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Raimondeau P, Ksouda S, Marande W, Fuchs AL, Gryta H, Theron A, Puyoou A, Dupin J, Cheptou PO, Vautrin S, Valière S, Manzi S, Baali-Cherif D, Chave J, Christin PA, Besnard G. A hemizygous supergene controls homomorphic and heteromorphic self-incompatibility systems in Oleaceae. Curr Biol 2024; 34:1977-1986.e8. [PMID: 38626764 DOI: 10.1016/j.cub.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/29/2024] [Accepted: 03/18/2024] [Indexed: 04/18/2024]
Abstract
Self-incompatibility (SI) has evolved independently multiple times and prevents self-fertilization in hermaphrodite angiosperms. Several groups of Oleaceae such as jasmines exhibit distylous flowers, with two compatibility groups each associated with a specific floral morph.1 Other Oleaceae species in the olive tribe have two compatibility groups without associated morphological variation.2,3,4,5 The genetic basis of both homomorphic and dimorphic SI systems in Oleaceae is unknown. By comparing genomic sequences of three olive subspecies (Olea europaea) belonging to the two compatibility groups, we first locate the genetic determinants of SI within a 700-kb hemizygous region present only in one compatibility group. We then demonstrate that the homologous hemizygous region also controls distyly in jasmine. Phylogenetic analyses support a common origin of both systems, following a segmental genomic duplication in a common ancestor. Examination of the gene content of the hemizygous region in different jasmine and olive species suggests that the mechanisms determining compatibility groups and floral phenotypes (whether homomorphic or dimorphic) in Oleaceae rely on the presence/absence of two genes involved in gibberellin and brassinosteroid regulation.
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Affiliation(s)
- Pauline Raimondeau
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France; Yale Institute of Biospheric Studies, New Haven, CT 06520, USA
| | - Sayam Ksouda
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - William Marande
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Anne-Laure Fuchs
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Hervé Gryta
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Anthony Theron
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Aurore Puyoou
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Julia Dupin
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Pierre-Olivier Cheptou
- CEFE (Centre d'Ecologie Fonctionnelle et Evolutive), UMR 5175, CNRS, Université de Montpellier, Université Paul Valéry, EPHE, IRD, 34293 Montpellier, France
| | - Sonia Vautrin
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Sophie Valière
- INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France
| | - Sophie Manzi
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Djamel Baali-Cherif
- Laboratoire de Recherche sur les Zones Arides, USTHB/ENSA, 16000 Alger, Algeria
| | - Jérôme Chave
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Guillaume Besnard
- CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), UMR 5300, CNRS, Université Paul Sabatier, IRD, INP Toulouse, 118 Route de Narbonne, 31062 Toulouse, France.
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Balboa RF, Bertola LD, Brüniche-Olsen A, Rasmussen MS, Liu X, Besnard G, Salmona J, Santander CG, He S, Zinner D, Pedrono M, Muwanika V, Masembe C, Schubert M, Kuja J, Quinn L, Garcia-Erill G, Stæger FF, Rakotoarivony R, Henrique M, Lin L, Wang X, Heaton MP, Smith TPL, Hanghøj K, Sinding MHS, Atickem A, Chikhi L, Roos C, Gaubert P, Siegismund HR, Moltke I, Albrechtsen A, Heller R. African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival. Nat Commun 2024; 15:172. [PMID: 38172616 PMCID: PMC10764920 DOI: 10.1038/s41467-023-44105-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1000-5000 years ago, concurrent with human arrival in Madagascar. These results shed light on the evolutionary history of an iconic and widespread African mammal and provide insight into the longstanding biogeographic puzzle surrounding the bushpig's presence in Madagascar.
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Affiliation(s)
- Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guillaume Besnard
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Jordi Salmona
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shixu He
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dietmar Zinner
- Cognitive Ecology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077, Göttingen, Germany
| | - Miguel Pedrono
- UMR ASTRE, CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Mikkel Schubert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Anagaw Atickem
- Department of Zoological Sciences, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Lounès Chikhi
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Kaniewski D, Marriner N, Morhange C, Khater C, Terral JF, Besnard G, Otto T, Luce F, Couillebault Q, Tsitsou L, Pourkerman M, Cheddadi R. Climate change threatens olive oil production in the Levant. Nat Plants 2023; 9:219-227. [PMID: 36702932 DOI: 10.1038/s41477-022-01339-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
The olive tree (Olea europaea L.) is one of the species best adapted to a Mediterranean-type climate1-8. Nonetheless, the Mediterranean Basin is deemed to be a climate change 'hotspot' by the Intergovernmental Panel on Climate Change9,10 because future model projections suggest considerable warming and drying11,12. Within this context, new environmental challenges will arise in the coming decades, which will both weaken and threaten olive-growing areas, leading to a loss of productivity and changes in fruit and oil quality13-15. Olive growing, a core of the Mediterranean economy, might soon be under stress. To probe the link between climate and olive trees, we here report 5,400 years of olive tree dynamics from the ancient city of Tyre, Lebanon. We show that optimal fruiting scales closely with temperature. Present-day and palaeo data define an optimal annual average temperature of 16.9 ± 0.3 °C for olive flowering that has existed at least since the Neolithic period. According to our projections, during the second half of the twenty-first century, temperature increases in Lebanon will have detrimental consequences on olive tree growth and olive oil production, especially in the country's southern regions, which will become too hot for optimal flowering and fruiting. These data provide a template to understand present and future thresholds of olive production under climate change.
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Affiliation(s)
- David Kaniewski
- TRACES, UMR 5608 CNRS, Université Toulouse Jean Jaurès, Toulouse, France.
- Département de Biologie et Géosciences, Université Paul Sabatier - Toulouse III, Toulouse, France.
| | - Nick Marriner
- CNRS, ThéMA, Université de Franche-Comté, UMR 6049, MSHE Ledoux, Besançon, France
| | - Christophe Morhange
- Aix Marseille Université, CNRS, IRD, INRA, Collège de France, CEREGE, Aix-en-Provence, France
- EPHE-Section des Sciences Historiques et Philologiques, AOROC, UMR 8546, CNRS/PSL, École Normale Supérieure, Paris, France
| | - Carla Khater
- Center for Remote Sensing, National Council for Scientific Research - Lebanon, Beirut, Lebanon
| | | | - Guillaume Besnard
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse, CNRS, UPS, IRD, Toulouse, France
| | - Thierry Otto
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, INP, UPS, Toulouse, France
| | - Frédéric Luce
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, INP, UPS, Toulouse, France
| | - Quentin Couillebault
- TRACES, UMR 5608 CNRS, Université Toulouse Jean Jaurès, Toulouse, France
- Aix Marseille Université, CNRS, CCJ, Aix en Provence, France
| | - Labrini Tsitsou
- Aix Marseille Université, CNRS, IRD, INRA, Collège de France, CEREGE, Aix-en-Provence, France
| | - Majid Pourkerman
- Iranian National Institute for Oceanography and Atmospheric Sciences (INIOAS), Tehran, Iran
| | - Rachid Cheddadi
- Université Montpellier II, CNRS-UM-IRD, ISEM, Montpellier, France
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4
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Salmona J, Dresen A, Ranaivoson AE, Manzi S, Le Pors B, Hong-Wa C, Razanatsoa J, Andriaholinirina NV, Rasoloharijaona S, Vavitsara ME, Besnard G. How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a microendemic Malagasy tree. Mol Ecol 2023; 32:299-315. [PMID: 36320175 PMCID: PMC10100191 DOI: 10.1111/mec.16759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]
Abstract
Understanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exceptions in areas such as the Loky-Manambato region (north) raise questions regarding the causes and age of forest fragmentation. The Loky-Manambato region also harbours a rich and endemic flora, whose evolutionary origin remains poorly understood. We assessed the genetic diversity of an endangered microendemic Malagasy olive species (Noronhia spinifolia Hong-Wa) to better understand the vegetation dynamics in the Loky-Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction-associated DNA sequencing data and chloroplast microsatellites. Combined population and landscape genetics analyses indicate that N. spinifolia diversity is largely explained by the current forest cover, highlighting a long-standing habitat mosaic in the region. This sustains a major and long-term role of riparian corridors in maintaining connectivity across these antique mosaic habitats, calling for the study of organismal interactions that promote gene flow.
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Affiliation(s)
- Jordi Salmona
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | - Axel Dresen
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | - Anicet E Ranaivoson
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France.,Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Sophie Manzi
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | | | - Cynthia Hong-Wa
- Claude E. Phillips Herbarium, Delaware State University, Dover, Delaware, USA
| | - Jacqueline Razanatsoa
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | | | | | | | - Guillaume Besnard
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
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5
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Curran EV, Scott MS, Olofsson JK, Nyirenda F, Sotelo G, Bianconi ME, Manzi S, Besnard G, Pereira L, Christin PA. Hybridization boosts dispersal of two contrasted ecotypes in a grass species. Proc Biol Sci 2022; 289:20212491. [PMID: 35078363 PMCID: PMC8790336 DOI: 10.1098/rspb.2021.2491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/23/2021] [Indexed: 11/12/2022] Open
Abstract
Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes and influence rates of hybridization. How these dynamics affect the emergence and spread of novel phenotypes remains only partially understood. Here, we use phylogenomics and population genomics to retrace the origin and spread of two geographically overlapping ecotypes of the African grass Alloteropsis angusta. In addition to an ecotype inhabiting wetlands, we report the existence of a previously undescribed ecotype inhabiting Miombo woodlands and grasslands. The two ecotypes are consistently associated with different nuclear groups, which represent an advanced stage of divergence with secondary low-level gene flow. However, the seed-transported chloroplast genomes are consistently shared by distinct ecotypes inhabiting the same region. These patterns suggest that the nuclear genome of one ecotype can enter the seeds of the other via occasional pollen movements with sorting of nuclear groups in subsequent generations. The contrasting ecotypes of A. angusta can thus use each other as a gateway to new locations across a large part of Africa, showing that hybridization can facilitate the geographical dispersal of distinct ecotypes of the same grass species.
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Affiliation(s)
- Emma V. Curran
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Matilda S. Scott
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jill K. Olofsson
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Graciela Sotelo
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Matheus E. Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Sophie Manzi
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III – Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Guillaume Besnard
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III – Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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Thi Phan N, Besnard G, Ouazahrou R, Sánchez WS, Gil L, Manzi S, Bellafiore S. Genome sequence of the coffee root-knot nematode Meloidogyne exigua. J Nematol 2021; 53:e2021-65. [PMID: 34296190 PMCID: PMC8290501 DOI: 10.21307/jofnem-2021-065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
Root-knot nematodes (Meloidogyne spp.) cause serious damages on most crops. Here, we report a high-quality genome sequence of Meloidogyne exigua (population Mex1, Costa Rica), a major pathogen of coffee. Its mitogenome (20,974 bp) was first assembled and annotated. The nuclear genome was then constructed consisting of 206 contigs, with an N50 length of 1.89 Mb and a total assembly length of 42.1 Mb.
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Affiliation(s)
- Ngan Thi Phan
- PHIM Plant Health Institute, University of Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Guillaume Besnard
- CNRS-UPS-IRD, UMR5174, EDB, 118 route de Narbonne, Université Paul Sabatier, 31062 Toulouse, France
| | | | | | - Lisa Gil
- US 1426, GeT-PlaGe, Genotoul, INRAE, Castanet-Tolosan, France
| | - Sophie Manzi
- CNRS-UPS-IRD, UMR5174, EDB, 118 route de Narbonne, Université Paul Sabatier, 31062 Toulouse, France
| | - Stéphane Bellafiore
- PHIM Plant Health Institute, University of Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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7
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Raimondeau P, Manzi S, Brucato N, Kinipi C, Leavesley M, Ricaut FX, Besnard G. Genome skims analysis of betel palms (Areca spp., Arecaceae) and development of a profiling method to assess their plastome diversity. Gene 2021; 800:145845. [PMID: 34274465 DOI: 10.1016/j.gene.2021.145845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022]
Abstract
The betel nut (Areca catechu L., Arecaceae) is a monoecious cultivated palm tree that is widespread in tropical regions. It is mainly cultivated for producing areca nuts, from which seeds are extracted and chewed by local populations principally in the Indo-Pacific region. Seeds contain alkaloids which are central nervous system stimulants and are highly addictive. Wild relatives of the betel nut are distributed in South Asia and Australasia, with ca. 40-50 Areca species currently recognized. The geographic origin(s) of the betel nut and its subsequent diffusion and diversification remains poorly documented. Here, a genome skimming approach was applied to screen nucleotidic variation in the most abundant genomic regions. Low coverage sequencing data allowed us to assemble full plastomes, mitochondrial regions (either full mitogenomes or the full set of mitochondrial genes) and the nuclear ribosomal DNA cluster for nine representatives of the Areca genus collected in the field and herbarium collections (including a 182-years old specimen collected during the Dumont d'Urville's expedition). These three genomic compartments provided similar phylogenetic signals, and revealed very low genomic diversity in our sample of cultivated betel nut. We finally developed a genotyping method targeting 34 plastid DNA microsatellites. This plastome profiling approach is useful for tracing the spread of matrilineages, and in combination with nuclear genomic data, can resolve the history of the betel nut. Our method also proves to be efficient for analyzing herbarium specimens, even those collected >100 years ago.
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Affiliation(s)
- Pauline Raimondeau
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Sophie Manzi
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Nicolas Brucato
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Christopher Kinipi
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea; CABAH & College of Arts, Society and Education, James Cook University, PO Box 6811, Cairns, QLD 4870, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France
| | - Guillaume Besnard
- Laboratoire Évolution & Diversité Biologique (EDB, UMR 5174), Université de Toulouse, CNRS-IRD-UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse, France.
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8
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Besnard G, Gorrilliot O, Raimondeau P, Génot B, El Bakkali A, Anthelme F, Baali-Cherif D. Contrasting Genetic Footprints among Saharan Olive Populations: Potential Causes and Conservation Implications. Plants (Basel) 2021; 10:plants10061207. [PMID: 34198539 PMCID: PMC8231981 DOI: 10.3390/plants10061207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
The Laperrine's olive is endemic to the Saharan Mountains. Adapted to arid environments, it may constitute a valuable genetic resource to improve water-stress tolerance in the cultivated olive. However, limited natural regeneration coupled with human pressures make it locally endangered in Central Sahara. Understanding past population dynamics is thus crucial to define management strategies. Nucleotide sequence diversity was first investigated on five nuclear genes and compared to the Mediterranean and African olives. These data confirm that the Laperrine's olive has a strong affinity with the Mediterranean olive, but it shows lower nucleotide diversity than other continental taxa. To investigate gene flows mediated by seeds and pollen, polymorphisms from nuclear and plastid microsatellites from 383 individuals from four Saharan massifs were analyzed. A higher genetic diversity in Ahaggar (Hoggar, Algeria) suggests that this population has maintained over the long term a larger number of individuals than other massifs. High-to-moderate genetic differentiation between massifs confirms the role of desert barriers in limiting gene flow. Yet contrasting patterns of isolation by distance were observed within massifs, and also between plastid and nuclear markers, stressing the role of local factors (e.g., habitat fragmentation, historical range shift) in seed and pollen dispersal. Implications of these results in the management of the Laperrine's olive genetic resources are discussed.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, CEDEX 9, 31062 Toulouse, France; (O.G.); (P.R.); (B.G.)
- Correspondence:
| | - Océane Gorrilliot
- CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, CEDEX 9, 31062 Toulouse, France; (O.G.); (P.R.); (B.G.)
| | - Pauline Raimondeau
- CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, CEDEX 9, 31062 Toulouse, France; (O.G.); (P.R.); (B.G.)
| | - Benoit Génot
- CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, CEDEX 9, 31062 Toulouse, France; (O.G.); (P.R.); (B.G.)
| | | | - Fabien Anthelme
- AMAP, University Montpellier, IRD, CIRAD, CNRS, INRA, 34398 Montpellier, France;
| | - Djamel Baali-Cherif
- Laboratoire de Recherche sur les Zones Arides, USTHB/INA, BP44, Alger 16000, Algeria;
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9
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Abstract
Size, structure, and sequence content lability of plant mitochondrial genome (mtDNA) across species has sharply limited its use in taxonomic studies. Historically, mtDNA variation has been first investigated with RFLPs, while the development of universal primers then allowed studying sequence polymorphisms within short genomic regions (<3 kb). The recent advent of NGS technologies now offers new opportunities by greatly facilitating the assembly of longer mtDNA regions, and even full mitogenomes. Phylogenetic works aiming at comparing signals from different genomic compartments (i.e., nucleus, chloroplast, and mitochondria) have been developed on a few plant lineages, and have been shown especially relevant in groups with contrasted inheritance of organelle genomes. This chapter first reviews the main characteristics of mtDNA and the application offered in taxonomic studies. It then presents tips for best sequencing protocol based on NGS data to be routinely used in mtDNA-based phylogenetic studies.
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Affiliation(s)
- Jérôme Duminil
- DIADE, University of Montpellier, IRD, Montpellier, France.
| | - Guillaume Besnard
- CNRS-UPS-IRD, UMR5174, EDB, Université Paul Sabatier, Toulouse, France
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10
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Bianconi ME, Hackel J, Vorontsova MS, Alberti A, Arthan W, Burke SV, Duvall MR, Kellogg EA, Lavergne S, McKain MR, Meunier A, Osborne CP, Traiperm P, Christin PA, Besnard G. Continued Adaptation of C4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses. Syst Biol 2020; 69:445-461. [PMID: 31589325 PMCID: PMC7672695 DOI: 10.1093/sysbio/syz066] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/18/2019] [Accepted: 09/26/2019] [Indexed: 11/29/2022] Open
Abstract
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}{}$_{4}$\end{document} photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} lineages is Andropogoneae, a group of \documentclass[12pt]{minimal}
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}{}$\sim $\end{document}1200 grass species that includes some of the world’s most important crops and species dominating tropical and some temperate grasslands. Previous efforts to understand C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} evolution in the group have compared a few model C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} plants to distantly related C\documentclass[12pt]{minimal}
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}{}$_{3}$\end{document} species so that changes directly responsible for the transition to C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} could not be distinguished from those that preceded or followed it. In this study, we analyze the genomes of 66 grass species, capturing the earliest diversification within Andropogoneae as well as their C\documentclass[12pt]{minimal}
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}{}$_{3}$\end{document} relatives. Phylogenomics combined with molecular dating and analyses of protein evolution show that many changes linked to the evolution of C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} photosynthesis in Andropogoneae happened in the Early Miocene, between 21 and 18 Ma, after the split from its C\documentclass[12pt]{minimal}
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}{}$_{3}$\end{document} sister lineage, and before the diversification of the group. This initial burst of changes was followed by an extended period of modifications to leaf anatomy and biochemistry during the diversification of Andropogoneae, so that a single C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} origin gave birth to a diversity of C\documentclass[12pt]{minimal}
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}{}$_{4}$\end{document} phenotypes during 18 million years of speciation events and migration across geographic and ecological spaces. Our comprehensive approach and broad sampling of the diversity in the group reveals that one key transition can lead to a plethora of phenotypes following sustained adaptation of the ancestral state. [Adaptive evolution; complex traits; herbarium genomics; Jansenelleae; leaf anatomy; Poaceae; phylogenomics.]
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Affiliation(s)
- Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Jan Hackel
- Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Adriana Alberti
- CEA - Institut de Biologie Francois-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Watchara Arthan
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
- School of Biological Sciences, University of Reading, Reading RG6 6AH, UK
| | - Sean V Burke
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Melvin R Duvall
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MI 63132, USA
| | - Sébastien Lavergne
- Laboratoire d’Ecologie Alpine, CNRS – Université Grenoble Alpes, UMR 5553, Grenoble, France
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, 500 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Alexandre Meunier
- Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Paweena Traiperm
- Department of Plant Science, Faculty of Science, Mahidol University, King Rama VI Road, Bangkok 10400, Thailand
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Guillaume Besnard
- Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France
- Correspondence to be sent to: Laboratoire Evolution & Diversité Biologique (EDB, UMR 5174), CNRS/IRD/Université Toulouse III, 118 route de Narbonne, 31062 Toulouse, France; E-mail:
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11
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Chapuis E, Ali N, Besnard G. Corrigendum to: Adaptive response to olive cultivation in a generalist parasitic nematode (Meloidogyne javanica). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elodie Chapuis
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Nadeen Ali
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Guillaume Besnard
- CNRS, UPS, IRD, UMR5174, EDB, Université Toulouse III Paul Sabatier, Toulouse Cedex, France
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12
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Lee C, Day J, Goodman SM, Pedrono M, Besnard G, Frantz L, Taylor PJ, Herrera MJ, Gongora J. Genetic origins and diversity of bushpigs from Madagascar (Potamochoerus larvatus, family Suidae). Sci Rep 2020; 10:20629. [PMID: 33244111 PMCID: PMC7693328 DOI: 10.1038/s41598-020-77279-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/09/2020] [Indexed: 11/08/2022] Open
Abstract
The island of Madagascar, situated off the southeast coast of Africa, shows the first evidence of human presence ~ 10,000 years ago; however, other archaeological data indicates a settlement of the modern peoples of the island distinctly more recent, perhaps > 1500 years ago. Bushpigs of the genus Potamochoerus (family Suidae), are today widely distributed in Madagascar and presumed to have been introduced from Africa at some stage by human immigrants to the island. However, disparities about their origins in Madagascar have been presented in the literature, including the possibility of endemic subspecies, and few empirical data are available. Furthermore, the separation of bushpigs in Madagascar from their mainland relatives may have favoured the evolution of a different repertoire of immune genes first due to a founder effect and then as a response to distinct pathogens compared to their ancestors. Molecular analysis confirmed the species status of the bushpig in Madagascar as P. larvatus, likely introduced from the central region of southern Africa, with no genetic evidence for the recognition of eastern and western subspecies as suggested from previous cranial morphology examination. Investigation of the immunologically important SLA-DQB1 peptide-binding region showed a different immune repertoire of bushpigs in Madagascar compared to those on the African mainland, with seventeen exon-2 haplotypes unique to bushpigs in Madagascar (2/28 haplotypes shared). This suggests that the MHC diversity of the Madagascar populations may have enabled Malagasy bushpigs to adapt to new environments.
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Affiliation(s)
- Carol Lee
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jenna Day
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Steven M Goodman
- Field Museum of Natural History, Chicago, IL, 60605, USA
- Association Vahatra, 101, Antananarivo, Madagascar
| | - Miguel Pedrono
- UMR ASTRE, INRAE, CIRAD, Université de Montpellier, 34398, Montpellier Cedex 5, France
| | - Guillaume Besnard
- CNRS, UPS, IRD, Laboratoire Evolution et Diversité Biologique, UMR5174, Université Toulouse III Paul Sabatier, 31062, Toulouse, France
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Peter J Taylor
- School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, Limpopo Province, South Africa
- Afromontane Research Unit and Zoology Department, University of the Free State, Qwa Qwa campus, Phuthaditjhaba, 9866, South Africa
| | - Michael J Herrera
- Archaeological Studies Program, University of the Philippines Diliman, 1101, Quezon City, Philippines
| | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia.
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13
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Bianconi ME, Dunning LT, Curran EV, Hidalgo O, Powell RF, Mian S, Leitch IJ, Lundgren MR, Manzi S, Vorontsova MS, Besnard G, Osborne CP, Olofsson JK, Christin PA. Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species. Proc Biol Sci 2020; 287:20201960. [PMID: 33171085 PMCID: PMC7735283 DOI: 10.1098/rspb.2020.1960] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C4 physiology away from its region of origin.
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Affiliation(s)
- Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Emma V Curran
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Oriane Hidalgo
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Robyn F Powell
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Sahr Mian
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Ilia J Leitch
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Sophie Manzi
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III - Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Guillaume Besnard
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III - Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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14
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Phan NT, Orjuela J, Danchin EGJ, Klopp C, Perfus‐Barbeoch L, Kozlowski DK, Koutsovoulos GD, Lopez‐Roques C, Bouchez O, Zahm M, Besnard G, Bellafiore S. Genome structure and content of the rice root-knot nematode ( Meloidogyne graminicola). Ecol Evol 2020; 10:11006-11021. [PMID: 33144944 PMCID: PMC7593179 DOI: 10.1002/ece3.6680] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/04/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022] Open
Abstract
Discovered in the 1960s, Meloidogyne graminicola is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294 kb, totaling 41.5 Mb). The completeness scores of our assembly are among the highest currently published for Meloidogyne genomes. We predicted 10,284 protein-coding genes spanning 75.5% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61% of the genome. These TEs might promote genomic plasticity putatively related to the evolution of M. graminicola parasitism. This high-quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies of Meloidogyne species. In particular, this will foster comparative genomic studies to trace back the evolutionary history of M. graminicola and its closest relatives.
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Affiliation(s)
- Ngan Thi Phan
- IRD‐CIRAD‐University of MontpellierUMR Interactions Plantes Microorganismes Environnement (IPME)MontpellierFrance
| | - Julie Orjuela
- IRD‐CIRAD‐University of MontpellierUMR Interactions Plantes Microorganismes Environnement (IPME)MontpellierFrance
| | | | - Christophe Klopp
- Plateforme BioInfo GenotoulUR875INRAECastanet‐Tolosan cedexFrance
| | | | - Djampa K. Kozlowski
- Institut Sophia AgrobiotechINRAECNRSUniversité Côte d’AzurSophia AntipolisFrance
| | | | | | | | - Margot Zahm
- Plateforme BioInfo GenotoulUR875INRAECastanet‐Tolosan cedexFrance
| | | | - Stéphane Bellafiore
- IRD‐CIRAD‐University of MontpellierUMR Interactions Plantes Microorganismes Environnement (IPME)MontpellierFrance
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15
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Chapuis E, Ali N, Noûs C, Besnard G. Adaptive response to olive cultivation in a generalist parasitic nematode (Meloidogyne javanica). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractCultivated plants usually differ from their wild progenitors in several morphological and/or physiological traits. Their microbe communities might also differ because of adaptation to new conditions related to cultivation. To test this hypothesis, we investigated morphological traits in a parthenogenetic root-knot nematode (Meloidogyne javanica) from natural and agricultural environments. Seventeen populations of M. javanica were sampled on cultivated and wild olives in Morocco, then maintained in controlled conditions for a ‘common garden’ experiment. We estimated the genetic variation based on three traits (stylet size, neck width and body width) by a quantitative genetic design (ten families per population and nine individuals per family were measured), and molecular variation was investigated with a mitochondrial marker to identify the genetic lineages of nematode isolates sampled from wild and cultivated olives. Significant morphological differences were detected between individuals from wild vs. cultivated hosts for the three traits, whereas no phylogenetic clustering was observed among isolates collected on those two hosts. Our results thus suggest an adaptive response of the asexual parasite, possibly related to the deep modification of soil nematode communities between natural olive stands and orchards.
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Affiliation(s)
- Elodie Chapuis
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Nadeen Ali
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Guillaume Besnard
- CNRS, UPS, IRD, UMR5174, EDB, Université Toulouse III Paul Sabatier, Toulouse Cedex, France
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16
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Penouilh-Suzette C, Fourré S, Besnard G, Godiard L, Pecrix Y. A simple method for high molecular-weight genomic DNA extraction suitable for long-read sequencing from spores of an obligate biotroph oomycete. J Microbiol Methods 2020; 178:106054. [PMID: 32926900 DOI: 10.1016/j.mimet.2020.106054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/09/2020] [Accepted: 09/07/2020] [Indexed: 10/23/2022]
Abstract
Long-read sequencing technologies are having a major impact on our approaches to studying non-model organisms and microbial communities. By significantly reducing the cost and facilitating the genome assembly pipelines, any laboratory can now develop its own genomics program regardless of the complexity of the genome studied. The most crucial current challenge is to develop efficient protocols for extracting genomic DNA (gDNA) with high quality and integrity adapted to the organism of interest. This can be particularly complex for obligate pathogens that must maintain intimate interactions inside infected host tissues. Here we propose a simple and cost-effective method for high molecular weight gDNA extraction from spores of Plasmopara halstedii, an obligate biotroph oomycete pathogen responsible for downy mildew in sunflower. We optimized the yield, the quality and the integrity of the extracted gDNA by fine-tuning three critical parameters, the grinding, the lysis temperature and the lysis duration. We obtained gDNA with a fragment size distribution reaching a peak ranging from 79 to 145 kb. More than half of the extracted gDNA consisted of DNA fragments larger than 42 kb, with 23% of fragments larger than 100 kb. We then demonstrated the relevance of this protocol for long-read sequencing using PacBio RSII technology. With this protocol, we were able to obtain a mean read length of 9.3 kb, a max read length of 71 kb and an N50 of 13.3 kb. The development of such DNA extraction protocols is an essential prerequisite for fully exploiting technologies requiring high molecular weight gDNA (e.g. long-read sequencing or optical mapping). These technological advances will help generate data to answer questions such as the role of newly duplicated gene clusters, repeated regions, genomic structural variations or to define number of chromosomes that still remains undefined in many species of pathogenic fungi and oomycetes.
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Affiliation(s)
- Charlotte Penouilh-Suzette
- LIPM (Laboratoire des Interactions Plantes Microorganismes), INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde-Rouge, BP 52627, F-31326 Castanet-Tolosan, France.
| | - Sandra Fourré
- GeT-PlaGe, INRAE Auzeville, US 1426, 24 Chemin de Borde-Rouge, BP 52627, F-31326 Castanet-Tolosan, France.
| | - Guillaume Besnard
- CNRS, Université Paul Sabatier, IRD, UMR 5174 EDB (Laboratoire Évolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France.
| | - Laurence Godiard
- LIPM (Laboratoire des Interactions Plantes Microorganismes), INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde-Rouge, BP 52627, F-31326 Castanet-Tolosan, France.
| | - Yann Pecrix
- LIPM (Laboratoire des Interactions Plantes Microorganismes), INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde-Rouge, BP 52627, F-31326 Castanet-Tolosan, France; CIRAD, UMR 53 Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Pole de Protection des Plantes, 7 chemin de l'IRAT, F-97410 Saint Pierre, Réunion, France.
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Wood D, Besnard G, Beerling DJ, Osborne CP, Christin PA. Phylogenomics indicates the "living fossil" Isoetes diversified in the Cenozoic. PLoS One 2020; 15:e0227525. [PMID: 32555586 PMCID: PMC7302493 DOI: 10.1371/journal.pone.0227525] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 05/14/2020] [Indexed: 11/19/2022] Open
Abstract
The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.
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Affiliation(s)
- Daniel Wood
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Guillaume Besnard
- CNRS, Université de Toulouse, IRD, UMR 5174, EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | - David J. Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Colin P. Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
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18
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Díaz-Rueda P, Franco-Navarro JD, Messora R, Espartero J, Rivero-Núñez CM, Aleza P, Capote N, Cantos M, García-Fernández JL, de Cires A, Belaj A, León L, Besnard G, Colmenero-Flores JM. SILVOLIVE, a Germplasm Collection of Wild Subspecies With High Genetic Variability as a Source of Rootstocks and Resistance Genes for Olive Breeding. Front Plant Sci 2020; 11:629. [PMID: 32547577 PMCID: PMC7270354 DOI: 10.3389/fpls.2020.00629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Wild subspecies of Olea europaea constitute a source of genetic variability with huge potential for olive breeding to face global changes in Mediterranean-climate regions. We intend to identify wild olive genotypes with optimal adaptability to different environmental conditions to serve as a source of rootstocks and resistance genes for olive breeding. The SILVOLIVE collection includes 146 wild genotypes representative of the six O. europaea subspecies and early-generations hybrids. These genotypes came either from olive germplasm collections or from direct prospection in Spain, continental Africa and the Macaronesian archipelago. The collection was genotyped with plastid and nuclear markers, confirming the origin of the genotypes and their high genetic variability. Morphological and architectural parameters were quantified in 103 genotypes allowing the identification of three major groups of correlative traits including vigor, branching habits and the belowground-to-aboveground ratio. The occurrence of strong phenotypic variability in these traits within the germplasm collection has been shown. Furthermore, wild olive relatives are of great significance to be used as rootstocks for olive cultivation. Thus, as a proof of concept, different wild genotypes used as rootstocks were shown to regulate vigor parameters of the grafted cultivar "Picual" scion, which could improve the productivity of high-density hedgerow orchards.
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Affiliation(s)
- Pablo Díaz-Rueda
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Juan D. Franco-Navarro
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Rita Messora
- Plant Physiology Laboratory, Dipartimento Sci Vita, Univ Modena & Reggio Emilia, Modena, Italy
| | - Joaquín Espartero
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Carlos M. Rivero-Núñez
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Nieves Capote
- Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA) Centro Las Torres, Seville, Spain
| | - Manuel Cantos
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Jose L. García-Fernández
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Alfonso de Cires
- Departamento de Biología Vegetal y Ecología, Fac Biología, Univ de Sevilla, Seville, Spain
| | - Angjelina Belaj
- Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA) Centro Alameda del Obispo, Córdoba, Spain
| | - Lorenzo León
- Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA) Centro Alameda del Obispo, Córdoba, Spain
| | - Guillaume Besnard
- CNRS-UPS-IRD, EDB, UMR 5174, Université Paul Sabatier, Toulouse, France
| | - Jose M. Colmenero-Flores
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
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19
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Salmona J, Olofsson JK, Hong-Wa C, Razanatsoa J, Rakotonasolo F, Ralimanana H, Randriamboavonjy T, Suescun U, Vorontsova MS, Besnard G. Late Miocene origin and recent population collapse of the Malagasy savanna olive tree (Noronhia lowryi). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Jordi Salmona
- CNRS, Université Paul Sabatier, IRD, UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Cynthia Hong-Wa
- Claude E. Phillips Herbarium, Delaware State University, Dover, DE, USA
| | - Jacqueline Razanatsoa
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | - Franck Rakotonasolo
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
- Kew Madagascar Conservation Centre, Lot II J 131 Ambodivoanjo, Ivandry, Antananarivo, Madagascar
| | - Hélène Ralimanana
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | | | - Uxue Suescun
- CNRS, Université Paul Sabatier, IRD, UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | - Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Guillaume Besnard
- CNRS, Université Paul Sabatier, IRD, UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
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20
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Besnard G, Cheptou P, Debbaoui M, Lafont P, Hugueny B, Dupin J, Baali‐Cherif D. Paternity tests support a diallelic self-incompatibility system in a wild olive ( Olea europaea subsp. laperrinei, Oleaceae). Ecol Evol 2020; 10:1876-1888. [PMID: 32128122 PMCID: PMC7042767 DOI: 10.1002/ece3.5993] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 01/31/2023] Open
Abstract
Self-incompatibility (SI) is the main mechanism that favors outcrossing in plants. By limiting compatible matings, SI interferes in fruit production and breeding of new cultivars. In the Oleeae tribe (Oleaceae), an unusual diallelic SI system (DSI) has been proposed for three distantly related species including the olive (Olea europaea), but empirical evidence has remained controversial for this latter. The olive domestication is a complex process with multiple origins. As a consequence, the mixing of S-alleles from two distinct taxa, the possible artificial selection of self-compatible mutants and the large phenological variation of blooming may constitute obstacles for deciphering SI in olive. Here, we investigate cross-genotype compatibilities in the Saharan wild olive (O. e. subsp. laperrinei). As this taxon was geographically isolated for thousands of years, SI should not be affected by human selection. A population of 37 mature individuals maintained in a collection was investigated. Several embryos per mother were genotyped with microsatellites in order to identify compatible fathers that contributed to fertilization. While the pollination was limited by distance inside the collection, our results strongly support the DSI hypothesis, and all individuals were assigned to two incompatibility groups (G1 and G2). No self-fertilization was observed in our conditions. In contrast, crosses between full or half siblings were frequent (ca. 45%), which is likely due to a nonrandom assortment of related trees in the collection. Finally, implications of our results for orchard management and the conservation of olive genetic resources are discussed.
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Affiliation(s)
| | - Pierre‐Olivier Cheptou
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valery Montpellier 3MontpellierFrance
| | - Malik Debbaoui
- EDBUMR 5174CNRS‐IRD‐UPSUniversité Paul SabatierToulouse cedexFrance
| | - Pierre Lafont
- EDBUMR 5174CNRS‐IRD‐UPSUniversité Paul SabatierToulouse cedexFrance
| | - Bernard Hugueny
- EDBUMR 5174CNRS‐IRD‐UPSUniversité Paul SabatierToulouse cedexFrance
| | - Julia Dupin
- EDBUMR 5174CNRS‐IRD‐UPSUniversité Paul SabatierToulouse cedexFrance
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21
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Khadari B, El Bakkali A, Essalouh L, Tollon C, Pinatel C, Besnard G. Cultivated Olive Diversification at Local and Regional Scales: Evidence From the Genetic Characterization of French Genetic Resources. Front Plant Sci 2019; 10:1593. [PMID: 31921243 PMCID: PMC6937215 DOI: 10.3389/fpls.2019.01593] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/13/2019] [Indexed: 05/11/2023]
Abstract
Molecular characterization of crop genetic resources is a powerful approach to elucidate the origin of varieties and facilitate local cultivar management. Here we aimed to decipher the origin and diversification of French local olive germplasm. The 113 olive accessions of the ex situ collection of Porquerolles were characterized with 20 nuclear microsatellites plus their plastid haplotype. We then compared this collection to Mediterranean olive varieties from the Worldwide Olive Germplasm Bank of Marrakech, Morocco. High genetic diversity was observed within local French varieties, indicating a high admixture level, with an almost equal contribution from the three main Mediterranean gene pools. Nearly identical and closely related genotypes were observed among French and Italian/Spanish varieties. A high number of parent-offspring relationships were also detected among French varieties and between French and two Italian varieties ('Frantoio' and 'Moraiolo') and the Spanish variety ('Gordal Sevillana'). Our investigations indicated that French olive germplasm resulted from the diffusion of material from multiple origins followed by diversification based on parentage relationships between varieties. We strongly suggest that farmers have been actively selecting olives based on local French varieties. French olive agroecosystems more affected by unexpected frosts than southernmost regions could also be seen as incubators and as a bridge between Italy and Spain that has enhanced varietal olive diversification.
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Affiliation(s)
- Bouchaib Khadari
- AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- Conservatoire Botanique National Méditerranéen de Porquerolles (CBNMed), UMR AGAP, Montpellier, France
| | - Ahmed El Bakkali
- INRA, UR Amélioration des Plantes et Conservation des Ressources Phytogénétiques, Meknès, Morocco
| | - Laila Essalouh
- AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- Établissement Public Local d’Enseignement et de Formation Professionnelle Agricoles Nîmes-Rodilhan-CFPPA du Gard, Rodilhan, France
| | - Christine Tollon
- AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Christian Pinatel
- Centre Technique de l’Olivier, Maison des Agriculteurs, Aix-en-Provence, France
| | - Guillaume Besnard
- CNRS-IRD-UPS EDB, UMR 5174, Université Paul Sabatier, Toulouse, France
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22
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Yamada K, Davydov II, Besnard G, Salamin N. Duplication history and molecular evolution of the rbcS multigene family in angiosperms. J Exp Bot 2019; 70:6127-6139. [PMID: 31498865 PMCID: PMC6859733 DOI: 10.1093/jxb/erz363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/12/2019] [Indexed: 05/22/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the main enzyme determining the rate of photosynthesis. The small subunit of the protein, encoded by the rbcS gene, has been shown to influence the catalytic efficiency, CO2 specificity, assembly, activity, and stability of RuBisCO. However, the evolution of the rbcS gene remains poorly studied. We inferred the phylogenetic tree of the rbcS gene in angiosperms using the nucleotide sequences and found that it is composed of two lineages that may have existed before the divergence of land plants. Although almost all species sampled carry at least one copy of lineage 1, genes of lineage 2 were lost in most angiosperm species. We found the specific residues that have undergone positive selection during the evolution of the rbcS gene. We detected intensive coevolution between each rbcS gene copy and the rbcL gene encoding the large subunit of RuBisCO. We tested the role played by each rbcS gene copy on the stability of the RuBisCO protein through homology modelling. Our results showed that this evolutionary constraint could limit the level of divergence seen in the rbcS gene, which leads to the similarity among the rbcS gene copies of lineage 1 within species.
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Affiliation(s)
- Kana Yamada
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
| | - Iakov I Davydov
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Guillaume Besnard
- Laboratoire Evolution et Diversité Biologique (EDB UMR5174), CNRS-UPS-IRD, University of Toulouse III, Toulouse Cedex, France
| | - Nicolas Salamin
- Department of Computational Biology, Génopode, University of Lausanne, Lausanne, Switzerland
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23
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Salmona J, Olofsson JK, Hong-Wa C, Razanatsoa J, Rakotonasolo F, Ralimanana H, Randriamboavonjy T, Suescun U, Vorontsova MS, Besnard G. Late Miocene origin and recent population collapse of the Malagasy savanna olive tree (Noronhia lowryi). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz164] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Debates regarding the origin of tropical savannas have attempted to disentangle the role of human, biotic and abiotic factors. Understanding the origins of savanna remains essential to identifying processes that gave rise to habitat mosaics, particularly those found in the Central Plateau of Madagascar. Documenting the evolutionary history and demography of native trees occurring in open habitats may reveal footprints left by past and recent environmental changes. We conducted a population genetic analysis of an endangered Malagasy shrub (Noronhia lowryi, Oleaceae) of the Central Plateau. Seventy-seven individuals were sampled from three sites and genotyped at 14 nuclear and 24 chloroplast microsatellites. We found a highly contrasting nuclear and plastid genetic structure, suggesting that pollen-mediated gene flow allows panmixia, while seed-based dispersal may rarely exceed tens of metres. From a phylogeny based on full plastomes, we dated the surprisingly old crown age of maternal lineages back to ~6.2 Mya, perhaps co-occurring with the global expansion of savanna. In contrast, recent demographic history inferred from nuclear data shows a bottleneck signature ~350 generations ago, probably reflecting an environmental shift during the Late Pleistocene or the Holocene. Ancient in situ adaptation and recent demographic collapse of an endangered woody plant highlight the unique value and vulnerability of the Malagasy savannas.
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Affiliation(s)
- Jordi Salmona
- CNRS, Université Paul Sabatier, IRD, UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | - Cynthia Hong-Wa
- Claude E. Phillips Herbarium, Delaware State University, Dover, DE, USA
| | - Jacqueline Razanatsoa
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | - Franck Rakotonasolo
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
- Kew Madagascar Conservation Centre, Ivandry, Antananarivo, Madagascar
| | - Hélène Ralimanana
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | | | - Uxue Suescun
- CNRS, Université Paul Sabatier, IRD, UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | - Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Guillaume Besnard
- CNRS, Université Paul Sabatier, IRD, UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
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24
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Gros‐Balthazard M, Besnard G, Sarah G, Holtz Y, Leclercq J, Santoni S, Wegmann D, Glémin S, Khadari B. Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication. Plant J 2019; 100:143-157. [PMID: 31192486 PMCID: PMC6851578 DOI: 10.1111/tpj.14435] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/11/2023]
Abstract
The olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio-economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA-sequencing data for 68 wild and cultivated olive trees to study the genetic diversity and structure both at the transcription and sequence levels. To localize putative genes or expression pathways targeted by artificial selection during domestication, we employed a two-step approach in which we identified differentially expressed genes and screened the transcriptome for signatures of selection. Our analyses support a major domestication event in the eastern part of the Mediterranean basin followed by dispersion towards the West and subsequent admixture with western wild olives. While we found large changes in gene expression when comparing cultivated and wild olives, we found no major signature of selection on coding variants and weak signals primarily affected transcription factors. Our results indicated that the domestication of olives resulted in only moderate genomic consequences and that the domestication syndrome is mainly related to changes in gene expression, consistent with its evolutionary history and life history traits.
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Affiliation(s)
- Muriel Gros‐Balthazard
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Present address:
New York University Abu Dhabi (NYUAD), Center for Genomics and Systems BiologySaadiyat IslandAbu DhabiUnited Arab Emirates
| | | | - Gautier Sarah
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Yan Holtz
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Julie Leclercq
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Sylvain Santoni
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
| | - Sylvain Glémin
- CNRSUniversité de RennesECOBIO (Ecosystèmes, biodiversité, évolution) − UMR 6553F‐35000RennesFrance
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Bouchaib Khadari
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Conservatoire Botanique National MéditerranéenUMR AGAPMontpellierFrance
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25
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Dunning LT, Moreno-Villena JJ, Lundgren MR, Dionora J, Salazar P, Adams C, Nyirenda F, Olofsson JK, Mapaura A, Grundy IM, Kayombo CJ, Dunning LA, Kentatchime F, Ariyarathne M, Yakandawala D, Besnard G, Quick WP, Bräutigam A, Osborne CP, Christin PA. Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata. J Exp Bot 2019; 70:3255-3268. [PMID: 30949663 PMCID: PMC6598098 DOI: 10.1093/jxb/erz149] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/19/2019] [Indexed: 05/23/2023]
Abstract
C4 photosynthesis is a complex trait that boosts productivity in tropical conditions. Compared with C3 species, the C4 state seems to require numerous novelties, but species comparisons can be confounded by long divergence times. Here, we exploit the photosynthetic diversity that exists within a single species, the grass Alloteropsis semialata, to detect changes in gene expression associated with different photosynthetic phenotypes. Phylogenetically informed comparative transcriptomics show that intermediates with a weak C4 cycle are separated from the C3 phenotype by increases in the expression of 58 genes (0.22% of genes expressed in the leaves), including those encoding just three core C4 enzymes: aspartate aminotransferase, phosphoenolpyruvate carboxykinase, and phosphoenolpyruvate carboxylase. The subsequent transition to full C4 physiology was accompanied by increases in another 15 genes (0.06%), including only the core C4 enzyme pyruvate orthophosphate dikinase. These changes probably created a rudimentary C4 physiology, and isolated populations subsequently improved this emerging C4 physiology, resulting in a patchwork of expression for some C4 accessory genes. Our work shows how C4 assembly in A. semialata happened in incremental steps, each requiring few alterations over the previous step. These create short bridges across adaptive landscapes that probably facilitated the recurrent origins of C4 photosynthesis through a gradual process of evolution.
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Affiliation(s)
- Luke T Dunning
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | | | - Marjorie R Lundgren
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | | | - Paolo Salazar
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Claire Adams
- Botany Department, Rhodes University, Grahamstown, South Africa
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Jill K Olofsson
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
| | | | - Isla M Grundy
- Institute of Environmental Studies, University of Zimbabwe, Harare, Zimbabwe
| | | | - Lucy A Dunning
- Department of Social Sciences, University of Sheffield, Sheffield, UK
| | | | - Menaka Ariyarathne
- Department of Botany, Faculty of Science, University of Peradeniya, Peradeiya, Sri Lanka
| | - Deepthi Yakandawala
- Department of Botany, Faculty of Science, University of Peradeniya, Peradeiya, Sri Lanka
| | - Guillaume Besnard
- Laboratoire Évolution et Diversité Biologique (EDB UMR5174), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - W Paul Quick
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | | | - Colin P Osborne
- Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, UK
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26
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Olofsson JK, Cantera I, Van de Paer C, Hong-Wa C, Zedane L, Dunning LT, Alberti A, Christin PA, Besnard G. Phylogenomics using low-depth whole genome sequencing: A case study with the olive tribe. Mol Ecol Resour 2019; 19:877-892. [PMID: 30934146 DOI: 10.1111/1755-0998.13016] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 12/20/2022]
Abstract
Species trees have traditionally been inferred from a few selected markers, and genome-wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historical species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these data sets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Here we evaluate different reference-based methods to infer phylogenies of large taxonomic groups from such data sets. Using the example of the Oleeae tribe, a worldwide-distributed group, we build phylogenies based on single nucleotide polymorphisms (SNPs) obtained using two reference genomes (the olive and ash trees). The inferred phylogenies are overall congruent, yet present differences that might reflect the effect of distance to the reference on the amount of missing data. To limit this issue, genome complexity was reduced by using pairs of orthologous coding sequences as the reference, thus allowing us to combine SNPs obtained using two distinct references. Concatenated and coalescence trees based on these combined SNPs suggest events of incomplete lineage sorting and/or hybridization during the diversification of this large phylogenetic group. Our results show that genome-wide phylogenetic trees can be inferred from low-depth sequence data sets for eukaryote groups with complex genomes, and histories of reticulate evolution. This opens new avenues for large-scale phylogenomics and biogeographical analyses covering both the extant and the historical diversity stored in museum collections.
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Affiliation(s)
- Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Isabel Cantera
- Laboratoire Évolution and Diversité Biologique (EDB, UMR5174), CNRS, UPS, IRD, Université de Toulouse, Toulouse, France
| | - Céline Van de Paer
- Laboratoire Évolution and Diversité Biologique (EDB, UMR5174), CNRS, UPS, IRD, Université de Toulouse, Toulouse, France
| | - Cynthia Hong-Wa
- Claude E. Phillips Herbarium, Delaware State University, Dover, Delaware
| | - Loubab Zedane
- Laboratoire Évolution and Diversité Biologique (EDB, UMR5174), CNRS, UPS, IRD, Université de Toulouse, Toulouse, France
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Adriana Alberti
- Genoscope, CEA - Institut de biologie François-Jacob, Evry Cedex, France
| | | | - Guillaume Besnard
- Laboratoire Évolution and Diversité Biologique (EDB, UMR5174), CNRS, UPS, IRD, Université de Toulouse, Toulouse, France
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27
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Lundgren MR, Dunning LT, Olofsson JK, Moreno-Villena JJ, Bouvier JW, Sage TL, Khoshravesh R, Sultmanis S, Stata M, Ripley BS, Vorontsova MS, Besnard G, Adams C, Cuff N, Mapaura A, Bianconi ME, Long CM, Christin PA, Osborne CP. C 4 anatomy can evolve via a single developmental change. Ecol Lett 2018; 22:302-312. [PMID: 30557904 PMCID: PMC6849723 DOI: 10.1111/ele.13191] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 01/05/2023]
Abstract
C4 photosynthesis is a complex trait that boosts productivity in warm environments. Paradoxically, it evolved independently in numerous plant lineages, despite requiring specialised leaf anatomy. The anatomical modifications underlying C4 evolution have previously been evaluated through interspecific comparisons, which capture numerous changes besides those needed for C4 functionality. Here, we quantify the anatomical changes accompanying the transition between non‐C4 and C4 phenotypes by sampling widely across the continuum of leaf anatomical traits in the grass Alloteropsis semialata. Within this species, the only trait that is shared among and specific to C4 individuals is an increase in vein density, driven specifically by minor vein development that yields multiple secondary effects facilitating C4 function. For species with the necessary anatomical preconditions, developmental proliferation of veins can therefore be sufficient to produce a functional C4 leaf anatomy, creating an evolutionary entry point to complex C4 syndromes that can become more specialised.
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Affiliation(s)
- Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Jose J Moreno-Villena
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Jacques W Bouvier
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Tammy L Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Roxana Khoshravesh
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Stefanie Sultmanis
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Matt Stata
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Brad S Ripley
- Botany Department, Rhodes University, Grahamstown, 6139, South Africa
| | - Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Guillaume Besnard
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174), Université de Toulouse, CNRS, ENSFEA, UPS, IRD, 118 route de Narbonne, 31062, Toulouse, France
| | - Claire Adams
- Botany Department, Rhodes University, Grahamstown, 6139, South Africa
| | - Nicholas Cuff
- Northern Territory Herbarium, Department of Environment and Natural Resources, PO Box 496, Palmerston, NT, 0831, Australia
| | | | - Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Christine M Long
- Department of Primary Industry and Fisheries, Northern Territory Government, Darwin, NT, 0801, Australia
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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28
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Solofondranohatra CL, Vorontsova MS, Hackel J, Besnard G, Cable S, Williams J, Jeannoda V, Lehmann CER. Grass Functional Traits Differentiate Forest and Savanna in the Madagascar Central Highlands. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00184] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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29
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Besnard G, Terral JF, Cornille A. On the origins and domestication of the olive: a review and perspectives. Ann Bot 2018; 121:385-403. [PMID: 29293871 PMCID: PMC5838823 DOI: 10.1093/aob/mcx145] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
Background Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully. Scope The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide. Conclusion The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENSFEA-IRD, EDB, UMR 5174, Université Paul Sabatier, Toulouse Cedex , France
| | - Jean-Frédéric Terral
- ISEM, UMR 5554, CNRS-Université de Montpellier-IRD-EPHE, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Montpellier Cedex, France
- International Associated Laboratory (LIA, CNRS) EVOLea, Zürich, Switzerland
| | - Amandine Cornille
- Center for Adaptation to a Changing Environment, ETH Zürich, Zürich, Switzerland
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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30
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Besnard G, Terral JF, Cornille A. On the origins and domestication of the olive: a review and perspectives. Ann Bot 2018; 121:587-588. [PMID: 29390111 PMCID: PMC5838833 DOI: 10.1093/aob/mcy002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
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31
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Bruxaux J, Gabrielli M, Ashari H, Prŷs-Jones R, Joseph L, Milá B, Besnard G, Thébaud C. Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds. Mol Phylogenet Evol 2018; 120:248-258. [DOI: 10.1016/j.ympev.2017.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
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Piot A, Hackel J, Christin PA, Besnard G. One-third of the plastid genes evolved under positive selection in PACMAD grasses. Planta 2018; 247:255-266. [PMID: 28956160 DOI: 10.1007/s00425-017-2781-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/18/2017] [Indexed: 05/10/2023]
Abstract
We demonstrate that rbcL underwent strong positive selection during the C 3 -C 4 photosynthetic transitions in PACMAD grasses, in particular the 3' end of the gene. In contrast, selective pressures on other plastid genes vary widely and environmental drivers remain to be identified. Plastid genomes have been widely used to infer phylogenetic relationships among plants, but the selective pressures driving their evolution have not been systematically investigated. In our study, we analyse all protein-coding plastid genes from 113 species of PACMAD grasses (Poaceae) to evaluate the selective pressures driving their evolution. Our analyses confirm that the gene encoding the large subunit of RubisCO (rbcL) evolved under strong positive selection after C3-C4 photosynthetic transitions. We highlight new codons in rbcL that underwent parallel changes, in particular those encoding the C-terminal part of the protein. C3-C4 photosynthetic shifts did not significantly affect the evolutionary dynamics of other plastid genes. Instead, while two-third of the plastid genes evolved under purifying selection or neutrality, 25 evolved under positive selection across the PACMAD clade. This set of genes encode for proteins involved in diverse functions, including self-replication of plastids and photosynthesis. Our results suggest that plastid genes widely adapt to changing ecological conditions, but factors driving this evolution largely remain to be identified.
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Affiliation(s)
- Anthony Piot
- Laboratoire Evolution and Diversité Biologique (EDB, UMR 5174), CNRS/ENSFEA/IRD/Université Toulouse III, 118 Route de Narbonne, 31062, Toulouse, France.
| | - Jan Hackel
- Laboratoire Evolution and Diversité Biologique (EDB, UMR 5174), CNRS/ENSFEA/IRD/Université Toulouse III, 118 Route de Narbonne, 31062, Toulouse, France
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Guillaume Besnard
- Laboratoire Evolution and Diversité Biologique (EDB, UMR 5174), CNRS/ENSFEA/IRD/Université Toulouse III, 118 Route de Narbonne, 31062, Toulouse, France.
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Van de Paer C, Bouchez O, Besnard G. Prospects on the evolutionary mitogenomics of plants: A case study on the olive family (Oleaceae). Mol Ecol Resour 2017; 18:407-423. [PMID: 29172252 DOI: 10.1111/1755-0998.12742] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/14/2017] [Accepted: 11/18/2017] [Indexed: 11/30/2022]
Abstract
The mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic male sterility (CMS) and of potentially contrasted organelle inheritance are known. We compare the diversity and the evolution of mitochondrial and chloroplast genomes by focusing on the olive complex and related genera. Using high-throughput techniques, we reconstructed complete mitogenomes (ca. 0.7 Mb) and plastomes (ca. 156 kb) for six olive accessions and one Chionanthus. A highly variable organization of mitogenomes was observed at the species level. In olive, two specific chimeric genes were identified in the mitogenome of lineage E3 and may be involved in CMS. Plastid-derived regions (mtpt) were observed in all reconstructed mitogenomes. Through phylogenetic reconstruction, we demonstrate that multiple integrations of mtpt regions have occurred in Oleaceae, but mtpt regions shared by all members of the olive complex derive from a common ancestor. We then assembled 52 conserved mitochondrial gene regions and complete plastomes of ten additional accessions belonging to tribes Oleeae, Fontanesieae and Forsythieae. Phylogenetic congruence between topologies based on mitochondrial regions and plastomes suggests a strong disequilibrium linkage between both organellar genomes. Finally, while phylogenetic reconstruction based on plastomes fails to resolve the evolutionary history of maternal olive lineages in the Mediterranean area, their phylogenetic relationships were successfully resolved with complete mitogenomes. Overall, our study demonstrates the great potential of using mitochondrial DNA in plant phylogeographic and metagenomic studies.
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Affiliation(s)
- Céline Van de Paer
- CNRS, Université de Toulouse, ENSFEA, IRD, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
| | - Olivier Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Guillaume Besnard
- CNRS, Université de Toulouse, ENSFEA, IRD, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), Toulouse, France
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34
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Ali N, Tavoillot J, Besnard G, Khadari B, Dmowska E, Winiszewska G, Fossati-Gaschignard O, Ater M, Aït Hamza M, El Mousadik A, El Oualkadi A, Moukhli A, Essalouh L, El Bakkali A, Chapuis E, Mateille T. How anthropogenic changes may affect soil-borne parasite diversity? Plant-parasitic nematode communities associated with olive trees in Morocco as a case study. BMC Ecol 2017; 17:4. [PMID: 28166763 PMCID: PMC5294739 DOI: 10.1186/s12898-016-0113-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 12/16/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Plant-parasitic nematodes (PPN) are major crop pests. On olive (Olea europaea), they significantly contribute to economic losses in the top-ten olive producing countries in the world especially in nurseries and under cropping intensification. The diversity and the structure of PPN communities respond to environmental and anthropogenic forces. The olive tree is a good host plant model to understand the impact of such forces on PPN diversity since it grows according to different modalities (wild, feral and cultivated olives). A wide soil survey was conducted in several olive-growing regions in Morocco. The taxonomical and the functional diversity as well as the structures of PPN communities were described and then compared between non-cultivated (wild and feral forms) and cultivated (traditional and high-density olive cultivation) olives. RESULTS A high diversity of PPN with the detection of 117 species and 47 genera was revealed. Some taxa were recorded for the first time on olive trees worldwide and new species were also identified. Anthropogenic factors (wild vs cultivated conditions) strongly impacted the PPN diversity and the functional composition of communities because the species richness, the local diversity and the evenness of communities significantly decreased and the abundance of nematodes significantly increased in high-density conditions. Furthermore, these conditions exhibited many more obligate and colonizer PPN and less persister PPN compared to non-cultivated conditions. Taxonomical structures of communities were also impacted: genera such as Xiphinema spp. and Heterodera spp. were dominant in wild olive, whereas harmful taxa such as Meloidogyne spp. were especially enhanced in high-density orchards. CONCLUSIONS Olive anthropogenic practices reduce the PPN diversity in communities and lead to changes of the community structures with the development of some damaging nematodes. The study underlined the PPN diversity as a relevant indicator to assess community pathogenicity. That could be taken into account in order to design control strategies based on community rearrangements and interactions between species instead of reducing the most pathogenic species.
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Affiliation(s)
- Nadine Ali
- Plant Protection Department, Faculty of Agriculture, Tishreen University, PO Box 2233, Latakia, Syrian Arab Republic
- IRD, UMR CBGP, 755 Avenue du Campus Agropolis, CS30016, 34988 Montferrier-sur-Lez Cedex, France
| | - Johannes Tavoillot
- IRD, UMR CBGP, 755 Avenue du Campus Agropolis, CS30016, 34988 Montferrier-sur-Lez Cedex, France
| | - Guillaume Besnard
- CNRS, UMR EDB, Université Toulouse III Paul Sabatier, Bâtiment 4R1, 118 Route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Bouchaib Khadari
- UMR AGAP, SUPAGRO, Campus CIRAD, TAA-108/03, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Ewa Dmowska
- Museum and Institute of Zoology PAS, Wilcza 64, 00-679 Warsaw, Poland
| | | | | | - Mohammed Ater
- Faculté des Sciences et Techniques, Université Abdelmalek Essaadi, BP 2062, 93030 Tétouan, Morocco
| | - Mohamed Aït Hamza
- Laboratoire LBVRN, Faculté des Sciences d’Agadir, Université Ibn Zohr, BP 8106, 80000 Agadir, Morocco
| | - Abdelhamid El Mousadik
- Laboratoire LBVRN, Faculté des Sciences d’Agadir, Université Ibn Zohr, BP 8106, 80000 Agadir, Morocco
| | | | | | - Laila Essalouh
- UMR AGAP, SUPAGRO, Campus CIRAD, TAA-108/03, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | | | - Elodie Chapuis
- IRD, UMR CBGP, 755 Avenue du Campus Agropolis, CS30016, 34988 Montferrier-sur-Lez Cedex, France
- IRD, UMR IPME (IRD/Université de Montpellier/CIRAD), 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
- UMR PVBMT, 3P-CIRAD, 7 chemin de l’Irat, Ligne paradis, 97410 Saint Pierre, Réunion
| | - Thierry Mateille
- IRD, UMR CBGP, 755 Avenue du Campus Agropolis, CS30016, 34988 Montferrier-sur-Lez Cedex, France
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35
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Silva C, Besnard G, Piot A, Razanatsoa J, Oliveira RP, Vorontsova MS. Museomics resolve the systematics of an endangered grass lineage endemic to north-western Madagascar. Ann Bot 2017; 119:339-351. [PMID: 28028020 PMCID: PMC5314640 DOI: 10.1093/aob/mcw208] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 07/28/2016] [Accepted: 08/24/2016] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Recent developments in DNA sequencing, so-called next-generation sequencing (NGS) methods, can help the study of rare lineages that are known from museum specimens. Here, the taxonomy and evolution of the Malagasy grass lineage Chasechloa was investigated with the aid of NGS. METHODS Full chloroplast genome data and some nuclear sequences were produced by NGS from old herbarium specimens, while some selected markers were generated from recently collected Malagasy grasses. In addition, a scanning electron microscopy analysis of the upper floret and cross-sections of the rachilla appendages followed by staining with Sudan IV were performed on Chasechloa to examine the morphology of the upper floret and the presence of oils in the appendages. KEY RESULTS Chasechloa was recovered within tribe Paniceae, sub-tribe Boivinellinae, contrary to its previous placement as a member of the New World genus Echinolaena (tribe Paspaleae). Chasechloa originated in Madagascar between the Upper Miocene and the Pliocene. It comprises two species, one of them collected only once in 1851. The genus is restricted to north-western seasonally dry deciduous forests. The appendages at the base of the upper floret of Chasechloa have been confirmed as elaiosomes, an evolutionary adaptation for myrmecochory. CONCLUSIONS Chasechloa is reinstated at the generic level and a taxonomic treatment is presented, including conservation assessments of its species. Our study also highlights the power of NGS technology to analyse relictual or probably extinct groups.
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Affiliation(s)
- Christian Silva
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Programa de Pós-graduação em Botânica, Av. Transnordestina s.n., Feira de Santana, Bahia 44036-900, Brazil
| | - Guillaume Besnard
- CNRS, Université de Toulouse, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France
| | - Anthony Piot
- CNRS, Université de Toulouse, ENFA, UMR5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, 31062 Toulouse, France
| | - Jacqueline Razanatsoa
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, BP 4096, Antananarivo 101, Madagascar
| | - Reyjane P Oliveira
- Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Programa de Pós-graduação em Botânica, Av. Transnordestina s.n., Feira de Santana, Bahia 44036-900, Brazil
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Olofsson JK, Bianconi M, Besnard G, Dunning LT, Lundgren MR, Holota H, Vorontsova MS, Hidalgo O, Leitch IJ, Nosil P, Osborne CP, Christin P. Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait. Mol Ecol 2016; 25:6107-6123. [PMID: 27862505 PMCID: PMC6849575 DOI: 10.1111/mec.13914] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 10/27/2016] [Accepted: 11/09/2016] [Indexed: 01/17/2023]
Abstract
Physiological novelties are often studied at macro-evolutionary scales such that their micro-evolutionary origins remain poorly understood. Here, we test the hypothesis that key components of a complex trait can evolve in isolation and later be combined by gene flow. We use C4 photosynthesis as a study system, a derived physiology that increases plant productivity in warm, dry conditions. The grass Alloteropsis semialata includes C4 and non-C4 genotypes, with some populations using laterally acquired C4 -adaptive loci, providing an outstanding system to track the spread of novel adaptive mutations. Using genome data from C4 and non-C4 A. semialata individuals spanning the species' range, we infer and date past migrations of different parts of the genome. Our results show that photosynthetic types initially diverged in isolated populations, where key C4 components were acquired. However, rare but recurrent subsequent gene flow allowed the spread of adaptive loci across genetic pools. Indeed, laterally acquired genes for key C4 functions were rapidly passed between populations with otherwise distinct genomic backgrounds. Thus, our intraspecific study of C4 -related genomic variation indicates that components of adaptive traits can evolve separately and later be combined through secondary gene flow, leading to the assembly and optimization of evolutionary innovations.
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Affiliation(s)
- Jill K. Olofsson
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Matheus Bianconi
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Guillaume Besnard
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174)Université de ToulouseCNRS, ENSFEA, UPS118 route de NarbonneF‐31062ToulouseFrance
| | - Luke T. Dunning
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Marjorie R. Lundgren
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Helene Holota
- Laboratoire Évolution & Diversité Biologique (EDB UMR5174)Université de ToulouseCNRS, ENSFEA, UPS118 route de NarbonneF‐31062ToulouseFrance
| | | | | | | | - Patrik Nosil
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Colin P. Osborne
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Pascal‐Antoine Christin
- Department of Animal and Plant SciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
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Vorontsova MS, Besnard G, Forest F, Malakasi P, Moat J, Clayton WD, Ficinski P, Savva GM, Nanjarisoa OP, Razanatsoa J, Randriatsara FO, Kimeu JM, Luke WRQ, Kayombo C, Linder HP. Madagascar's grasses and grasslands: anthropogenic or natural? Proc Biol Sci 2016; 283:rspb.2015.2262. [PMID: 26791612 PMCID: PMC4795014 DOI: 10.1098/rspb.2015.2262] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Grasses, by their high productivity even under very low pCO2, their ability to survive repeated burning and to tolerate long dry seasons, have transformed the terrestrial biomes in the Neogene and Quaternary. The expansion of grasslands at the cost of biodiverse forest biomes in Madagascar is often postulated as a consequence of the Holocene settlement of the island by humans. However, we show that the Malagasy grass flora has many indications of being ancient with a long local evolutionary history, much predating the Holocene arrival of humans. First, the level of endemism in the Madagascar grass flora is well above the global average for large islands. Second, a survey of many of the more diverse areas indicates that there is a very high spatial and ecological turnover in the grass flora, indicating a high degree of niche specialization. We also find some evidence that there are both recently disturbed and natural stable grasslands: phylogenetic community assembly indicates that recently severely disturbed grasslands are phylogenetically clustered, whereas more undisturbed grasslands tend to be phylogenetically more evenly distributed. From this evidence, it is likely that grass communities existed in Madagascar long before human arrival and so were determined by climate, natural grazing and other natural factors. Humans introduced zebu cattle farming and increased fire frequency, and may have triggered an expansion of the grasslands. Grasses probably played the same role in the modification of the Malagasy environments as elsewhere in the tropics.
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Affiliation(s)
- Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Guillaume Besnard
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France
| | - Félix Forest
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Panagiota Malakasi
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Justin Moat
- Bioinformatics and Spatial Analysis, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK School of Geography, University of Nottingham, Nottingham NG7 2RD, UK
| | - W Derek Clayton
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Paweł Ficinski
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - George M Savva
- School of Health Sciences, University of East Anglia, Norwich, Norfolk NR4 7TJ, UK
| | - Olinirina P Nanjarisoa
- Kew Madagascar Conservation Centre, II J 131 B, Ambodivoanjo, Ivandry, Antananarivo 101, Madagascar
| | | | - Fetra O Randriatsara
- Kew Madagascar Conservation Centre, II J 131 B, Ambodivoanjo, Ivandry, Antananarivo 101, Madagascar Ecole Supérieure des Sciences Agronomiques, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - John M Kimeu
- National Museums of Kenya, Museum Hill Road, PO Box 45166, Nairobi 00100, Kenya
| | - W R Quentin Luke
- National Museums of Kenya, Museum Hill Road, PO Box 45166, Nairobi 00100, Kenya
| | - Canisius Kayombo
- Forestry Training Institute, Olmotonyi, PO Box 943, Arusha, Tanzania
| | - H Peter Linder
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, Zurich 8008, Switzerland
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Besnard G, Cuneo P. An ecological and evolutionary perspective on the parallel invasion of two cross-compatible trees. AoB Plants 2016; 8:plw056. [PMID: 27519914 PMCID: PMC5018386 DOI: 10.1093/aobpla/plw056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 08/01/2016] [Indexed: 05/29/2023]
Abstract
Invasive trees are generally seen as ecosystem-transforming plants that can have significant impacts on native vegetation, and often require management and control. Understanding their history and biology is essential to guide actions of land managers. Here, we present a summary of recent research into the ecology, phylogeography and management of invasive olives, which are now established outside of their native range as high ecological impact invasive trees. The parallel invasion of European and African olive in different climatic zones of Australia provides an interesting case study of invasion, characterized by early genetic admixture between domesticated and wild taxa. Today, the impact of the invasive olives on native vegetation and ecosystem function is of conservation concern, with European olive a declared weed in areas of South Australia, and African olive a declared weed in New South Wales and Pacific islands. Population genetics was used to trace the origins and invasion of both subspecies in Australia, indicating that both olive subspecies have hybridized early after introduction. Research also indicates that African olive populations can establish from a low number of founder individuals even after successive bottlenecks. Modelling based on distributional data from the native and invasive range identified a shift of the realized ecological niche in the Australian invasive range for both olive subspecies, which was particularly marked for African olive. As highly successful and long-lived invaders, olives offer further opportunities to understand the genetic basis of invasion, and we propose that future research examines the history of introduction and admixture, the genetic basis of adaptability and the role of biotic interactions during invasion. Advances on these questions will ultimately improve predictions on the future olive expansion and provide a solid basis for better management of invasive populations.
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Affiliation(s)
- Guillaume Besnard
- CNRS, UPS, ENFA, Laboratoire Evolution & Diversité Biologique, UMR 5174, 31062 Toulouse 4, France
| | - Peter Cuneo
- The Australian PlantBank, Royal Botanic Gardens and Domain Trust, The Australian Botanic Garden, Mount Annan, NSW 2567, Australia
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Lundgren MR, Christin PA, Escobar EG, Ripley BS, Besnard G, Long CM, Hattersley PW, Ellis RP, Leegood RC, Osborne CP. Evolutionary implications of C3 -C4 intermediates in the grass Alloteropsis semialata. Plant Cell Environ 2016; 39:1874-1885. [PMID: 26524631 DOI: 10.1111/pce.12665] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 10/21/2015] [Accepted: 10/25/2015] [Indexed: 06/05/2023]
Abstract
C4 photosynthesis is a complex trait resulting from a series of anatomical and biochemical modifications to the ancestral C3 pathway. It is thought to evolve in a stepwise manner, creating intermediates with different combinations of C4 -like components. Determining the adaptive value of these components is key to understanding how C4 photosynthesis can gradually assemble through natural selection. Here, we decompose the photosynthetic phenotypes of numerous individuals of the grass Alloteropsis semialata, the only species known to include both C3 and C4 genotypes. Analyses of δ(13) C, physiology and leaf anatomy demonstrate for the first time the existence of physiological C3 -C4 intermediate individuals in the species. Based on previous phylogenetic analyses, the C3 -C4 individuals are not hybrids between the C3 and C4 genotypes analysed, but instead belong to a distinct genetic lineage, and might have given rise to C4 descendants. C3 A. semialata, present in colder climates, likely represents a reversal from a C3 -C4 intermediate state, indicating that, unlike C4 photosynthesis, evolution of the C3 -C4 phenotype is not irreversible.
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Affiliation(s)
- Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Emmanuel Gonzalez Escobar
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Brad S Ripley
- Botany Department, Rhodes University, Grahamstown, 6139, South Africa
| | - Guillaume Besnard
- CNRS, Université de Toulouse, ENFA, UMR5174 EDB (Laboratoire Évolution and Diversité Biologique), 118 Route de Narbonne, Toulouse, 31062, France
| | - Christine M Long
- Department of Primary Industry and Fisheries, Northern Territory Government, Darwin, NT, 0801, Australia
| | - Paul W Hattersley
- School of Chemistry and Biochemistry (honorary research fellow), University of Western Australia, Crawley, WA, 6009, Australia
| | | | - Richard C Leegood
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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Besnard G, Thèves C, Mata X, Holota H, Rakotozafy LMA, Pedrono M. Shotgun sequencing of the mitochondrial genome of the Aldabra giant tortoise (Aldabrachelys gigantea). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:4543-4544. [PMID: 27159683 DOI: 10.3109/19401736.2015.1101554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the Aldabra giant tortoise [Aldabrachelys gigantea (Schweigger, 1812): Reptilia, Testudines, Testudinidae] was sequenced using a shotgun approach on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA). This genome was 16 467 bp long and presents the typical organization found in vertebrates. The mean coverage of sequencing was 116×. A phylogenetic analysis of the Testudinidae confirms the placement of Aldabrachelys in an Indian Ocean group (including Madagascar). This mitogenome constitutes a reference for ancient DNA analyses of the extinct Madagascan lineages of Aldabrachelys.
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Affiliation(s)
| | - Catherine Thèves
- b Laboratoire AMIS , UMR 5288, Université de Toulouse/CNRS , Toulouse , France
| | - Xavier Mata
- b Laboratoire AMIS , UMR 5288, Université de Toulouse/CNRS , Toulouse , France
| | - Hélène Holota
- a Laboratoire EDB , UMR5174, CNRS-UPS-ENFA , Toulouse , France
| | - Lucien M A Rakotozafy
- c Laboratoire de Zooarchéologie , Institut des Civilisations, Musée d'Art et d'Archéologie de l'Université d'Antananarivo , Antananarivo , Madagascar
| | - Miguel Pedrono
- d CIRAD, UPR AGIRs , Antananarivo , Madagascar.,e CIRAD, UPR AGIRs, Campus International de Baillarguet , Montpellier , France
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, 31062, Toulouse Cedex 9, France
| | - Rafael Rubio de Casas
- Estación Experimental de Zonas Áridas, EEZA-CSIC, Carretera de Sacramento s/n, 04120, Almería, Spain
- UMR 5175 CEFE-Centre d'Ecologie Fonctionnelle et Evolutive (CNRS), 1919 Route de Mende, 34293, Montpellier Cedex 05, France
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Lundgren MR, Besnard G, Ripley BS, Lehmann CER, Chatelet DS, Kynast RG, Namaganda M, Vorontsova MS, Hall RC, Elia J, Osborne CP, Christin PA. Photosynthetic innovation broadens the niche within a single species. Ecol Lett 2015; 18:1021-9. [DOI: 10.1111/ele.12484] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 07/03/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Marjorie R. Lundgren
- Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Sheffield S10 2TN UK
| | - Guillaume Besnard
- CNRS; Université Toulouse III - Paul Sabatier; ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); 118 route de Narbonne 31062 Toulouse France
| | - Brad S. Ripley
- Department of Botany; Rhodes University; Grahamstown 6139 South Africa
| | - Caroline E. R. Lehmann
- School of GeoSciences; University of Edinburgh; Crew Building The King's Buildings Alexander Crum Brown Road Edinburgh EH9 3FF UK
| | - David S. Chatelet
- Department of Ecology and Evolutionary Biology; Brown University; Providence RI USA
| | | | - Mary Namaganda
- Department of Biological Sciences; Makerere University; PO Box 7062 Kampala Uganda
| | | | - Russell C. Hall
- Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Sheffield S10 2TN UK
| | - John Elia
- National Herbarium of Tanzania; Arusha Tanzania
| | - Colin P. Osborne
- Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Sheffield S10 2TN UK
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Sheffield S10 2TN UK
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Bellafiore S, Jougla C, Chapuis É, Besnard G, Suong M, Vu PN, De Waele D, Gantet P, Thi XN. Intraspecific variability of the facultative meiotic parthenogenetic root-knot nematode (Meloidogyne graminicola) from rice fields in Vietnam. C R Biol 2015; 338:471-83. [PMID: 26026576 DOI: 10.1016/j.crvi.2015.04.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 04/05/2015] [Accepted: 04/06/2015] [Indexed: 11/15/2022]
Abstract
Twenty years ago, the facultative meiotic parthenogenetic root-knot nematode (RKN), Meloidogyne graminicola, was recognised as an important rice pathogen in South Vietnam. Although this country is one of the most important rice exporters worldwide, a comprehensive picture of the occurrence of M. graminicola in Vietnamese rice fields is still not available. Therefore a nematode survey was carried out with the aim of better understanding the geographical distribution, and the pathogenic and genetic variability of the RKN in Vietnam. From the fields surveyed in a range of ecosystems, 21 RKN populations were recovered from infected rice roots. A diagnostic SCAR marker was developed showing that all Vietnamese populations belong to M. graminicola. Furthermore, sequencing of the Internal Transcribed Spacer (ITS) of the rDNA genes confirmed this identification. These populations were then characterised using morphometrics and pathogenicity tests (host plant range diversity, reproduction and virulence diversity) revealing intraspecific variability. We showed that morphometric traits are mainly genetically heritable characters with significant differences among the studied populations. Finally, a distinctive trait signature was found for the populations isolated from the upland rice cultures. All together, our study reveals the prevalence of M. graminicola populations in Vietnamese rice. Further investigations need to be developed to explore the population dynamics and evolutionary history of this species in South East Asia.
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Affiliation(s)
- Stéphane Bellafiore
- IRD Institut de recherche pour le développement, UMR 186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France; IRD, LMI RICE, University of Science and Technology of Hanoi, Agricultural Genetics Institute, Hanoi, Viet Nam.
| | - Claire Jougla
- IRD Institut de recherche pour le développement, UMR 186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| | - Élodie Chapuis
- IRD Institut de recherche pour le développement, UMR 186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| | - Guillaume Besnard
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire « Évolution & diversité biologique »), 118, route de Narbonne, 31062 Toulouse, France
| | - Malyna Suong
- IRD Institut de recherche pour le développement, UMR 186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France; IRD, LMI RICE, University of Science and Technology of Hanoi, Agricultural Genetics Institute, Hanoi, Viet Nam
| | - Phong Nguyen Vu
- IRD Institut de recherche pour le développement, UMR 186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France; Department of Biotechnology, Nong Lam University, Ho Chi Minh City, Viet Nam
| | - Dirk De Waele
- Laboratory of Tropical Crop Improvement, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven (KU Leuven), Willem de Croylaan 42, 3001 Heverlee, Belgium; International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines; Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, 2520 Potchefstroom, South Africa
| | - Pascal Gantet
- IRD, LMI RICE, University of Science and Technology of Hanoi, Agricultural Genetics Institute, Hanoi, Viet Nam; University of Montpellier-2, UMR DIADE, Montpellier, France
| | - Xuyen Ngo Thi
- Department of Plant Pathology, Faculty of Agronomy, Hanoi University of Agriculture Trau Qui, Gia Lam, Hanoi, Viet Nam
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Zedane L, Hong-Wa C, Murienne J, Jeziorski C, Baldwin BG, Besnard G. Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12509] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Loubab Zedane
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Cynthia Hong-Wa
- Missouri Botanical Garden; PO Box 299 St. Louis MO 63166-0299 USA
| | - Jérôme Murienne
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Céline Jeziorski
- INRA; UAR1209; département de Génétique Animale; INRA Auzeville 31326; Castanet-Tolosan France
- GeT-PlaGe; Genotoul; INRA Auzeville 31326; Castanet-Tolosan France
| | - Bruce G. Baldwin
- Jepson Herbarium and Department of Integrative Biology; University of California; Berkeley CA 94720-2465 USA
| | - Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174; EDB (Laboratoire Evolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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45
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Besnard G, Bertrand JAM, Delahaie B, Bourgeois YXC, Lhuillier E, Thébaud C. Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12494] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Joris A. M. Bertrand
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Institute of Oceanography; National Taiwan University; n°1, sec. 4, Roosevelt Road, Daan District Taipei 10617 Taiwan
| | - Boris Delahaie
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Yann X. C. Bourgeois
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Zoological Institute; Department of Evolutionary Biology; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Emeline Lhuillier
- INRA; GeT-PlaGe; UAR 1209 Département de Génétique Animale; INRA Auzeville; 31326 Castanet-Tolosan France
| | - Christophe Thébaud
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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46
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Besnard G, Christin PA, Malé PJG, Lhuillier E, Lauzeral C, Coissac E, Vorontsova MS. From museums to genomics: old herbarium specimens shed light on a C3 to C4 transition. J Exp Bot 2014; 65:6711-21. [PMID: 25258360 DOI: 10.1093/jxb/eru395] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Collections of specimens held by natural history museums are invaluable material for biodiversity inventory and evolutionary studies, with specimens accumulated over 300 years readily available for sampling. Unfortunately, most museum specimens yield low-quality DNA. Recent advances in sequencing technologies, so called next-generation sequencing, are revolutionizing phylogenetic investigations at a deep level. Here, the Illumina technology (HiSeq) was used on herbarium specimens of Sartidia (subfamily Aristidoideae, Poaceae), a small African-Malagasy grass lineage (six species) characteristic of wooded savannas, which is the C3 sister group of Stipagrostis, an important C4 genus from Africa and SW Asia. Complete chloroplast and nuclear ribosomal sequences were assembled for two Sartidia species, one of which (S. perrieri) is only known from a single specimen collected in Madagascar 100 years ago. Partial sequences of a few single-copy genes encoding phosphoenolpyruvate carboxylases (ppc) and malic enzymes (nadpme) were also assembled. Based on these data, the phylogenetic position of Malagasy Sartidia in the subfamily Aristidoideae was investigated and the biogeographical history of this genus was analysed with full species sampling. The evolutionary history of two genes for C4 photosynthesis (ppc-aL1b and nadpme-IV) in the group was also investigated. The gene encoding the C4 phosphoenolpyruvate caroxylase of Stipagrostis is absent from S. dewinteri suggesting that it is not essential in C3 members of the group, which might have favoured its recruitment into a new metabolic pathway. Altogether, the inclusion of historical museum specimens in phylogenomic analyses of biodiversity opens new avenues for evolutionary studies.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France
| | | | - Pierre-Jean G Malé
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Emeline Lhuillier
- GeT-PlaGe, Campus INRA-Auzeville, F-31326 Castanet-Tolosan, France; INRA, UAR 1209 Département de Génétique Animale, INRA Auzeville, F-31326 Castanet-Tolosan, France
| | - Christine Lauzeral
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France
| | - Eric Coissac
- Laboratoire d'écologie Alpine (LECA), UMR5553, CNRS/Université Joseph Fourier-Grenoble I, Université de Savoie, F-38041 Grenoble, France
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Hesson JC, Rettich F, Merdić E, Vignjević G, Ostman O, Schäfer M, Schaffner F, Foussadier R, Besnard G, Medlock J, Scholte EJ, Lundström JO. The arbovirus vector Culex torrentium is more prevalent than Culex pipiens in northern and central Europe. Med Vet Entomol 2014; 28:179-186. [PMID: 23947434 DOI: 10.1111/mve.12024] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 06/11/2013] [Accepted: 06/24/2013] [Indexed: 06/02/2023]
Abstract
Two species of arbovirus vector, Culex torrentium and Culex pipiens (Diptera: Culicidae), occur in several European countries, but difficulties in their accurate identification and discrimination have hampered both detailed and large-scale distribution and abundance studies. Using a molecular identification method, we identified to species 2559 larvae of Cx. pipiens/torrentium collected from 138 sites in 13 European countries ranging from Scandinavia to the Mediterranean coast. In addition, samples of 1712 males of Cx. pipiens/torrentium collected at several sites in the Czech Republic were identified to species based on the morphology of their hypopygia. We found that the two species occur together in large areas of Europe, and that Cx. torrentium dominates in northern Europe and Cx. pipiens dominates south of the Alps. The transition in dominance occurs in central Europe, where both species are roughly equally common. There was a strong correlation between the length of the growing season at different sites and occurrences of the two species. As the growing season increases, the proportion and detection of Cx. torrentium decrease, whereas those of Cx. pipiens increase. The present findings have important consequences for the interpretation of the results of studies on major enzootic and link-vectors of mosquito-borne bird-associated viruses (i.e. Sindbis, West Nile and Usutu viruses), especially in central Europe and Scandinavia.
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Affiliation(s)
- J C Hesson
- Population Conservation Biology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Besnard G, Jühling F, Chapuis É, Zedane L, Lhuillier É, Mateille T, Bellafiore S. Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing. C R Biol 2014; 337:295-301. [PMID: 24841955 DOI: 10.1016/j.crvi.2014.03.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 10/25/2022]
Abstract
Little is known about the variations of nematode mitogenomes (mtDNA). Sequencing a complete mtDNA using a PCR approach remains a challenge due to frequent genome reorganizations and low sequence similarities between divergent nematode lineages. Here, a genome skimming approach based on HiSeq sequencing (shotgun) was used to assemble de novo the first complete mtDNA sequence of a root-knot nematode (Meloidogyne graminicola). An AT-rich genome (84.3%) of 20,030 bp was obtained with a mean sequencing depth superior to 300. Thirty-six genes were identified with a semi-automated approach. A comparison with a gene map of the M. javanica mitochondrial genome indicates that the gene order is conserved within this nematode lineage. However, deep genome rearrangements were observed when comparing with other species of the superfamily Hoplolaimoidea. Repeat elements of 111 bp and 94 bp were found in a long non-coding region of 7.5 kb, as similarly reported in M. javanica and M. hapla. This study points out the power of next generation sequencing to produce complete mitochondrial genomes, even without a reference sequence, and possibly opening new avenues for species/race identification, phylogenetics and population genetics of nematodes.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Évolution & Diversité biologique), 118, route de Narbonne, 31062 Toulouse, France.
| | - Frank Jühling
- University of Leipzig, Interdisciplinary Center for Bioinformatics, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Élodie Chapuis
- IRD, UMR186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| | - Loubab Zedane
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Évolution & Diversité biologique), 118, route de Narbonne, 31062 Toulouse, France
| | - Émeline Lhuillier
- INRA, GeT-PlaGe, UAR 1209 Département de génétique animale, INRA Auzeville, 31326 Castanet-Tolosan, France
| | - Thierry Mateille
- IRD, UMR 022 Centre de biologie pour la gestion des populations, campus de Baillarguet, CS30016, 34988 Montferrier-sur-Lez cedex, France
| | - Stéphane Bellafiore
- IRD, UMR186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
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Malé PJG, Bardon L, Besnard G, Coissac E, Delsuc F, Engel J, Lhuillier E, Scotti-Saintagne C, Tinaut A, Chave J. Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Mol Ecol Resour 2014; 14:966-75. [DOI: 10.1111/1755-0998.12246] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/09/2014] [Accepted: 02/22/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Pierre-Jean G. Malé
- UMR 5174 Laboratoire Évolution & Diversité Biologique; CNRS; Université Paul Sabatier; ENFA; 118 route de Narbonne F-31062 Toulouse France
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto ON M5S 3G5 Canada
| | - Léa Bardon
- UMR 5174 Laboratoire Évolution & Diversité Biologique; CNRS; Université Paul Sabatier; ENFA; 118 route de Narbonne F-31062 Toulouse France
| | - Guillaume Besnard
- UMR 5174 Laboratoire Évolution & Diversité Biologique; CNRS; Université Paul Sabatier; ENFA; 118 route de Narbonne F-31062 Toulouse France
| | - Eric Coissac
- Laboratoire d'Ecologie Alpine CNRS; UMR5553; Université Joseph Fourier; BP 53 F-38041 Grenoble Cedex 9 France
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution; UMR 5554-CNRS; Université Montpellier 2; Place Eugène Bataillon Montpellier France
| | - Julien Engel
- UMR ECOFOG; INRA; Université Antilles-Guyane; CNRS; CIRAD; AgroParisTech; Campus agronomique BP 709 F-97387 Kourou Cedex France
| | - Emeline Lhuillier
- INRA; UAR 1209 Département de Génétique Animale; INRA Auzeville; F-31326 Castanet-Tolosan France
- GeT-PlaGe; Genotoul; INRA Auzeville; F-31326 Castanet-Tolosan France
| | - Caroline Scotti-Saintagne
- UMR ECOFOG; INRA; Université Antilles-Guyane; CNRS; CIRAD; AgroParisTech; Campus agronomique BP 709 F-97387 Kourou Cedex France
| | - Alexandra Tinaut
- UMR ECOFOG; INRA; Université Antilles-Guyane; CNRS; CIRAD; AgroParisTech; Campus agronomique BP 709 F-97387 Kourou Cedex France
| | - Jérôme Chave
- UMR 5174 Laboratoire Évolution & Diversité Biologique; CNRS; Université Paul Sabatier; ENFA; 118 route de Narbonne F-31062 Toulouse France
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Besnard G, El Bakkali A. Sequence analysis of single-copy genes in two wild olive subspecies: nucleotide diversity and potential use for testing admixture. Genome 2014; 57:145-53. [PMID: 24884690 DOI: 10.1139/gen-2014-0001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The wild olive distribution extends from the Mediterranean region to south Asia and Austral Africa. The species is also invasive, particularly in Australia. Here, we investigated the sequence variation at five nuclear single-copy genes in 41 native and invasive accessions of the Mediterranean and African olive subspecies. The nucleotide diversity was assessed and the phylogenetic relationships between alleles were depicted with haplotype networks. A Bayesian clustering method (STRUCTURE) was applied to identify the main gene pools. We found an average of 18.4 alleles per locus. Native Mediterranean and African olives only share one allele, which testifies for ancient admixture on the Red Sea hills. The presence of divergent alleles in the Mediterranean olive, as well as the identification of two main genetic clusters, suggests a complex origin with two highly differentiated gene pools from the eastern and western Mediterranean that recently admixed. In the invasive range, relatively high nucleotide diversity is observed as a consequence of the introduction of alleles from two subspecies. Our data confirm that four invasive individuals are early-generation hybrids. Finally, the utility of single-copy gene sequences in olive population genomic and phylogenetic studies is briefly discussed.
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Affiliation(s)
- G Besnard
- a CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, 31062 Toulouse cedex 9, France
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