm PEBP genes provide novel insight into the functional evolution of this gene family.
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Affiliation(s)
- Yan-Yan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Ke-Zhen Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiao-Xin Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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66
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Beekman M, Nieuwenhuis B, Ortiz-Barrientos D, Evans JP. Sexual selection in hermaphrodites, sperm and broadcast spawners, plants and fungi. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150541. [PMID: 27619704 PMCID: PMC5031625 DOI: 10.1098/rstb.2015.0541] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/12/2022] Open
Abstract
Darwin was the first to recognize that sexual selection is a strong evolutionary force. Exaggerated traits allow same-sex individuals to compete over access to mates and provide a mechanism by which mates are selected. It is relatively easy to appreciate how inter- and intrasexual selection work in organisms with the sensory capabilities to perceive physical or behavioural traits that signal mate quality or mate compatibility, and to assess the relative quality of competitors. It is therefore not surprising that most studies of sexual selection have focused on animals with separate sexes and obvious adaptations that function in the context of reproductive competition. Yet, many sexual organisms are both male and female at the same time, often lack sexual dimorphism and never come into direct contact at mating. How does sexual selection act in such species, and what can we learn from them? Here, we address these questions by exploring the potential for sexual selection in simultaneous hermaphrodites, sperm- and broadcast spawners, plants and fungi. Our review reveals a range of mechanisms of sexual selection, operating primarily after gametes have been released, which are common in many of these groups and also quite possibly in more familiar (internally fertilizing and sexually dimorphic) organisms.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Madeleine Beekman
- School of Life and Environmental Sciences, University of Sydney, 2006 New South Wales, Australia
| | - Bart Nieuwenhuis
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | | | - Jonathan P Evans
- Centre for Evolutionary Biology, School of Animal Biology, University of Western Australia, 6009 Western Australia, Australia
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67
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Frank SA. Puzzles in modern biology. II. Language, cancer and the recursive processes of evolutionary innovation. F1000Res 2016; 5:2289. [PMID: 28184282 PMCID: PMC5288677 DOI: 10.12688/f1000research.9568.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/06/2016] [Indexed: 11/20/2022] Open
Abstract
Human language emerged abruptly. Diverse body forms evolved suddenly. Seed-bearing plants spread rapidly. How do complex evolutionary innovations arise so quickly? Resolving alternative claims remains difficult. The great events of the past happened a long time ago. Cancer provides a model to study evolutionary innovation. A tumor must evolve many novel traits to become an aggressive cancer. I use what we know or could study about cancer to describe the key processes of innovation. In general, evolutionary systems form a hierarchy of recursive processes. Those recursive processes determine the rates at which innovations are generated, spread and transmitted. I relate the recursive processes to abrupt evolutionary innovation.
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Affiliation(s)
- Steven A. Frank
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, 92697–2525, USA
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68
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O'Meara BC, Beaulieu JM. Past, future, and present of state-dependent models of diversification. AMERICAN JOURNAL OF BOTANY 2016; 103:792-795. [PMID: 27208347 DOI: 10.3732/ajb.1600012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 03/25/2016] [Indexed: 06/05/2023]
Affiliation(s)
- Brian C O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996-1610 USA
| | - Jeremy M Beaulieu
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996-1610 USA
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Considine MJ, Considine JA. On the language and physiology of dormancy and quiescence in plants. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3189-203. [PMID: 27053719 DOI: 10.1093/jxb/erw138] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The language of dormancy is rich and poetic, as researchers spanning disciplines and decades have attempted to understand the spell that entranced 'Sleeping Beauty', and how she was gently awoken. The misleading use of 'dormancy', applied to annual axillary buds, for example, has confounded progress. Language is increasingly important as genetic and genomic approaches become more accessible to species of agricultural and ecological importance. Here we examine how terminology has been applied to different eco-physiological states in plants, and with pertinent reference to quiescent states described in other domains of life, in order to place plant quiescence and dormancy in a more complete context than previously described. The physiological consensus defines latency or quiescence as opportunistic avoidance states, where growth resumes in favourable conditions. In contrast, the dormant state in higher plants is entrained in the life history of the organism. Competence to resume growth requires quantitative and specific conditioning. This definition applies only to the embryo of seeds and specialized meristems in higher plants; however, mechanistic control of dormancy extends to mobile signals from peripheral tissues and organs, such as the endosperm of seed or subtending leaf of buds. The distinction between dormancy, quiescence, and stress-hardiness remains poorly delineated, most particularly in buds of winter perennials, which comprise multiple meristems of differing organogenic states. Studies in seeds have shown that dormancy is not a monogenic trait, and limited study has thus far failed to canalize dormancy as seen in seeds and buds. We argue that a common language, based on physiology, is central to enable further dissection of the quiescent and dormant states in plants. We direct the topic largely to woody species showing a single cycle of growth and reproduction per year, as these bear the majority of global timber, fruit, and nut production, as well being of great ecological value. However, for context and hypotheses, we draw on knowledge from annuals and other specialized plant conditions, from a perspective of the major physical, metabolic, and molecular cues that regulate cellular activity.
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Affiliation(s)
- Michael J Considine
- School of Plant Biology, and The Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia Department of Agriculture and Food Western Australia, South Perth, WA 6151 Australia Centre for Plant Sciences, University of Leeds, Leeds, Yorkshire LS2 9JT, UK
| | - John A Considine
- School of Plant Biology, and The Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
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Niu S, Yuan H, Sun X, Porth I, Li Y, El-Kassaby YA, Li W. A transcriptomics investigation into pine reproductive organ development. THE NEW PHYTOLOGIST 2016; 209:1278-1289. [PMID: 26406997 DOI: 10.1111/nph.13680] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/20/2015] [Indexed: 06/05/2023]
Abstract
The development of reproductive structures in gymnosperms is still poorly studied because of a lack of genomic information and useful genetic tools. The hermaphroditic reproductive structure derived from unisexual gymnosperms is an even less studied aspect of seed plant evolution. To extend our understanding of the molecular mechanism of hermaphroditism and the determination of sexual identity of conifer reproductive structures in general, unisexual and bisexual cones from Pinus tabuliformis were profiled for gene expression using 60K microarrays. Expression patterns of genes during progression of sexual cone development were analysed using RNA-seq. The results showed that, overall, the transcriptomes of male structures in bisexual cones were more similar to those of female cones. However, the expression of several MADS-box genes in the bisexual cones was similar to that of male cones at the more juvenile developmental stage, while despite these expression shifts, male structures of bisexual cones and normal male cones were histologically indistinguishable and cone development was continuous. This study represents a starting point for in-depth analysis of the molecular regulation of cone development and also the origin of hermaphroditism in pine.
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Affiliation(s)
- Shihui Niu
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of biological sciences and technology, Beijing Forestry University, Beijing, 100083, China
| | - Huwei Yuan
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of biological sciences and technology, Beijing Forestry University, Beijing, 100083, China
| | - Xinrui Sun
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of biological sciences and technology, Beijing Forestry University, Beijing, 100083, China
| | - Ilga Porth
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Département des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et de Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Yue Li
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of biological sciences and technology, Beijing Forestry University, Beijing, 100083, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Wei Li
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of biological sciences and technology, Beijing Forestry University, Beijing, 100083, China
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71
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Nicholson DB, Ross AJ, Mayhew PJ. Fossil evidence for key innovations in the evolution of insect diversity. Proc Biol Sci 2015; 281:rspb.2014.1823. [PMID: 25165766 DOI: 10.1098/rspb.2014.1823] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Explaining the taxonomic richness of the insects, comprising over half of all described species, is a major challenge in evolutionary biology. Previously, several evolutionary novelties (key innovations) have been posited to contribute to that richness, including the insect bauplan, wings, wing folding and complete metamorphosis, but evidence over their relative importance and modes of action is sparse and equivocal. Here, a new dataset on the first and last occurrences of fossil hexapod (insects and close relatives) families is used to show that basal families of winged insects (Palaeoptera, e.g. dragonflies) show higher origination and extinction rates in the fossil record than basal wingless groups (Apterygota, e.g. silverfish). Origination and extinction rates were maintained at levels similar to Palaeoptera in the more derived Polyneoptera (e.g. cockroaches) and Paraneoptera (e.g. true bugs), but extinction rates subsequently reduced in the very rich group of insects with complete metamorphosis (Holometabola, e.g. beetles). Holometabola show evidence of a recent slow-down in their high net diversification rate, whereas other winged taxa continue to diversify at constant but low rates. These data suggest that wings and complete metamorphosis have had the most effect on family-level insect macroevolution, and point to specific mechanisms by which they have influenced insect diversity through time.
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Affiliation(s)
- David B Nicholson
- Department of Biology, University of York, York YO10 5YW, UK Department of Natural Sciences, National Museum of Scotland, Chambers Street, Edinburgh, Midlothian EH1 1JF, UK Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Andrew J Ross
- Department of Natural Sciences, National Museum of Scotland, Chambers Street, Edinburgh, Midlothian EH1 1JF, UK
| | - Peter J Mayhew
- Department of Biology, University of York, York YO10 5YW, UK
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72
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Xiao B, Cui LQ, Chen TM, Lian B. Stochastic effects in adaptive reconstruction of body damage: implied the creativity of natural selection. J Cell Mol Med 2015; 19:2521-9. [PMID: 26153081 PMCID: PMC4627558 DOI: 10.1111/jcmm.12647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/02/2015] [Indexed: 12/28/2022] Open
Abstract
After an injury occurs, mechanical/biochemical loads on muscles influence the composition and structure of recovering muscles; this effect likely occurs in other tissues, cells and biological molecules as well owing to the similarity, interassociation and interaction among biochemical reactions and molecules. The 'damage and reconstruction' model provides an explanation for how an ideal cytoarchitecture is created by reducing components not suitable for bearing loads; in this model, adaptive changes are induced by promoting the stochasticity of biochemical reactions. Biochemical and mechanical loads can direct the stochasticity of biochemical reactions, which can in turn induce cellular changes. Thus, mechanical and biochemical loads, under natural selection pressure, modify the direction of cell- and tissue-level changes and guide the formation of new structures and traits, thereby influencing microevolution. In summary, the 'damage and reconstruction' model accounts for the role of natural selection in the formation of new organisms, helps explain punctuated equilibrium, and illustrates how macroevolution arises from microevolution.
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Affiliation(s)
- Bo Xiao
- Key Laboratory for Ecology and Pollution Control of Coastal Wetlands, School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Li-Qiang Cui
- Key Laboratory for Ecology and Pollution Control of Coastal Wetlands, School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Tian-Ming Chen
- Key Laboratory for Ecology and Pollution Control of Coastal Wetlands, School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Bin Lian
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Key Lab for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
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73
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Sanderson MJ. Back to the past: a new take on the timing of flowering plant diversification. THE NEW PHYTOLOGIST 2015; 207:257-259. [PMID: 26096201 DOI: 10.1111/nph.13462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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74
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Magallón S, Gómez-Acevedo S, Sánchez-Reyes LL, Hernández-Hernández T. A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. THE NEW PHYTOLOGIST 2015; 207:437-453. [PMID: 25615647 DOI: 10.1111/nph.13264] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/21/2014] [Indexed: 05/03/2023]
Abstract
The establishment of modern terrestrial life is indissociable from angiosperm evolution. While available molecular clock estimates of angiosperm age range from the Paleozoic to the Late Cretaceous, the fossil record is consistent with angiosperm diversification in the Early Cretaceous. The time-frame of angiosperm evolution is here estimated using a sample representing 87% of families and sequences of five plastid and nuclear markers, implementing penalized likelihood and Bayesian relaxed clocks. A literature-based review of the palaeontological record yielded calibrations for 137 phylogenetic nodes. The angiosperm crown age was bound within a confidence interval calculated with a method that considers the fossil record of the group. An Early Cretaceous crown angiosperm age was estimated with high confidence. Magnoliidae, Monocotyledoneae and Eudicotyledoneae diversified synchronously 135-130 million yr ago (Ma); Pentapetalae is 126-121 Ma; and Rosidae (123-115 Ma) preceded Asteridae (119-110 Ma). Family stem ages are continuously distributed between c. 140 and 20 Ma. This time-frame documents an early phylogenetic proliferation that led to the establishment of major angiosperm lineages, and the origin of over half of extant families, in the Cretaceous. While substantial amounts of angiosperm morphological and functional diversity have deep evolutionary roots, extant species richness was probably acquired later.
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Affiliation(s)
- Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sandra Gómez-Acevedo
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luna L Sánchez-Reyes
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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75
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Jensen MK, Vogt JK, Bressendorff S, Seguin-Orlando A, Petersen M, Sicheritz-Pontén T, Mundy J. Transcriptome and genome size analysis of the Venus flytrap. PLoS One 2015; 10:e0123887. [PMID: 25886597 PMCID: PMC4401711 DOI: 10.1371/journal.pone.0123887] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/23/2015] [Indexed: 11/30/2022] Open
Abstract
The insectivorous Venus flytrap (Dionaea muscipula) is renowned from Darwin’s studies of plant carnivory and the origins of species. To provide tools to analyze the evolution and functional genomics of D. muscipula, we sequenced a normalized cDNA library synthesized from mRNA isolated from D. muscipula flowers and traps. Using the Oases transcriptome assembler 79,165,657 quality trimmed reads were assembled into 80,806 cDNA contigs, with an average length of 679 bp and an N50 length of 1,051 bp. A total of 17,047 unique proteins were identified, and assigned to Gene Ontology (GO) and classified into functional categories. A total of 15,547 full-length cDNA sequences were identified, from which open reading frames were detected in 10,941. Comparative GO analyses revealed that D. muscipula is highly represented in molecular functions related to catalytic, antioxidant, and electron carrier activities. Also, using a single copy sequence PCR-based method, we estimated that the genome size of D. muscipula is approx. 3 Gb. Our genome size estimate and transcriptome analyses will contribute to future research on this fascinating, monotypic species and its heterotrophic adaptations.
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Affiliation(s)
| | - Josef Korbinian Vogt
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Morten Petersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail: (TS); (JM)
| | - John Mundy
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (TS); (JM)
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76
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Silva CS, Puranik S, Round A, Brennich M, Jourdain A, Parcy F, Hugouvieux V, Zubieta C. Evolution of the Plant Reproduction Master Regulators LFY and the MADS Transcription Factors: The Role of Protein Structure in the Evolutionary Development of the Flower. FRONTIERS IN PLANT SCIENCE 2015; 6:1193. [PMID: 26779227 PMCID: PMC4701952 DOI: 10.3389/fpls.2015.01193] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/11/2015] [Indexed: 05/21/2023]
Abstract
Understanding the evolutionary leap from non-flowering (gymnosperms) to flowering (angiosperms) plants and the origin and vast diversification of the floral form has been one of the focuses of plant evolutionary developmental biology. The evolving diversity and increasing complexity of organisms is often due to relatively small changes in genes that direct development. These "developmental control genes" and the transcription factors (TFs) they encode, are at the origin of most morphological changes. TFs such as LEAFY (LFY) and the MADS-domain TFs act as central regulators in key developmental processes of plant reproduction including the floral transition in angiosperms and the specification of the male and female organs in both gymnosperms and angiosperms. In addition to advances in genome wide profiling and forward and reverse genetic screening, structural techniques are becoming important tools in unraveling TF function by providing atomic and molecular level information that was lacking in purely genetic approaches. Here, we summarize previous structural work and present additional biophysical and biochemical studies of the key master regulators of plant reproduction - LEAFY and the MADS-domain TFs SEPALLATA3 and AGAMOUS. We discuss the impact of structural biology on our understanding of the complex evolutionary process leading to the development of the bisexual flower.
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Affiliation(s)
- Catarina S. Silva
- CNRS, Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, University of Grenoble AlpesGrenoble, France
- Commissariat à l´Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Laboratoire de Physiologie Cellulaire & Végétale, Institut de Recherches en Technologies et Sciences pour le VivantGrenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, Institut National de la Recherche AgronomiqueGrenoble, France
| | - Sriharsha Puranik
- European Synchrotron Radiation Facility, Structural Biology GroupGrenoble, France
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble OutstationGrenoble, France
- Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRSGrenoble, France
- Faculty of Natural Sciences, Keele UniversityKeele, UK
| | - Martha Brennich
- European Synchrotron Radiation Facility, Structural Biology GroupGrenoble, France
| | - Agnès Jourdain
- CNRS, Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, University of Grenoble AlpesGrenoble, France
- Commissariat à l´Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Laboratoire de Physiologie Cellulaire & Végétale, Institut de Recherches en Technologies et Sciences pour le VivantGrenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, Institut National de la Recherche AgronomiqueGrenoble, France
| | - François Parcy
- CNRS, Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, University of Grenoble AlpesGrenoble, France
- Commissariat à l´Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Laboratoire de Physiologie Cellulaire & Végétale, Institut de Recherches en Technologies et Sciences pour le VivantGrenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, Institut National de la Recherche AgronomiqueGrenoble, France
| | - Veronique Hugouvieux
- CNRS, Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, University of Grenoble AlpesGrenoble, France
- Commissariat à l´Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Laboratoire de Physiologie Cellulaire & Végétale, Institut de Recherches en Technologies et Sciences pour le VivantGrenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, Institut National de la Recherche AgronomiqueGrenoble, France
| | - Chloe Zubieta
- CNRS, Laboratoire de Physiologie Cellulaire & Végétale, UMR 5168Grenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, University of Grenoble AlpesGrenoble, France
- Commissariat à l´Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Laboratoire de Physiologie Cellulaire & Végétale, Institut de Recherches en Technologies et Sciences pour le VivantGrenoble, France
- Laboratoire de Physiologie Cellulaire & Végétale, Institut National de la Recherche AgronomiqueGrenoble, France
- *Correspondence: Chloe Zubieta,
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77
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Moubayidin L, Ostergaard L. Dynamic control of auxin distribution imposes a bilateral-to-radial symmetry switch during gynoecium development. Curr Biol 2014; 24:2743-8. [PMID: 25455035 PMCID: PMC4245708 DOI: 10.1016/j.cub.2014.09.080] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 09/29/2014] [Accepted: 09/29/2014] [Indexed: 01/28/2023]
Abstract
Symmetry formation is a remarkable feature of biological life forms associated with evolutionary advantages and often with great beauty. Several examples exist in which organisms undergo a transition in symmetry during development [1, 2, 3, 4]. Such transitions are almost exclusively in the direction from radial to bilateral symmetry [5, 6, 7, 8]. Here, we describe the dynamics of symmetry establishment during development of the Arabidopsis gynoecium. We show that the apical style region undergoes an unusual transition from a bilaterally symmetric stage ingrained in the gynoecium due to its evolutionary origin to a radially symmetric structure. We also identify two transcription factors, INDEHISCENT [9] and SPATULA [10], that are both necessary and sufficient for the radialization process. Our work furthermore shows that these two transcription factors control style symmetry by directly regulating auxin distribution. Establishment of specific auxin-signaling foci and the subsequent development of a radially symmetric auxin ring at the style are required for the transition to radial symmetry, because genetic manipulations of auxin transport can either cause loss of radialization in a wild-type background or rescue mutants with radialization defects. Whereas many examples have described how auxin provides polarity and specific identity to cells in a range of developmental contexts, our data presented here demonstrate that auxin can also be recruited to impose uniform identity to a group of cells that are otherwise differentially programmed. Apex of the Arabidopsis gynoecium undergoes a bilateral-to-radial symmetry transition Transcription factors IND/SPT are necessary and sufficient for organ radialization IND and SPT regulate auxin transport to achieve radial symmetry Spatiotemporal auxin dynamics control growth and symmetry of the gynoecium
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Affiliation(s)
- Laila Moubayidin
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lars Ostergaard
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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78
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Scutt CP, Vandenbussche M. Current trends and future directions in flower development research. ANNALS OF BOTANY 2014; 114:1399-406. [PMID: 25335868 PMCID: PMC4204790 DOI: 10.1093/aob/mcu224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 09/24/2014] [Indexed: 05/05/2023]
Abstract
Flowers, the reproductive structures of the approximately 400 000 extant species of flowering plants, exist in a tremendous range of forms and sizes, mainly due to developmental differences involving the number, arrangement, size and form of the floral organs of which they consist. However, this tremendous diversity is underpinned by a surprisingly robust basic floral structure in which a central group of carpels forms on an axis of determinate growth, almost invariably surrounded by two successive zones containing stamens and perianth organs, respectively. Over the last 25 years, remarkable progress has been achieved in describing the molecular mechanisms that control almost all aspects of flower development, from the phase change that initiates flowering to the final production of fruits and seeds. However, this work has been performed almost exclusively in a small number of eudicot model species, chief among which is Arabidopsis thaliana. Studies of flower development must now be extended to a much wider phylogenetic range of flowering plants and, indeed, to their closest living relatives, the gymnosperms. Studies of further, more wide-ranging models should provide insights that, for various reasons, cannot be obtained by studying the major existing models alone. The use of further models should also help to explain how the first flowering plants evolved from an unknown, although presumably gymnosperm-like ancestor, and rapidly diversified to become the largest major plant group and to dominate the terrestrial flora. The benefits for society of a thorough understanding of flower development are self-evident, as human life depends to a large extent on flowering plants and on the fruits and seeds they produce. In this preface to the Special Issue, we introduce eleven articles on flower development, representing work in both established and further models, including gymnosperms. We also present some of our own views on current trends and future directions of the flower development field.
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Affiliation(s)
- Charlie P Scutt
- Laboratoire de Reproduction et Développement des Plantes, (Unité mixte de recherche 5667: CNRS-INRA-Université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Michiel Vandenbussche
- Laboratoire de Reproduction et Développement des Plantes, (Unité mixte de recherche 5667: CNRS-INRA-Université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
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79
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Zeng L, Zhang Q, Sun R, Kong H, Zhang N, Ma H. Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nat Commun 2014; 5:4956. [PMID: 25249442 PMCID: PMC4200517 DOI: 10.1038/ncomms5956] [Citation(s) in RCA: 236] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 08/11/2014] [Indexed: 11/08/2022] Open
Abstract
Angiosperms are the most successful plants and support human livelihood and ecosystems. Angiosperm phylogeny is the foundation of studies of gene function and phenotypic evolution, divergence time estimation and biogeography. The relationship of the five divergent groups of the Mesangiospermae (~99.95% of extant angiosperms) remains uncertain, with multiple hypotheses reported in the literature. Here transcriptome data sets are obtained from 26 species lacking sequenced genomes, representing each of the five groups: eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae. Phylogenetic analyses using 59 carefully selected low-copy nuclear genes resulted in highly supported relationships: sisterhood of eudicots and a clade containing Chloranthaceae and Ceratophyllaceae, with magnoliids being the next sister group, followed by monocots. Our topology allows a re-examination of the evolutionary patterns of 110 morphological characters. The molecular clock estimates of Mesangiospermae diversification during the late to middle Jurassic correspond well to the origins of some insects, which may have been a factor facilitating early angiosperm radiation.
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Affiliation(s)
- Liping Zeng
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 220 Handan Road, Yangpu District, Shanghai 200433, China
| | - Qiang Zhang
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Guilin 541006, China
| | - Renran Sun
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 220 Handan Road, Yangpu District, Shanghai 200433, China
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ning Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 220 Handan Road, Yangpu District, Shanghai 200433, China
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington DC 20560, USA
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 220 Handan Road, Yangpu District, Shanghai 200433, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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80
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Abstract
A new study shows that birds plucking anthers of the Melastome, Axinaea, demonstrate a novel bird pollination mechanism. Each stamen of Axinaea offers a nutrient-rich, berry-like food body that, when bitten, releases a puff of pollen allowing transfer to stigmas by wind or the pollen-dusted bird.
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Affiliation(s)
- Joan Edwards
- Biology Department, Thompson Biology Lab, Williams College, Williamstown, MA, USA.
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81
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Moghe GD, Shiu SH. The causes and molecular consequences of polyploidy in flowering plants. Ann N Y Acad Sci 2014; 1320:16-34. [PMID: 24903334 DOI: 10.1111/nyas.12466] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Polyploidy is an important force shaping plant genomes. All flowering plants are descendants of an ancestral polyploid species, and up to 70% of extant vascular plant species are believed to be recent polyploids. Over the past century, a significant body of knowledge has accumulated regarding the prevalence and ecology of polyploid plants. In this review, we summarize our current understanding of the causes and molecular consequences of polyploidization in angiosperms. We also provide a discussion on the relationships between polyploidy and adaptation and suggest areas where further research may provide a better understanding of polyploidy.
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82
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Lin IW, Sosso D, Chen LQ, Gase K, Kim SG, Kessler D, Klinkenberg PM, Gorder MK, Hou BH, Qu XQ, Carter CJ, Baldwin IT, Frommer WB. Nectar secretion requires sucrose phosphate synthases and the sugar transporter SWEET9. Nature 2014; 508:546-9. [PMID: 24670640 DOI: 10.1038/nature13082] [Citation(s) in RCA: 244] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 01/27/2014] [Indexed: 01/09/2023]
Abstract
Angiosperms developed floral nectaries that reward pollinating insects. Although nectar function and composition have been characterized, the mechanism of nectar secretion has remained unclear. Here we identify SWEET9 as a nectary-specific sugar transporter in three eudicot species: Arabidopsis thaliana, Brassica rapa (extrastaminal nectaries) and Nicotiana attenuata (gynoecial nectaries). We show that SWEET9 is essential for nectar production and can function as an efflux transporter. We also show that sucrose phosphate synthase genes, encoding key enzymes for sucrose biosynthesis, are highly expressed in nectaries and that their expression is also essential for nectar secretion. Together these data are consistent with a model in which sucrose is synthesized in the nectary parenchyma and subsequently secreted into the extracellular space via SWEET9, where sucrose is hydrolysed by an apoplasmic invertase to produce a mixture of sucrose, glucose and fructose. The recruitment of SWEET9 for sucrose export may have been a key innovation, and could have coincided with the evolution of core eudicots and contributed to the evolution of nectar secretion to reward pollinators.
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Affiliation(s)
- I Winnie Lin
- 1] Department of Biology, Stanford University, Stanford, California 94305, USA [2] Carnegie Institution for Science, 260 Panama Street, Stanford, California 94305, USA
| | - Davide Sosso
- 1] Department of Biology, Stanford University, Stanford, California 94305, USA [2] Carnegie Institution for Science, 260 Panama Street, Stanford, California 94305, USA
| | - Li-Qing Chen
- Carnegie Institution for Science, 260 Panama Street, Stanford, California 94305, USA
| | - Klaus Gase
- Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Sang-Gyu Kim
- Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Danny Kessler
- Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Peter M Klinkenberg
- 1] Department of Biology, University of Minnesota Duluth, Duluth, Minnesota 55812, USA [2] Department of Plant Biology, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Molly K Gorder
- 1] Department of Biology, University of Minnesota Duluth, Duluth, Minnesota 55812, USA [2] Department of Plant Biology, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Bi-Huei Hou
- Carnegie Institution for Science, 260 Panama Street, Stanford, California 94305, USA
| | - Xiao-Qing Qu
- 1] Carnegie Institution for Science, 260 Panama Street, Stanford, California 94305, USA [2] Key Laboratory of Plant and Soil Interactions, College of Resources and Environmental Sciences, China Agricultural University, 100193 Beijing, China
| | - Clay J Carter
- 1] Department of Biology, University of Minnesota Duluth, Duluth, Minnesota 55812, USA [2] Department of Plant Biology, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Ian T Baldwin
- Max Planck Institute for Chemical Ecology, Jena D-07745, Germany
| | - Wolf B Frommer
- 1] Department of Biology, Stanford University, Stanford, California 94305, USA [2] Carnegie Institution for Science, 260 Panama Street, Stanford, California 94305, USA
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83
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Galbraith DW. Endoreduplicative standards for calibration of flow cytometric C-Value measurements. Cytometry A 2014; 85:368-74. [PMID: 24415326 DOI: 10.1002/cyto.a.22440] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/05/2013] [Accepted: 12/27/2013] [Indexed: 01/13/2023]
Abstract
It has been estimated that there are, globally, as many as 400,000 species of the angiosperms (the flowering plants). Of these, a minimal proportion has been characterized at the cytological level. Urgency is required in initiating a systematic and comprehensive census, due to species extinction as a consequence of anthropogenic activities. Fundamental to eukaryotes is the 2C-value, the amount of DNA contained within the nucleus of the unreduced gametes. Flow cytometry provides an ideal method for determining C-values, but the values archived in the Kew Plant C-value Database represent <2% of these species. Complicating the issue is a proliferation of different, and inconsistent standards for C-value measurements utilizing flow cytometry, and variability associated with different instrument platforms and using different staining procedures. In previous work, the use of flow cytometry for analysis of plant nuclear DNA contents for species spanning much of the range of genome sizes found in the angiosperms was described. For this work, an endoreduplicative species (Arabidopsis thaliana L.) was particularly helpful as an internal standard for genome size calibration. Such a standard is compromised if it overlaps in DNA content than that of the species whose genome size is sought. This report describes the use of a second species displaying endoreduplication, Capsicum annuum L., for similar standardization. The results (a) indicate accurate reporting of nuclear DNA contents across a range 0.32-423.68 pg, (b) confirm that endoreduplication increases nuclear DNA contents by complete replication of the genome, and (c) provide a means for quality control of linearity in instrumentation over defined dynamic ranges.
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Affiliation(s)
- David W Galbraith
- School of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, Arizona
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84
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Abstract
The flower itself, which comprises most of the evolutionary innovations of flowering plants, bears special significance for understanding the origin and diversification of angiosperms. The sudden origin of angiosperms in the fossil record poses unanswered questions on both the origins of flowering plants and their rapid spread and diversification. Central to these questions is the role that the flower, and floral diversity, played. Recent clarifications of angiosperm phylogeny provide the foundation for investigating evolutionary transitions in floral features and the underlying genetic mechanisms of stasis and change. The general features of floral diversity can best be addressed by considering key patterns of variation: an undifferentiated versus a differentiated perianth; elaboration of perianth organs in size and color; merosity of the flower; and phyllotaxy of floral organs. Various models of gene expression now explain the regulation of floral organization and floral organ identity; the best understood are the ABC(E) model and its modifications, but other gene systems are important in specific clades and require further study. Furthermore, the propensity for gene and genome duplications in angiosperms provides abundant raw material for novel floral features--emphasizing the importance of understanding the conservation and diversification of gene lineages and functions in studies of macroevolution.
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85
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Rock CD. Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development? TRENDS IN PLANT SCIENCE 2013; 18:601-10. [PMID: 23993483 PMCID: PMC3818397 DOI: 10.1016/j.tplants.2013.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/12/2013] [Accepted: 07/31/2013] [Indexed: 05/19/2023]
Abstract
The facility and versatility of microRNAs (miRNAs) to evolve and change likely underlies how they have become dominant constituents of eukaryotic genomes. In this opinion article I propose that trans-acting small interfering RNA gene 4 (TAS4) evolution may be important for biosynthesis of polyphenolics, arbuscular symbiosis, and bacterial pathogen etiologies. Expression-based and phylogenetic evidence shows that TAS4 targets two novel grape (Vitis vinifera L.) MYB transcription factors (VvMYBA6, VvMYBA7) that spawn phased small interfering RNAs (siRNAs) which probably function in nutraceutical bioflavonoid biosynthesis and fruit development. Characterization of the molecular mechanisms of TAS4 control of plant development and integration into biotic and abiotic stress- and nutrient-signaling regulatory networks has applicability to molecular breeding and the development of strategies for engineering healthier foods.
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Affiliation(s)
- Christopher D Rock
- Department of Biological Sciences, Texas Tech University (TTU), Lubbock, TX 79409-3131, USA.
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86
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Haller BC, Hendry AP. SOLVING THE PARADOX OF STASIS: SQUASHED STABILIZING SELECTION AND THE LIMITS OF DETECTION. Evolution 2013; 68:483-500. [PMID: 24102172 DOI: 10.1111/evo.12275] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 09/10/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin C. Haller
- Department of Biology and Redpath Museum; McGill University; 859 Sherbrooke Street West Montreal Quebec Canada H3A 0C4
| | - Andrew P. Hendry
- Department of Biology and Redpath Museum; McGill University; 859 Sherbrooke Street West Montreal Quebec Canada H3A 0C4
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87
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Baluška F, Mancuso S. Microorganism and filamentous fungi drive evolution of plant synapses. Front Cell Infect Microbiol 2013; 3:44. [PMID: 23967407 PMCID: PMC3744040 DOI: 10.3389/fcimb.2013.00044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/26/2013] [Indexed: 12/23/2022] Open
Abstract
In the course of plant evolution, there is an obvious trend toward an increased complexity of plant bodies, as well as an increased sophistication of plant behavior and communication. Phenotypic plasticity of plants is based on the polar auxin transport machinery that is directly linked with plant sensory systems impinging on plant behavior and adaptive responses. Similar to the emergence and evolution of eukaryotic cells, evolution of land plants was also shaped and driven by infective and symbiotic microorganisms. These microorganisms are the driving force behind the evolution of plant synapses and other neuronal aspects of higher plants; this is especially pronounced in the root apices. Plant synapses allow synaptic cell–cell communication and coordination in plants, as well as sensory-motor integration in root apices searching for water and mineral nutrition. These neuronal aspects of higher plants are closely linked with their unique ability to adapt to environmental changes.
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Affiliation(s)
- František Baluška
- IZMB, Department of Plant Cell Biology, University of Bonn Bonn, Germany.
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88
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Cardinal S, Danforth BN. Bees diversified in the age of eudicots. Proc Biol Sci 2013; 280:20122686. [PMID: 23363629 PMCID: PMC3574388 DOI: 10.1098/rspb.2012.2686] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 01/04/2013] [Indexed: 11/12/2022] Open
Abstract
Reliable estimates on the ages of the major bee clades are needed to further understand the evolutionary history of bees and their close association with flowering plants. Divergence times have been estimated for a few groups of bees, but no study has yet provided estimates for all major bee lineages. To date the origin of bees and their major clades, we first perform a phylogenetic analysis of bees including representatives from every extant family, subfamily and almost all tribes, using sequence data from seven genes. We then use this phylogeny to place 14 time calibration points based on information from the fossil record for an uncorrelated relaxed clock divergence time analysis taking into account uncertainties in phylogenetic relationships and the fossil record. We explore the effect of placing a hard upper age bound near the root of the tree and the effect of different topologies on our divergence time estimates. We estimate that crown bees originated approximately 123 Ma (million years ago) (113-132 Ma), concurrently with the origin or diversification of the eudicots, a group comprising 75 per cent of angiosperm species. All of the major bee clades are estimated to have originated during the Middle to Late Cretaceous, which is when angiosperms became the dominant group of land plants.
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Affiliation(s)
- Sophie Cardinal
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Ottawa, Ontario, Canada.
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89
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90
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Seymour GB, Østergaard L, Chapman NH, Knapp S, Martin C. Fruit development and ripening. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:219-41. [PMID: 23394500 DOI: 10.1146/annurev-arplant-050312-120057] [Citation(s) in RCA: 323] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fruiting structures in the angiosperms range from completely dry to highly fleshy organs and provide many of our major crop products, including grains. In the model plant Arabidopsis, which has dry fruits, a high-level regulatory network of transcription factors controlling fruit development has been revealed. Studies on rare nonripening mutations in tomato, a model for fleshy fruits, have provided new insights into the networks responsible for the control of ripening. It is apparent that there are strong similarities between dry and fleshy fruits in the molecular circuits governing development and maturation. Translation of information from tomato to other fleshy-fruited species indicates that regulatory networks are conserved across a wide spectrum of angiosperm fruit morphologies. Fruits are an essential part of the human diet, and recent developments in the sequencing of angiosperm genomes have provided the foundation for a step change in crop improvement through the understanding and harnessing of genome-wide genetic and epigenetic variation.
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Affiliation(s)
- Graham B Seymour
- Plant and Crop Science Division, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom.
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91
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Starr TN, Gadek KE, Yoder JB, Flatz R, Smith CI. Asymmetric hybridization and gene flow between Joshua trees (Agavaceae:Yucca) reflect differences in pollinator host specificity. Mol Ecol 2012. [DOI: 10.1111/mec.12124] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tyler N. Starr
- Department of Biology; Willamette University; 900 State Street Salem OR 97301 USA
| | - Katherine E. Gadek
- Department of Biology; Willamette University; 900 State Street Salem OR 97301 USA
| | - Jeremy B. Yoder
- Department of Biological Sciences; University of Idaho; Moscow ID 83844 USA
| | - Ramona Flatz
- Department of Biology; Willamette University; 900 State Street Salem OR 97301 USA
| | - Christopher I. Smith
- Department of Biology; Willamette University; 900 State Street Salem OR 97301 USA
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92
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Williams JH. Pollen Tube Growth Rates and the Diversification of Flowering Plant Reproductive Cycles. INTERNATIONAL JOURNAL OF PLANT SCIENCES 2012. [PMID: 0 DOI: 10.1086/665822] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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93
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Leitch AR, Leitch IJ. Ecological and genetic factors linked to contrasting genome dynamics in seed plants. THE NEW PHYTOLOGIST 2012; 194:629-646. [PMID: 22432525 DOI: 10.1111/j.1469-8137.2012.04105.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The large-scale replacement of gymnosperms by angiosperms in many ecological niches over time and the huge disparity in species numbers have led scientists to explore factors (e.g. polyploidy, developmental systems, floral evolution) that may have contributed to the astonishing rise of angiosperm diversity. Here, we explore genomic and ecological factors influencing seed plant genomes. This is timely given the recent surge in genomic data. We compare and contrast the genomic structure and evolution of angiosperms and gymnosperms and find that angiosperm genomes are more dynamic and diverse, particularly amongst the herbaceous species. Gymnosperms typically have reduced frequencies of a number of processes (e.g. polyploidy) that have shaped the genomes of other vascular plants and have alternative mechanisms to suppress genome dynamism (e.g. epigenetics and activity of transposable elements). Furthermore, the presence of several characters in angiosperms (e.g. herbaceous habit, short minimum generation time) has enabled them to exploit new niches and to be viable with small population sizes, where the power of genetic drift can outweigh that of selection. Together these processes have led to increased rates of genetic divergence and faster fixation times of variation in many angiosperms compared with gymnosperms.
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Affiliation(s)
- A R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, UK
| | - I J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
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94
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Airoldi CA, Davies B. Gene Duplication and the Evolution of Plant MADS-box Transcription Factors. J Genet Genomics 2012; 39:157-65. [DOI: 10.1016/j.jgg.2012.02.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 02/14/2012] [Accepted: 02/15/2012] [Indexed: 11/17/2022]
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95
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de Boer HJ, Eppinga MB, Wassen MJ, Dekker SC. A critical transition in leaf evolution facilitated the Cretaceous angiosperm revolution. Nat Commun 2012; 3:1221. [PMID: 23187621 PMCID: PMC3514505 DOI: 10.1038/ncomms2217] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 10/23/2012] [Indexed: 11/21/2022] Open
Abstract
The revolutionary rise of broad-leaved (flowering) angiosperm plant species during the Cretaceous initiated a global ecological transformation towards modern biodiversity. Still, the mechanisms involved in this angiosperm radiation remain enigmatic. Here we show that the period of rapid angiosperm evolution initiated after the leaf interior (post venous) transport path length for water was reduced beyond the leaf interior transport path length for CO2 at a critical leaf vein density of 2.5-5 mm mm(-2). Data and our modelling approaches indicate that surpassing this critical vein density was a pivotal moment in leaf evolution that enabled evolving angiosperms to profit from developing leaves with more and smaller stomata in terms of higher carbon returns from equal water loss. Surpassing the critical vein density may therefore have facilitated evolving angiosperms to develop leaves with higher gas exchange capacities required to adapt to the Cretaceous CO2 decline and outcompete previously dominant coniferous species in the upper canopy.
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Affiliation(s)
- Hugo Jan de Boer
- Department of Environmental Sciences, Faculty of Geosciences, Utrecht University, Heidelberglaan 2, PO box 80115, Utrecht 3508 TC, The Netherlands.
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96
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Lee EK, Cibrian-Jaramillo A, Kolokotronis SO, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, DeSalle R. A functional phylogenomic view of the seed plants. PLoS Genet 2011; 7:e1002411. [PMID: 22194700 PMCID: PMC3240601 DOI: 10.1371/journal.pgen.1002411] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 10/21/2011] [Indexed: 12/01/2022] Open
Abstract
A novel result of the current research is the development and implementation of a unique functional phylogenomic approach that explores the genomic origins of seed plant diversification. We first use 22,833 sets of orthologs from the nuclear genomes of 101 genera across land plants to reconstruct their phylogenetic relationships. One of the more salient results is the resolution of some enigmatic relationships in seed plant phylogeny, such as the placement of Gnetales as sister to the rest of the gymnosperms. In using this novel phylogenomic approach, we were also able to identify overrepresented functional gene ontology categories in genes that provide positive branch support for major nodes prompting new hypotheses for genes associated with the diversification of angiosperms. For example, RNA interference (RNAi) has played a significant role in the divergence of monocots from other angiosperms, which has experimental support in Arabidopsis and rice. This analysis also implied that the second largest subunit of RNA polymerase IV and V (NRPD2) played a prominent role in the divergence of gymnosperms. This hypothesis is supported by the lack of 24nt siRNA in conifers, the maternal control of small RNA in the seeds of flowering plants, and the emergence of double fertilization in angiosperms. Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification.
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Affiliation(s)
- Ernest K. Lee
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Angelica Cibrian-Jaramillo
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Cullman Program in Molecular Systematics, The New York Botanical Garden, Bronx, New York, United States of America
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Sergios-Orestis Kolokotronis
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Manpreet S. Katari
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | | | - Michael Ott
- Department of Computer Science, Technische Universität München, Munich, Germany
| | - Joanna C. Chiu
- Department of Entomology, University of California Davis, Davis, California, United States of America
| | - Damon P. Little
- Cullman Program in Molecular Systematics, The New York Botanical Garden, Bronx, New York, United States of America
| | - Dennis Wm. Stevenson
- Cullman Program in Molecular Systematics, The New York Botanical Garden, Bronx, New York, United States of America
| | - W. Richard McCombie
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Gloria Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
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97
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Chen R, Binder BM, Garrett WM, Tucker ML, Chang C, Cooper B. Proteomic responses in Arabidopsis thaliana seedlings treated with ethylene. MOLECULAR BIOSYSTEMS 2011; 7:2637-50. [PMID: 21713283 DOI: 10.1039/c1mb05159h] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Ethylene (ET) is a volatile hormone that modulates fruit ripening, plant growth, development and stress responses. Key components of the ET-signaling pathway identified by genetic dissection in Arabidopsis thaliana include five ET receptors, the negative regulator CTR1 and the positive regulator EIN2, all of which localize to the endoplasmic reticulum. Mechanisms of signaling among these proteins are still unresolved and targets of ET responses are not fully known. So, we used mass spectrometry to identify proteins in microsomal membrane preparations from etiolated A. thaliana seedlings maintained in ambient air or treated with ET for 3 h. We compared 3814 proteins from ET-exposed seedlings and controls and identified 304 proteins with significant accumulation changes. The proteins with increased accumulation were involved in ET biosynthesis, cell morphogenesis, oxidative stress and vesicle secretion while those with decreased accumulation were ribosomal proteins and proteins positively regulated by brassinosteroid, another hormone involved in cell elongation. Several proteins, including EIN2, appeared to be differentially phosphorylated upon ET treatment, which suggests that the activity or stability of these proteins may be controlled by phosphorylation. TUA3, a component of microtubules that contributes to cellular morphological change, exhibited both increased accumulation and differential phosphorylation upon ET treatment. To verify the role of TUA3 in the ET response, tua3 mutants were evaluated. Mutant seedlings had altered ET-associated growth movements. The data indicate that ET perception leads to rapid proteomic change and that these changes are an important part of signaling and development. The data serve as a foundation for exploring ET signaling through systems biology.
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Affiliation(s)
- Ruiqiang Chen
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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98
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Abstract
In Trimenia moorei, an extant member of the ancient angiosperm clade Austrobaileyales, we found a remarkable pattern of female gametophyte (egg-producing structure) development that strikingly resembles that of pollen tubes and their intrasexual competition within the maternal pollen tube transmitting tissues of most flowers. In contrast with most other flowering plants, in Trimenia, multiple female gametophytes are initiated at the base (chalazal end) of each ovule. Female gametophytes grow from their tips and compete over hundreds of micrometers to reach the apex of the nucellus and the site of fertilization. Here, the successful female gametophyte will mate with a pollen tube to produce an embryo and an endosperm. Moreover, the central tissue within the ovules of Trimenia, through which the embryo sacs grow, contains starch and other carbohydrates similar to the pollen tube transmitting tissues in the styles of most flowers. The pattern of female gametophyte development found in Trimenia is rare but by no means unique in angiosperms. Importantly, it seems that multiple female gametophytes are occasionally or frequently initiated in members of other ancient angiosperm lineages. The intensification of pollen tube (male gametophyte) competition and enhanced maternal selection among competing pollen tubes are considered to have been major contributors to the rise of angiosperms. Based on insights from Trimenia, we posit that prefertilization female gametophyte (egg) competition within individual ovules in addition to male gametophyte (sperm) competition and maternal mate choice may have been key features of the earliest angiosperms.
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99
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Abstract
A recent phylogenomic study has provided new evidence for two ancient whole genome duplications in plants, with potential importance for the evolution of seed and flowering plants.
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Affiliation(s)
- Yves Van de Peer
- Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent, Belgium.
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100
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Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. Proc Natl Acad Sci U S A 2010; 107:22570-5. [PMID: 21149731 DOI: 10.1073/pnas.1013395108] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The origin and rapid diversification of the angiosperms (Darwin's "Abominable Mystery") has engaged generations of researchers. Here, we examine the floral genetic programs of phylogenetically pivotal angiosperms (water lily, avocado, California poppy, and Arabidopsis) and a nonflowering seed plant (a cycad) to obtain insight into the origin and subsequent evolution of the flower. Transcriptional cascades with broadly overlapping spatial domains, resembling the hypothesized ancestral gymnosperm program, are deployed across morphologically intergrading organs in water lily and avocado flowers. In contrast, spatially discrete transcriptional programs in distinct floral organs characterize the more recently derived angiosperm lineages represented by California poppy and Arabidopsis. Deep evolutionary conservation in the genetic programs of putatively homologous floral organs traces to those operating in gymnosperm reproductive cones. Female gymnosperm cones and angiosperm carpels share conserved genetic features, which may be associated with the ovule developmental program common to both organs. However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants.
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