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Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM. Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodivers Data J 2023; 11:e102317. [PMID: 38327316 PMCID: PMC10848826 DOI: 10.3897/bdj.11.e102317] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 02/09/2024] Open
Abstract
Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.
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Affiliation(s)
- Giada Ferrari
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Lore Esselens
- Royal Museum for Central Africa, Tervuren, BelgiumRoyal Museum for Central AfricaTervurenBelgium
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Michelle L Hart
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Steven Janssens
- Meise Botanic Garden, Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Leuven Plant Institute, Department of Biology, Leuven, BelgiumLeuven Plant Institute, Department of BiologyLeuvenBelgium
| | - Catherine Kidner
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Flávia Pezzini
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of African Zoology, Tervuren, BelgiumRoyal Museum for Central Africa, Department of African ZoologyTervurenBelgium
| | - Peter M Hollingsworth
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
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Yi H, Dong S, Yang L, Wang J, Kidner C, Kang M. Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns. Mol Phylogenet Evol 2023; 184:107801. [PMID: 37088242 DOI: 10.1016/j.ympev.2023.107801] [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: 12/06/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 04/25/2023]
Abstract
Discovery of cryptic diversity is essential to understanding both the process of speciation and the conservation of species. Determining species boundaries in fern lineages represents a major challenge due to lack of morphologically diagnostic characters and frequent hybridization. Genomic data has substantially enhanced our understanding of the speciation process, increased the resolution of species delimitation studies, and led to the discovery of cryptic diversity. Here, we employed restriction-site-associated DNA sequencing (RAD-seq) and integrated phylogenomic and population genomic analyses to investigate phylogenetic relationships and evolutionary history of 16 tree ferns with marginate scales (Cyatheaceae) from China and Vietnam. We conducted multiple species delimitation analyses using the multispecies coalescent (MSC) model and novel approaches based on genealogical divergence index (gdi) and isolation by distance (IBD). In addition, we inferred species trees using concatenation and several coalescent-based methods, and assessed hybridization patterns and rate of gene flow across the phylogeny. We obtained highly supported and generally congruent phylogenies inferred from concatenated and summary-coalescent methods, and the monophyly of all currently recognized species were strongly supported. Our results revealed substantial evidence of cryptic diversity in three widely distributed Gymnosphaera species, each of which was composite of two highly structure lineages that may correspond to cryptic species. We found that hybridization was fairly common between not only closely related species, but also distantly related species. Collectively, it appears that scaly tree ferns may contain cryptic diversity and hybridization has played an important role throughout the evolutionary history of this group.
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Affiliation(s)
- Huiqin Yi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Shiying Dong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China
| | - Catherine Kidner
- Institute of Molecular Plant Sciences, University of Edinburgh, Daniel Rutherford Building Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, UK; Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; South China National Botanical Garden, Guangzhou 510650, China.
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3
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Li L, Chen X, Fang D, Dong S, Guo X, Li N, Campos‐Dominguez L, Wang W, Liu Y, Lang X, Peng Y, Tian D, Thomas DC, Mu W, Liu M, Wu C, Yang T, Zhang S, Yang L, Yang J, Liu Z, Zhang L, Zhang X, Chen F, Jiao Y, Guo Y, Hughes M, Wang W, Liu X, Zhong C, Li A, Sahu SK, Yang H, Wu E, Sharbrough J, Lisby M, Liu X, Xu X, Soltis DE, Van de Peer Y, Kidner C, Zhang S, Liu H. Genomes shed light on the evolution of Begonia, a mega-diverse genus. New Phytol 2022; 234:295-310. [PMID: 34997964 PMCID: PMC7612470 DOI: 10.1111/nph.17949] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 07/10/2021] [Accepted: 12/20/2021] [Indexed: 05/02/2023]
Abstract
Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with c. 2000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana and B. peltatifolia), and whole genome shotgun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22 059-23 444 protein-coding genes. Synteny analysis revealed a lineage-specific whole-genome duplication (WGD) that occurred just before the diversification of Begonia. Functional enrichment of gene families retained after WGD highlights the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade.
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Canales NA, Pérez-Escobar OA, Powell RF, Töpel M, Kidner C, Nesbitt M, Maldonado C, Barnes CJ, Rønsted N, Przelomska NAS, Leitch IJ, Antonelli A. A highly contiguous, scaffold-level nuclear genome assembly for the fever tree ( Cinchona pubescens Vahl) as a novel resource for Rubiaceae research. GigaByte 2022; 2022:gigabyte71. [PMID: 36950143 PMCID: PMC10027117 DOI: 10.46471/gigabyte.71] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/29/2022] [Indexed: 11/12/2022] Open
Abstract
The Andean fever tree (Cinchona L.; Rubiaceae) is a source of bioactive quinine alkaloids used to treat malaria. C. pubescens Vahl is a valuable cash crop within its native range in northwestern South America, however, genomic resources are lacking. Here we provide the first highly contiguous and annotated nuclear and plastid genome assemblies using Oxford Nanopore PromethION-derived long-read and Illumina short-read data. Our nuclear genome assembly comprises 603 scaffolds with a total length of 904 Mbp (∼82% of the full genome based on a genome size of 1.1 Gbp/1C). Using a combination of de novo and reference-based transcriptome assemblies we annotated 72,305 coding sequences comprising 83% of the BUSCO gene set and 4.6% fragmented sequences. Using additional plastid and nuclear datasets we place C. pubescens in the Gentianales order. This first genomic resource for C. pubescens opens new research avenues, including the analysis of alkaloid biosynthesis in the fever tree.
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Affiliation(s)
- Nataly Allasi Canales
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Oscar A. Pérez-Escobar
- Royal Botanic Gardens, Kew, Richmond, UK
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Corresponding authors. E-mail: ;
| | | | - Mats Töpel
- University of Gothenburg, Department of Marine Sciences, Gothenburg, Sweden
| | | | | | - Carla Maldonado
- Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | | | - Nina Rønsted
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- National Tropical Botanical Garden, Kalaheo, Hawaii, USA
| | | | - Ilia J. Leitch
- Royal Botanic Gardens, Kew, Richmond, UK
- Corresponding authors. E-mail: ;
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, UK
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Plant Sciences, University of Oxford, Oxford, UK
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Emelianova K, Martínez Martínez A, Campos-Dominguez L, Kidner C. Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family. Sci Rep 2021; 11:17773. [PMID: 34493743 PMCID: PMC8423730 DOI: 10.1038/s41598-021-96854-y] [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: 04/08/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Begonia is an important horticultural plant group, as well as one of the most speciose Angiosperm genera, with over 2000 described species. Genus wide studies of genome size have shown that Begonia has a highly variable genome size, and analysis of paralog pairs has previously suggested that Begonia underwent a whole genome duplication. We address the contribution of gene duplication to the generation of diversity in Begonia using a multi-tissue RNA-seq approach. We chose to focus on chalcone synthase (CHS), a gene family having been shown to be involved in biotic and abiotic stress responses in other plant species, in particular its importance in maximising the use of variable light levels in tropical plants. We used RNA-seq to sample six tissues across two closely related but ecologically and morphologically divergent species, Begonia conchifolia and B. plebeja, yielding 17,012 and 19,969 annotated unigenes respectively. We identified the chalcone synthase gene family members in our Begonia study species, as well as in Hillebrandia sandwicensis, the monotypic sister genus to Begonia, Cucumis sativus, Arabidopsis thaliana, and Zea mays. Phylogenetic analysis suggested the CHS gene family has high duplicate turnover, all members of CHS identified in Begonia arising recently, after the divergence of Begonia and Cucumis. Expression profiles were similar within orthologous pairs, but we saw high inter-ortholog expression variation. Sequence analysis showed relaxed selective constraints on some ortholog pairs, with substitutions at conserved sites. Evidence of pseudogenisation and species specific duplication indicate that lineage specific differences are already beginning to accumulate since the divergence of our study species. We conclude that there is evidence for a role of gene duplication in generating diversity through sequence and expression divergence in Begonia.
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Affiliation(s)
- Katie Emelianova
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988Dementia Research Institute at the University of Edinburgh, Edinburgh, UK
| | - Andrea Martínez Martínez
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988School of Biological Sciences, University of Edinburgh, King’s Buildings, Mayfield Rd, Edinburgh, EH9 3JU UK
| | - Lucia Campos-Dominguez
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988School of Biological Sciences, University of Edinburgh, King’s Buildings, Mayfield Rd, Edinburgh, EH9 3JU UK
| | - Catherine Kidner
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988School of Biological Sciences, University of Edinburgh, King’s Buildings, Mayfield Rd, Edinburgh, EH9 3JU UK
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Koenen EJ, Kidner C, de Souza ÉR, Simon MF, Iganci JR, Nicholls JA, Brown GK, de Queiroz LP, Luckow M, Lewis GP, Pennington RT, Hughes CE. Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation. Am J Bot 2020; 107:1710-1735. [PMID: 33253423 PMCID: PMC7839790 DOI: 10.1002/ajb2.1568] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 05/15/2020] [Accepted: 08/07/2020] [Indexed: 05/05/2023]
Abstract
PREMISE Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the "tree of life" are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species-rich and taxonomically challenging ingoids. METHODS We generated transcriptomes to select low-copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids. RESULTS Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well-supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids. CONCLUSIONS Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation.
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Affiliation(s)
- Erik J. M. Koenen
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Catherine Kidner
- School of Biological SciencesUniversity of EdinburghKing’s Buildings, Mayfield RoadEdinburghUK
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
| | - Élvia R. de Souza
- Departamento Ciências BiológicasUniversidade Estadual de Feira de SantanaAvenida Transnordestina s/n—Novo Horizonte44036‐900Feira de SantanaBrazil
| | - Marcelo F. Simon
- Embrapa Recursos Genéticos e BiotecnologiaParque Estação Biológica (PqEB)Avenida W5 norte70770‐917BrasíliaBrazil
| | - João R. Iganci
- Instituto de BiologiaUniversidade Federal de PelotasCampus Universitário Capão do LeãoTravessa André Dreyfus s/nCapão do Leão96010‐900Rio Grande do SulBrazil
| | - James A. Nicholls
- School of Biological SciencesUniversity of EdinburghKing’s Buildings, Mayfield RoadEdinburghUK
- Australian National Insect CollectionCSIROClunies Ross StActonACT 2601Australia
| | - Gillian K. Brown
- Queensland HerbariumBrisbane Botanic GardensMount Coot‐tha, Mt Coot‐tha RoadToowong4066QueenslandAustralia
| | - Luciano P. de Queiroz
- Departamento Ciências BiológicasUniversidade Estadual de Feira de SantanaAvenida Transnordestina s/n—Novo Horizonte44036‐900Feira de SantanaBrazil
| | - Melissa Luckow
- L.H. Bailey HortoriumDepartment of Plant BiologyCornell University412 Mann Library BuildingIthacaNew York14853USA
| | - Gwilym P. Lewis
- Comparative Plant and Fungal Biology DepartmentRoyal Botanic GardensKew, RichmondSurreyTW9 3AEUK
| | - R. Toby Pennington
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
- GeographyUniversity of ExeterAmory Building, Rennes DriveExeterEX4 4RJUK
| | - Colin E. Hughes
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
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7
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Koenen EJM, Ojeda DI, Bakker FT, Wieringa JJ, Kidner C, Hardy OJ, Pennington RT, Herendeen PS, Bruneau A, Hughes CE. The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous-Paleogene (K-Pg) Mass Extinction Event. Syst Biol 2020; 70:508-526. [PMID: 32483631 PMCID: PMC8048389 DOI: 10.1093/sysbio/syaa041] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/06/2020] [Accepted: 05/25/2020] [Indexed: 12/17/2022] Open
Abstract
The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events]
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Affiliation(s)
- Erik J M Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Dario I Ojeda
- Service Évolution Biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Avenue Franklin Roosevelt 50, 1050, Brussels, Belgium.,Norwegian Institute of Bioeconomy Research, Høgskoleveien 8, 1433 Ås, Norway
| | - Freek T Bakker
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jan J Wieringa
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Catherine Kidner
- Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK.,School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Rd, Edinburgh, EH9 3JU, UK
| | - Olivier J Hardy
- Service Évolution Biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Avenue Franklin Roosevelt 50, 1050, Brussels, Belgium
| | - R Toby Pennington
- Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK.,Geography, University of Exeter, Amory Building, Rennes Drive, Exeter, EX4 4RJ, UK
| | | | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, Canada
| | - Colin E Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
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Koenen EJM, Ojeda DI, Steeves R, Migliore J, Bakker FT, Wieringa JJ, Kidner C, Hardy OJ, Pennington RT, Bruneau A, Hughes CE. Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies. New Phytol 2020; 225:1355-1369. [PMID: 31665814 PMCID: PMC6972672 DOI: 10.1111/nph.16290] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [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: 06/28/2019] [Accepted: 09/14/2019] [Indexed: 05/02/2023]
Abstract
Phylogenomics is increasingly used to infer deep-branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep-branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome-scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear-encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as 'basal' or 'early-diverging' with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.
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Affiliation(s)
- Erik J. M. Koenen
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107CH‐8008ZurichSwitzerland
| | - Dario I. Ojeda
- Service Évolution Biologique et ÉcologieFaculté des SciencesUniversité Libre de BruxellesAvenue Franklin Roosevelt 501050BrusselsBelgium
- Norwegian Institute of Bioeconomy ResearchHøgskoleveien 81433ÅsNorway
| | - Royce Steeves
- Institut de Recherche en Biologie Végétale and Département de Sciences BiologiquesUniversité de Montréal4101 Sherbrooke St EMontrealQCH1X 2B2Canada
- Fisheries & Oceans CanadaGulf Fisheries Center343 Université AveMonctonNBE1C 5K4Canada
| | - Jérémy Migliore
- Service Évolution Biologique et ÉcologieFaculté des SciencesUniversité Libre de BruxellesAvenue Franklin Roosevelt 501050BrusselsBelgium
| | - Freek T. Bakker
- Biosystematics GroupWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Jan J. Wieringa
- Naturalis Biodiversity Center, LeidenDarwinweg 22333 CRLeidenthe Netherlands
| | - Catherine Kidner
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
- School of Biological SciencesUniversity of EdinburghKing's Buildings, Mayfield RdEdinburghEH9 3JUUK
| | - Olivier J. Hardy
- Service Évolution Biologique et ÉcologieFaculté des SciencesUniversité Libre de BruxellesAvenue Franklin Roosevelt 501050BrusselsBelgium
| | - R. Toby Pennington
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
- GeographyUniversity of ExeterAmory Building, Rennes DriveExeterEX4 4RJUK
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences BiologiquesUniversité de Montréal4101 Sherbrooke St EMontrealQCH1X 2B2Canada
| | - Colin E. Hughes
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107CH‐8008ZurichSwitzerland
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Kidner C, Groover A, Thomas DC, Emelianova K, Soliz-Gamboa C, Lens F. First steps in studying the origins of secondary woodiness inBegonia(Begoniaceae): combining anatomy, phylogenetics, and stem transcriptomics. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12492] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Catherine Kidner
- Royal Botanic Gardens; Edinburgh UK
- Institute of Molecular Plant Sciences; University of Edinburgh; Edinburgh UK
| | - Andrew Groover
- US Forest Service; Pacific Southwest Research Station; Davis CA USA
- Department of Plant Biology; UC Davis; Davis CA USA
| | - Daniel C. Thomas
- Naturalis Biodiversity Center; Leiden University; P.O. Box 9517 2300RA Leiden the Netherlands
- School of Biological Sciences; University of Hong Kong; Hong Kong
- Research and Conservation Branch; Singapore Botanic Gardens; Singapore
| | - Katie Emelianova
- Royal Botanic Gardens; Edinburgh UK
- Institute of Molecular Plant Sciences; University of Edinburgh; Edinburgh UK
| | - Claudia Soliz-Gamboa
- Naturalis Biodiversity Center; Leiden University; P.O. Box 9517 2300RA Leiden the Netherlands
| | - Frederic Lens
- Naturalis Biodiversity Center; Leiden University; P.O. Box 9517 2300RA Leiden the Netherlands
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Nishii K, Möller M, Kidner C, Spada A, Mantegazza R, Wang CN, Nagata T. A complex case of simple leaves: indeterminate leaves co-express ARP and KNOX1 genes. Dev Genes Evol 2010; 220:25-40. [PMID: 20502914 DOI: 10.1007/s00427-010-0326-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 04/15/2010] [Indexed: 10/19/2022]
Abstract
The mutually exclusive relationship between ARP and KNOX1 genes in the shoot apical meristem and leaf primordia in simple leaved plants such as Arabidopsis has been well characterized. Overlapping expression domains of these genes in leaf primordia have been described for many compound leaved plants such as Solanum lycopersicum and Cardamine hirsuta and are regarded as a characteristic of compound leaved plants. Here, we present several datasets illustrating the co-expression of ARP and KNOX1 genes in the shoot apical meristem, leaf primordia, and developing leaves in plants with simple leaves and simple primordia. Streptocarpus plants produce unequal cotyledons due to the continued activity of a basal meristem and produce foliar leaves termed "phyllomorphs" from the groove meristem in the acaulescent species Streptocarpus rexii and leaves from a shoot apical meristem in the caulescent Streptocarpus glandulosissimus. We demonstrate that the simple leaves in both species possess a greatly extended basal meristematic activity that persists over most of the leaf's growth. The area of basal meristem activity coincides with the co-expression domain of ARP and KNOX1 genes. We suggest that the co-expression of ARP and KNOX1 genes is not exclusive to compound leaved plants but is associated with foci of meristematic activity in leaves.
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Affiliation(s)
- Kanae Nishii
- Institute of Ecology and Evolutionary Biology, Department of Life Science, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China.
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Nishii K, Moeller M, Kidner C, Spada A, Mantegazza R, Hsu HC, Nagata T, Wang CN. 03-P089 A simple leaf with compound gene expression: Indeterminate leaves co-express ARP and KNOX genes. Mech Dev 2009. [DOI: 10.1016/j.mod.2009.06.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Abstract
MicroRNAs (miRNAs) have a vital role in the generation of plant forms through post-transcriptional regulation of the accumulation of developmental regulators. Analysis of their roles requires detailed knowledge of their expression patterns. We describe an in situ hybridization technique we have used to study the patterns of miRNA accumulation in Arabidopsis and in maize.
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Affiliation(s)
- Catherine Kidner
- Institute of Molecular Plant Sciences, edinburgh University and Royal Botanic Gardens, Edinburgh, Scotland
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13
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Abstract
Eukaryotic heterochromatin is characterized by a high density of repeats and transposons, as well as by modified histones, and influences both gene expression and chromosome segregation. In the fission yeast Schizosaccharomyces pombe, we deleted the argonaute, dicer, and RNA-dependent RNA polymerase gene homologs, which encode part of the machinery responsible for RNA interference (RNAi). Deletion results in the aberrant accumulation of complementary transcripts from centromeric heterochromatic repeats. This is accompanied by transcriptional de-repression of transgenes integrated at the centromere, loss of histone H3 lysine-9 methylation, and impairment of centromere function. We propose that double-stranded RNA arising from centromeric repeats targets formation and maintenance of heterochromatin through RNAi.
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MESH Headings
- Centromere/physiology
- Chromosomal Proteins, Non-Histone/metabolism
- DNA Methylation
- DNA Transposable Elements
- Endoribonucleases/genetics
- Endoribonucleases/metabolism
- Gene Deletion
- Gene Silencing
- Genes, Fungal
- Heterochromatin/genetics
- Heterochromatin/metabolism
- Histones/metabolism
- Lysine/metabolism
- Methylation
- Models, Genetic
- RNA, Double-Stranded/metabolism
- RNA, Fungal/metabolism
- RNA, Small Interfering
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- RNA-Dependent RNA Polymerase/genetics
- RNA-Dependent RNA Polymerase/metabolism
- Repetitive Sequences, Nucleic Acid
- Ribonuclease III
- Schizosaccharomyces/genetics
- Schizosaccharomyces/metabolism
- Schizosaccharomyces pombe Proteins/genetics
- Schizosaccharomyces pombe Proteins/metabolism
- Transcription, Genetic
- Transgenes
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Affiliation(s)
- Thomas A Volpe
- Cold Spring Harbor Laboratory, Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA
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15
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16
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Abstract
Variation among vascular plants in the initiation and patterning of leaves results in a diverse array of leaf shape, including the strap-like leaf of many grasses and the broad lamina of most eudicots. Recent findings highlight the importance of interactions between the shoot apical meristem (SAM) and developing leaf primordia in axis specification and the establishment of leaf shape. Global regulators of epigenetic states have been implicated in these interactions and may play a role in distinguishing founder cells and stem cells within the SAM.
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Affiliation(s)
- M Byrne
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York 11724, USA
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17
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Kidner C, Sundaresan V, Roberts K, Dolan L. Clonal analysis of the Arabidopsis root confirms that position, not lineage, determines cell fate. Planta 2000; 211:191-199. [PMID: 10945213 DOI: 10.1007/s004250000284] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The cellular organization of the Arabidopsis thaliana (L.) Heynh. root meristem suggests that a regular pattern of cell divisions occurs in the root tip. Deviations from this pattern of division might be expected to disrupt the organization of cells and tissues in the root. A clonal analysis of the 3-d-old primary root meristem was carried out to determine if there is variability in division patterns, and if so to discover their effect on cellular organization in the root. Clones induced in the seedling meristem largely confirmed the predicted pattern of cell divisions. However, the cellular initials that normally give rise to the different cell files in the root were shown to exhibit some instability. For example, it was calculated that a lateral root cap/epidermal initial is displaced every 13 d. Furthermore, the existence of large marked clones that included more than two adjacent cell layers suggests that intrusive growth followed by cell division may occur at low frequency, perhaps in response to local cell deaths in the meristem. These findings support the view that even in plant organs with stereotypical cell division patterns, positional information is still the key determinant of cell fate.
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Affiliation(s)
- C Kidner
- Department of Cell Biology, John Innes Centre, Norwich, UK
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19
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Kidner C. Untwisting RNAs in plant development. Trends Genet 2000. [DOI: 10.1016/s0168-9525(99)01953-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kidner C. Argonaute catapults new gene family to prominence. Trends Genet 1998. [DOI: 10.1016/s0168-9525(98)01512-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Dolan L, Linstead P, Kidner C, Boudonck K, Cao XF, Berger F. Cell fate in plants. Lessons from the Arabidopsis root. Symp Soc Exp Biol 1998; 51:11-7. [PMID: 10645418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Classical studies in plant development have indicated that the fate of plant cells is fixed late, after cell division has ceased. Earlier commitment events are therefore considered reversible. To gain a mechanisatic understanding of the processes involved in specification and fixation of cell fate in plants, we are using the Arabidopsis root epidermis as a model system. The Arabidopsis root epidermis is composed of two cell types whose pattern of differentiation is directed by positional cues during development. Examination of mutations has identified genes involved in the establishment of cell fate specification in this tissue. TRANSPARENT TESTA GLABRA (TTG) and GLABRA2 (GL2) are positive regulators of non-hair fate and are active during the early differentiation of the epidermis in the meristem. GL2 encodes a homeobox protein which is expressed in non-hair cells in the meristem and is positively regulated by TTG. Mutations in genes involved in the regulation of ethylene biosynthesis and signal transduction indicate that ethylene is a positive regulator of hair cell fate. Treatment of ttg and gl2 plants with modulators of ethylene biosynthesis indicate that ethylene acts down stream of TTG and GL2 during the fate specification process. The relationship between meristem organisation and the mechanism underpinning the establishment of cell fate in other systems is also discussed.
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Affiliation(s)
- L Dolan
- Department of Cell Biology, John Innes Centre, Norwich, UK
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