1
|
Valdés-Florido A, González-Toral C, Maguilla E, Cires E, Díaz-Lifante Z, Andrés-Camacho C, Nieto Feliner G, Arroyo J, Escudero M. Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae). ANNALS OF BOTANY 2024; 134:247-262. [PMID: 38687133 PMCID: PMC11232519 DOI: 10.1093/aob/mcae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND AND AIMS Polyploidy is considered one of the main mechanisms of plant evolution and speciation. In the Mediterranean Basin, polyploidy has contributed to making this region a biodiversity hotspot, along with its geological and climatic history and other ecological and biogeographical factors. The Mediterranean genus Centaurium (Gentianaceae) comprises ~25 species, of which 60 % are polyploids, including tetraploids and hexaploids. To date, the evolutionary history of centauries has been studied using Sanger sequencing phylogenies, which have been insufficient to fully understand the phylogenetic relationships in this lineage. The goal of this study is to gain a better understanding of the evolutionary history of Centaurium by exploring the mechanisms that have driven its diversification, specifically hybridization and polyploidy. We aim to identify the parentage of hybrid species, at the species or clade level, as well as assessing whether morphological traits are associated with particular ploidy levels. METHODS We sequenced RADseq markers from 42 samples of 28 Centaurium taxa, and performed phylogenomic analyses using maximum likelihood, summary coalescent SVDquartets and Neighbor-Net approaches. To identify hybrid taxa, we used PhyloNetworks and the fastSTRUCTURE algorithm. To infer the putative parental species of the allopolyploids, we employed genomic analyses (SNIPloid). The association between different traits and particular ploidy levels was explored with non-metric multidimensional scaling. KEY RESULTS Our phylogenetic analyses confirmed the long-suspected occurrence of recurrent hybridization. The allopolyploid origin of the tetraploid C. serpentinicola and the hexaploids C. mairei, C. malzacianum and C. centaurioides was also confirmed, unlike that of C. discolor. We inferred additional signatures of hybridization events within the genus and identified morphological traits differentially distributed in different ploidy levels. CONCLUSIONS This study highlights the important role that hybridization has played in the evolution of a Mediterranean genus such as Centaurium, leading to a polyploid complex, which facilitated its diversification and may exemplify that of other Mediterranean groups.
Collapse
Affiliation(s)
- Ana Valdés-Florido
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | | | - Enrique Maguilla
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, 41013, Spain
| | - Eduardo Cires
- Department of Organisms and Systems Biology, University of Oviedo, Oviedo, 33071, Spain
- Institute of Natural Resources and Territorial Planning (INDUROT), Campus de Mieres, Mieres, 33600, Spain
| | - Zoila Díaz-Lifante
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | - Cristina Andrés-Camacho
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | | | - Juan Arroyo
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| | - Marcial Escudero
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, 41012, Spain
| |
Collapse
|
2
|
Scutt CP. Model Species to Investigate the Origin of Flowers. Methods Mol Biol 2023; 2686:83-109. [PMID: 37540355 DOI: 10.1007/978-1-0716-3299-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The angiosperms, or flowering plants, arose at least 135 million years ago (Ma) and rapidly diversified to form over 300,000 species alive today. This group appears, however, to have separated from its closest living relatives, the extant gymnosperms, much earlier: over 300 Ma. Representatives of basally-diverging angiosperm lineages are of key importance to studies aimed at reconstructing the most recent common ancestor of living angiosperms, including its morphological, anatomical, eco-physiological and molecular aspects. Furthermore, evo-devo comparisons of angiosperms with living gymnosperms may help to determine how the many novel aspects of angiosperms, including those of the flower, first came about. This chapter reviews literature on the origin of angiosperms and focusses on basally-diverging angiosperms and gymnosperms that show advantages as potential experimental models, reviewing information and protocols for the use of these species in an evo-devo context. The final section suggests a means by which data from living and fossil groups could be integrated to better elucidate evolutionary events that took place on the long stem-lineage that apparently preceded the radiation of living angiosperms.
Collapse
Affiliation(s)
- Charles P Scutt
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon-1, CNRS, INRA, Lyon, France.
| |
Collapse
|
3
|
Culley TM. Editorial: Growing up and moving forward: Discontinuing Primer Notes. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11293. [PMID: 31667021 PMCID: PMC6814178 DOI: 10.1002/aps3.11293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Theresa M Culley
- Department of Biological Sciences University of Cincinnati 614 Rieveschl Hall Cincinnati Ohio 45221-0006 USA
| |
Collapse
|
4
|
Marques I, Loureiro J, Draper D, Castro M, Castro S. How much do we know about the frequency of hybridisation and polyploidy in the Mediterranean region? PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20 Suppl 1:21-37. [PMID: 28963818 DOI: 10.1111/plb.12639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
Natural hybridisation and polyploidy are currently recognised as drivers of biodiversity, despite early scepticism about their importance. The Mediterranean region is a biodiversity hotspot where geological and climatic events have created numerous opportunities for speciation through hybridisation and polyploidy. Still, our knowledge on the frequency of these mechanisms in the region is largely limited, despite both phenomena are frequently cited in studies of Mediterranean plants. We reviewed information available from biodiversity and cytogenetic databases to provide the first estimates of hybridisation and polyploidy frequency in the Mediterranean region. We also inspected the most comprehensive modern Mediterranean Flora (Flora iberica) to survey the frequency and taxonomic distribution of hybrids and polyploids in Iberian Peninsula. We found that <6% of Mediterranean plants were hybrids, although a higher frequency was estimated for the Iberian Peninsula (13%). Hybrids were concentrated in few families and in even fewer genera. The overall frequency of polyploidy (36.5%) was comparable with previous estimates in other regions; however our estimates increased when analysing the Iberian Peninsula (48.8%). A surprisingly high incidence of species harbouring two or more ploidy levels was also observed (21.7%). A review of the available literature also showed that the ecological factors driving emergence and establishment of new entities are still poorly studied in the Mediterranean flora, although geographic barriers seem to play a major role in polyploid complexes. Finally, this study reveals several gaps and limitations in our current knowledge about the frequency of hybridisation and polyploidy in the Mediterranean region. The obtained estimates might change in the future with the increasing number of studies; still, rather than setting the complete reality, we hope that this work triggers future studies on hybridisation and polyploidy in the Mediterranean region.
Collapse
Affiliation(s)
- I Marques
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
| | - J Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - D Draper
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Universidade de Lisboa, Lisbon, Portugal
- UBC Botanical Garden & Centre for Plant Research, and Department of Botany, University of British Columbia, Vancouver, Canada
| | - M Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - S Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Botanic Garden of the University of Coimbra, Coimbra, Portugal
| |
Collapse
|
5
|
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.
Collapse
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
- )
| |
Collapse
|
6
|
Barker MS, Husband BC, Pires JC. Spreading Winge and flying high: The evolutionary importance of polyploidy after a century of study. AMERICAN JOURNAL OF BOTANY 2016; 103:1139-45. [PMID: 27480249 DOI: 10.3732/ajb.1600272] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 05/10/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 USA
| |
Collapse
|
7
|
Barker MS, Li Z, Kidder TI, Reardon CR, Lai Z, Oliveira LO, Scascitelli M, Rieseberg LH. Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae. AMERICAN JOURNAL OF BOTANY 2016; 103:1203-11. [PMID: 27313199 DOI: 10.3732/ajb.1600113] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 05/06/2016] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Like many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature. METHODS We sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy. KEY RESULTS We found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia. CONCLUSIONS Our analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high density Lactuca linkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and that most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.
Collapse
Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, P. O. Box 210088, Tucson, Arizona 85721 USA
| | - Zheng Li
- Department of Ecology & Evolutionary Biology, University of Arizona, P. O. Box 210088, Tucson, Arizona 85721 USA
| | - Thomas I Kidder
- Department of Ecology & Evolutionary Biology, University of Arizona, P. O. Box 210088, Tucson, Arizona 85721 USA
| | - Chris R Reardon
- Department of Ecology & Evolutionary Biology, University of Arizona, P. O. Box 210088, Tucson, Arizona 85721 USA
| | - Zhao Lai
- Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana 47405 USA
| | - Luiz O Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa 36570-900, Viçosa, Brazil
| | - Moira Scascitelli
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4 Canada
| | - Loren H Rieseberg
- Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana 47405 USA Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4 Canada
| |
Collapse
|