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Lopes JC, Fonseca LHM, Johnson DM, Luebert F, Murray N, Nge FJ, Rodrigues-Vaz C, Soulé V, Onstein RE, Lohmann LG, Couvreur TLP. Dispersal from Africa to the Neotropics was followed by multiple transitions across Neotropical biomes facilitated by frugivores. ANNALS OF BOTANY 2024; 133:659-676. [PMID: 37968940 PMCID: PMC11082516 DOI: 10.1093/aob/mcad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
BACKGROUND AND AIM Plant disjunctions have fascinated biogeographers and ecologists for a long time. We use tribe Bocageeae (Annonaceae), a predominantly Neotropical plant group distributed across several present-day Neotropical biomes and with an African-American disjunction, to investigate long-distance dispersal mediated by frugivorous animals at both intercontinental and intracontinental scales. METHODS We reconstructed a species-level phylogeny of tribe Bocageeae with a dataset composed of 116 nuclear markers. We sampled 70 % of Bocageeae species, covering their geographical range and representing all eight genera. We estimated divergence times using BEAST, inferred ancestral range distributions and reconstructed ancestral states for fruit traits related to long-distance dispersal in a Bayesian framework. KEY RESULTS The ancestral Bocageeae date to the Early Eocene and were inferred to occur in Africa and proto-Amazonia. Their ancestral fruits were large and dehiscent. The first lineage split gave rise to an exclusively Neotropical clade during the Middle Eocene, in proto-Amazonia. Range exchange between the Amazon and the Atlantic Forest occurred at least once during the Miocene, and from Amazonia to Central America and Mexico during the Early Miocene. Transitions in different sets of fruit morphologies were inferred to be related to dispersal events across South American regions/biomes. CONCLUSIONS In Bocageeae, mammals might have been responsible for long-distance dispersal through the Boreotropics. In the Neotropics, proto-Amazonia is proposed to be the source for dispersal to other tropical American biomes. Long-distance dispersal might have happened via a wide range of dispersal guilds, depending on frugivore radiations, diversity and abundance in particular time periods and places. Hence, inter- and intracontinental dispersal might not rely on a single dispersal syndrome or guild, but more on the availability of frugivorous lineages for seed dispersal.
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Affiliation(s)
- Jenifer C Lopes
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA, USA
| | | | - David M Johnson
- Department of Biological Sciences, Ohio Wesleyan University, Delaware, OH, USA
| | - Federico Luebert
- Departamento de Ciencias Ambientales y Recursos Naturales Renovables Universidad de Chile, Santiago, Chile
- Departmento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Nancy Murray
- Department of Biological Sciences, Ohio Wesleyan University, Delaware, OH, USA
| | - Francis J Nge
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Carlos Rodrigues-Vaz
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle-CNRS-SU-EPHE-UA, Paris, France
| | - Vincent Soulé
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Renske E Onstein
- Naturalis Biodiversity Center, Leiden, The Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Lúcia G Lohmann
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- University and Jepson Herbaria, and Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Thomas L P Couvreur
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
- Naturalis Biodiversity Center, Leiden, The Netherlands
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Dagallier LPMJ, Condamine FL, Couvreur TLP. Sequential diversification with Miocene extinction and Pliocene speciation linked to mountain uplift explains the diversity of the African rain forest clade Monodoreae (Annonaceae). ANNALS OF BOTANY 2024; 133:677-696. [PMID: 37659091 PMCID: PMC11082524 DOI: 10.1093/aob/mcad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
BACKGROUND AND AIMS Throughout the Cenozoic, Africa underwent several climatic and geological changes impacting the evolution of tropical rain forests (TRFs). African TRFs are thought to have extended from east to west in a 'pan-African' TRF, followed by several events of fragmentation during drier climate periods. During the Miocene, climate cooling and mountain uplift led to the aridification of tropical Africa and open habitats expanded at the expense of TRFs, which probably experienced local extinctions. However, in plants, these drivers were previously inferred using limited taxonomic and molecular data. Here, we tested the impact of climate and geological changes on diversification within the diverse clade Monodoreae (Annonaceae) composed of 90 tree species restricted to African TRFs. METHODS We reconstructed a near-complete phylogenetic tree, based on 32 nuclear genes, and dated using relaxed clocks and fossil calibrations in a Bayesian framework. We inferred the biogeographical history and the diversification dynamics of the clade using multiple birth-death models. KEY RESULTS Monodoreae originated in East African TRFs ~25 million years ago (Ma) and expanded toward Central Africa during the Miocene. We inferred range contractions during the middle Miocene and document important connections between East and West African TRFs after 15-13 Ma. Our results indicated a sudden extinction event during the late Miocene, followed by an increase in speciation rates. Birth-death models suggested that African elevation change (orogeny) is positively linked to speciation in this clade. CONCLUSION East Africa is inferred as an important source of Monodoreae species, and possibly for African plant diversity in general. Our results support a 'sequential scenario of diversification' in which increased aridification triggered extinction of TRF species in Monodoreae. This was quickly followed by fragmentation of rain forests, subsequently enhancing lagged speciation resulting from vicariance and improved climate conditions. In contrast to previous ideas, the uplift of East Africa is shown to have played a positive role in Monodoreae diversification.
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Affiliation(s)
- Léo-Paul M J Dagallier
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458, USA
| | - Fabien L Condamine
- CNRS, Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier), Place Eugène Bataillon, 34095 Montpellier, France
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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Dagallier LMJ, Michelangeli FA. An updated and extended version of the Melastomataceae probe set for target capture. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11564. [PMID: 38369977 PMCID: PMC10873813 DOI: 10.1002/aps3.11564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/27/2023] [Accepted: 10/01/2023] [Indexed: 02/20/2024]
Abstract
Premise A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae. Methods In order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version. Results The final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery. Discussion This updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant-targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available.
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Dagallier LPMJ, Mbago FM, Couderc M, Gaudeul M, Grall A, Loup C, Wieringa JJ, Sonké B, Couvreur TLP. Phylogenomic inference of the African tribe Monodoreae (Annonaceae) and taxonomic revision of Dennettia, Uvariodendron and Uvariopsis. PHYTOKEYS 2023; 233:1-200. [PMID: 37811332 PMCID: PMC10552675 DOI: 10.3897/phytokeys.233.103096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023]
Abstract
Monodoreae (Annonaceae) is a tribe composed of 11 genera and 90 species restricted to the tropical African rain forests. All the genera are taxonomically well circumscribed except the species rich genera Uvariodendron and Uvariopsis which lack a recent taxonomic revision. Here, we used a robust phylogenomic approach, including all the 90 currently accepted species, with several specimens per species, and based on more than 300 Annonaceae-specific nuclear genes, to infer the phylogenetic tree of the Monodoreae and test the limits between the genera and species. We recover all the genera as monophyletic, except the genus Uvariopsis for which the species Uvariopsistripetala falls outside this clade. We thus reinstate the monotypic genus Dennettia for its single species Dennettiatripetala. We also erect a new tribe, Ophrypetaleae trib. nov., to accommodate the genera Ophrypetalum and Sanrafaelia, as we recover them excluded from the Monodoreae tribe with good support. Below the genus level, the genera Isolona, Monodora, Uvariastrum, Uvariodendron and Uvariopsis show weakly supported nodes and phylogenetic conflicts, suggesting that population level processes of evolution might occur in these clades. Our results also support, at the molecular level, the description of several new species of Uvariodendron and Uvariopsis, as well as several new synonymies. Finally, we present a taxonomic revision of the genera Dennettia, Uvariodendron and Uvariopsis, which contain one, 18 and 17 species respectively. We provide a key to the 11 genera of the Monodoraeae and describe four new species to science: Uvariodendronkimbozaense Dagallier & Couvreur, sp. nov., Uvariodendronmossambicense Robson ex Dagallier & Couvreur, sp. nov., Uvariodendronpilosicarpum Dagallier & Couvreur, sp. nov. and Uvariopsisoligocarpa Dagallier & Couvreur, sp. nov., and provide provisional descriptions of three putatively new species. We also present lectotypifications and nomenclatural changes implying synonymies and new combinations (Uvariodendroncitriodorum (Le Thomas) Dagallier & Couvreur, comb. et stat. nov., Uvariodendronfuscumvar.magnificum (Verdc.) Dagallier & Couvreur, comb. et stat. nov., Uvariopsiscongensisvar.angustifolia Dagallier & Couvreur, var. nov., Uvariopsisguineensisvar.globiflora (Keay) Dagallier & Couvreur, comb. et stat. nov., and Uvariopsissolheidiivar.letestui (Pellegr.) Dagallier & Couvreur, comb. et stat. nov.).
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Affiliation(s)
- Léo-Paul M. J. Dagallier
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, New York 10458, USA
| | - Frank M. Mbago
- The Herbarium, Botany Department, Box 35060, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Marie Couderc
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France
| | - Aurélie Grall
- Herbaria Basel, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Caroline Loup
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Jan J. Wieringa
- Herbier MPU, DCSPH – CC 99010, Université de Montpellier, 163 rue A. Broussonnet, F-34090 Montpellier, France
| | - Bonaventure Sonké
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, Netherlands
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Martínez-Velarde MF, Rodrigues-Vaz C, Soulé V, Nge FJ, Schatz GE, Couvreur TLP, Ortiz-Rodriguez AE. Desmopsisterriflora, an extraordinary new species of Annonaceae with flagelliflory. PHYTOKEYS 2023; 227:181-198. [PMID: 37396012 PMCID: PMC10314296 DOI: 10.3897/phytokeys.227.102279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/03/2023] [Indexed: 07/04/2023]
Abstract
Flagelliflory refers to the production of inflorescences exclusively on long, whip-like branches which emerge from the main trunk and extend along the ground or below it. It is the rarest type of cauliflory and only a few cases have been reported in the world. Here, a new species of Annonaceae with flagelliflory is described and illustrated. The phylogenetic relationships of the new species were inferred using a hybrid-capture phylogenomic approach and we present some notes on its reproductive ecology and pollen characteristics. The new species, namely Desmopsisterriflorasp. nov., is part of a clade composed of Mexican species of Stenanona with long, awned petals. Desmopsisterriflora is distinguished by its flageliflorous inflorescences, basely fused sepals, thick red petals, reduced number of ovules per carpel, pollen grains with a weakly rugulate to fossulate exine ornamentation, and its globose, apiculate fruits with a woody testa. The morphological characteristics of the flagella suggest that these are specialized branches rather than inflorescences, and the absence of ramiflory implies an exclusively reproductive function. The flowers are infrequently visited by insects, their potential pollinators being flies and ants.
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Affiliation(s)
| | - Carlos Rodrigues-Vaz
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d‘Histoire Naturelle-CNRS-SU-EPHE-UA, Paris, France
| | - Vincent Soulé
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d‘Histoire Naturelle-CNRS-SU-EPHE-UA, Paris, France
| | - Francis J. Nge
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d‘Histoire Naturelle-CNRS-SU-EPHE-UA, Paris, France
| | - George E. Schatz
- DIADE, Université de Montpellier, CIRAD, IRD, Montpellier, France
| | - Thomas L. P. Couvreur
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d‘Histoire Naturelle-CNRS-SU-EPHE-UA, Paris, France
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Liu SH, Hung KH, Hsu TW, Hoch PC, Peng CI, Chiang TY. New insights into polyploid evolution and dynamic nature of Ludwigia section Isnardia (Onagraceae). BOTANICAL STUDIES 2023; 64:14. [PMID: 37269434 DOI: 10.1186/s40529-023-00387-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/17/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND While polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies, Ludwigia sect. Isnardia (comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies of Isnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa. RESULTS Phylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings on L. repens and L. sphaerocarpa were consistent with earlier studies; L. arcuata was reported as a multi-origin taxon here, and an additional evolutionary scenario of L. sphaerocarpa was uncovered, both for the first time. Furthermore, estimated Isnardia TMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations of Isnardia taxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows among Isnardia taxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported. CONCLUSIONS The present research gives new perceptions of the reticulate evolution and dynamic nature of Isnardia and points to gaps in current knowledge about allopolyploid evolution.
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Affiliation(s)
- Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan
| | - Tsai-Wen Hsu
- Endemic Species Research Institute, Nantou, 552, Taiwan
| | - Peter C Hoch
- Missouri Botanical Garden, St. Louis, MO, 63166, USA
| | - Ching-I Peng
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
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San HT, Chaowasku T, Khine HEE, Chaotham C, Rodsiri R, Sritularak B, Buraphaka H, Putalun W, Likhitwitayawuid K. Chemical Constituents of Huberantha jenkinsii Leaves and Their Glucose Uptake Stimulatory, Anti-Adipogenic, and Neuroprotective Activities. Chem Nat Compd 2022. [DOI: 10.1007/s10600-022-03889-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Couvreur TLP, Dagallier LPMJ, Crozier F, Ghogue JP, Hoekstra PH, Kamdem NG, Johnson DM, Murray NA, Sonké B. Flora of Cameroon - Annonaceae Vol 45. PHYTOKEYS 2022; 207:1-532. [PMID: 36760862 PMCID: PMC9849070 DOI: 10.3897/phytokeys.207.61432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 06/23/2022] [Indexed: 06/18/2023]
Abstract
Annonaceae is a major pantropical family with 113 genera and about 2550 species. Cameroon is one of the most biodiverse countries in Africa but its flora remains incompletely known. In this volume of the Flora of Cameroon, we describe 166 native taxa representing 163 species in 28 native genera within the family Annonaceae. A total of 22 species (about 13%) are endemic to the country. We provide keys to all native genera, species, and infraspecific taxa. For each species a detailed morphological description and a map of its distribution in Cameroon are provided. Distribution maps and diversity analyses are based on a taxonomically verified database of 2073 collections. Across Africa, Cameroon is a center of diversity for Annonaceae harboring one of the highest numbers of species and genera. For example, Cameroon harbors the highest number of African species for the only pantropical genus of Annonaceae, Xylopia. Annonaceae are found across all 10 administrative regions of Cameroon but diversity is concentrated within the tropical rain forest areas situated in the south and South-West. The areas around Bipindi and Mount Cameroon show the highest levels of diversity, but this is correlated with collection effort. Line drawings and/or photographs accompany most species. One species new to science Uvariopsisetugeana Dagallier & Couvreur sp. nov. is described. We also undertake a number of nomenclatural changes such as lectotypifications, six new synonymies and two new combinations (Uvariaanisotricha (Le Thomas) Couvreur, comb. nov.; Uvariodendronfuscumvar.giganteum (Engl.) Dagallier & Couvreur, comb. nov.).
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Affiliation(s)
- Thomas L. P. Couvreur
- IRD, DIADE, Univ Montpellier, Montpellier, FranceNaturalis Biodiversity CenterLeidenNetherlands
- Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d’Ecologie, B.P. 047, Yaoundé, CameroonUniv MontpellierMontpellierFrance
- Naturalis Biodiversity Center, Botany Section, Darwinweg 2, 2333 CR Leiden, NetherlandsUniversité de Yaoundé IYaoundéCameroon
| | | | - Francoise Crozier
- IRD, DIADE, Univ Montpellier, Montpellier, FranceNaturalis Biodiversity CenterLeidenNetherlands
| | - Jean-Paul Ghogue
- Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d’Ecologie, B.P. 047, Yaoundé, CameroonUniv MontpellierMontpellierFrance
- Green Connexion, Environmental Group, siège face GP Mélen, à côté de l’immeuble Palais des verres. Yaoundé, CamerounGreen ConnexionYaoundéCameroon
| | - Paul H. Hoekstra
- Naturalis Biodiversity Center, Botany Section, Darwinweg 2, 2333 CR Leiden, NetherlandsUniversité de Yaoundé IYaoundéCameroon
| | - Narcisse G. Kamdem
- Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d’Ecologie, B.P. 047, Yaoundé, CameroonUniv MontpellierMontpellierFrance
| | - David M. Johnson
- Department of Botany-Microbiology, Ohio Wesleyan University, Delaware, OH, 43015, USAOhio Wesleyan UniversityDelawareUnited States of America
| | - Nancy A. Murray
- Department of Botany-Microbiology, Ohio Wesleyan University, Delaware, OH, 43015, USAOhio Wesleyan UniversityDelawareUnited States of America
| | - Bonaventure Sonké
- Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d’Ecologie, B.P. 047, Yaoundé, CameroonUniv MontpellierMontpellierFrance
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Acha S, Majure LC. A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae. Genes (Basel) 2022; 13:genes13020350. [PMID: 35205394 PMCID: PMC8871817 DOI: 10.3390/genes13020350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/04/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies.
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Maeda G, Gilissen PJ, Rudenko A, van der Wal J, Bourgard C, Gupta AK, Sunnerhagen P, Munissi JJE, Nyandoro SS, Erdélyi M. Oxygenated Cyclohexene Derivatives from the Stem and Root Barks of Uvaria pandensis. JOURNAL OF NATURAL PRODUCTS 2021; 84:3080-3089. [PMID: 34802242 PMCID: PMC8713284 DOI: 10.1021/acs.jnatprod.1c00811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 05/13/2023]
Abstract
Five new cyclohexene derivatives, dipandensin A and B (1 and 2) and pandensenols A-C (3-5), and 16 known secondary metabolites (6-21) were isolated from the methanol-soluble extracts of the stem and root barks of Uvaria pandensis. The structures were characterized by NMR spectroscopic and mass spectrometric analyses, and that of 6-methoxyzeylenol (6) was further confirmed by single-crystal X-ray crystallography, which also established its absolute configuration. The isolated metabolites were evaluated for antibacterial activity against the Gram-positive bacteria Bacillus subtilis and Staphylococcus epidermidis and the Gram-negative bacteria Enterococcus raffinosus, Escherichia coli, Paraburkholderia caledonica, Pectobacterium carotovorum, and Pseudomonas putida, as well as for cytotoxicity against the MCF-7 human breast cancer cell line. A mixture of uvaretin (20) and isouvaretin (21) exhibited significant antibacterial activity against B. subtilis (EC50 8.7 μM) and S. epidermidis (IC50 7.9 μM). (8'α,9'β-Dihydroxy)-3-farnesylindole (12) showed strong inhibitory activity (EC50 9.8 μM) against B. subtilis, comparable to the clinical reference ampicillin (EC50 17.9 μM). None of the compounds showed relevant cytotoxicity against the MCF-7 human breast cancer cell line.
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Affiliation(s)
- Gasper Maeda
- Chemistry
Department, College of Natural and Applied Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania
- Department
of Chemistry−BMC, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Pieter J. Gilissen
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Anastasia Rudenko
- Department
of Chemistry and Molecular Biology, University of Gothenburg,
and Centre for Antibiotic Resistance Research (CARe)
at the University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Jelle van der Wal
- Department
of Chemistry and Molecular Biology, University of Gothenburg,
and Centre for Antibiotic Resistance Research (CARe)
at the University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Catarina Bourgard
- Department
of Chemistry and Molecular Biology, University of Gothenburg,
and Centre for Antibiotic Resistance Research (CARe)
at the University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Arvind Kumar Gupta
- Department
of Chemistry−Ångström, Uppsala University, SE-751
20 Uppsala, Sweden
| | - Per Sunnerhagen
- Department
of Chemistry and Molecular Biology, University of Gothenburg,
and Centre for Antibiotic Resistance Research (CARe)
at the University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Joan J. E. Munissi
- Chemistry
Department, College of Natural and Applied Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Stephen S. Nyandoro
- Chemistry
Department, College of Natural and Applied Sciences, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Máté Erdélyi
- Department
of Chemistry−BMC, Uppsala University, SE-751 23 Uppsala, Sweden
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12
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Diversity of Insect Flower Visitors of Xylopia aromatica (Magnoliales, Annonaceae) in a Brazilian Savanna. DIVERSITY 2021. [DOI: 10.3390/d13120661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Small beetles are important pollinators of Annonaceae whose flower chambers are small and have diurnal and/or nocturnal anthesis. The pollinators of these flowers belong to the families Nitidulidae, Staphylinidae, Chrysomelidae, and Curculionidae. In this study, the first conducted in the Cerrado of Chapada dos Guimarães, Mato Grosso, Brazil, the behavior of the insect flower visitors of Xylopia aromatica was observed, in both the field and the laboratory. The chambers of 253 flowers were collected from 11 plants, and the biological aspects of their visitors were analyzed quantitatively and qualitatively. The most abundant visitors were thrips and beetles. Coleoptera was represented by four morphospecies occurring frequently in the floral chambers (>70% of individuals). Among beetles, one species belonged to Nitidulidae (Cillaeinae, Conotelus sp. 1) and two belonged to Staphylinidae (Aleocharinae sp. 1 and Aleocharinae sp. 2). These three morphospecies of small elongate beetles have setae where pollen may adhere. In addition, they were present on both male and female phases of the flowers, indicating potential cross-pollination. In the study area, X. aromatica possesses mixed pollination promoted by Thysanoptera and small Nitidulidae and Staphylinidae beetles. This study brings the first record of Lamprosomatinae (Chrysomelidae) and, especially, of Conotelus (Nitidulidae) in the flower chambers of X. aromatica, with new information on behavior of floral visitors coupled with their morphological traits that may promote cross-pollination in this plant species.
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13
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Larson DA, Vargas OM, Vicentini A, Dick CW. Admixture may be extensive among hyperdominant Amazon rainforest tree species. THE NEW PHYTOLOGIST 2021; 232:2520-2534. [PMID: 34389989 PMCID: PMC9292926 DOI: 10.1111/nph.17675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/04/2021] [Indexed: 05/25/2023]
Abstract
Admixture is a mechanism by which species of long-lived plants may acquire novel alleles. However, the potential role of admixture in the origin and maintenance of tropical plant diversity is unclear. We ask whether admixture occurs in an ecologically important clade of Eschweilera (Parvifolia clade, Lecythidaceae), which includes some of the most widespread and abundant tree species in Amazonian forests. Using target capture sequencing, we conducted a detailed phylogenomic investigation of 33 species in the Parvifolia clade and investigated specific hypotheses of admixture within a robust phylogenetic framework. We found strong evidence of admixture among three ecologically dominant species, E. coriacea, E. wachenheimii and E. parviflora, but a lack of evidence for admixture among other lineages. Accepted species were largely distinguishable from one another, as was geographic structure within species. We show that hybridization may play a role in the evolution of the most widespread and ecologically variable Amazonian tree species. While admixture occurs among some species of Eschweilera, it has not led to widespread erosion of most species' genetic or morphological identities. Therefore, current morphological based species circumscriptions appear to provide a useful characterization of the clade's lineage diversity.
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Affiliation(s)
- Drew A. Larson
- Department of Ecology & Evolutionary BiologyUniversity of MichiganAnn ArborMI48109USA
| | - Oscar M. Vargas
- Department of Biological SciencesHumboldt State UniversityArcataCA95521USA
| | - Alberto Vicentini
- Instituto Nacional de Pesquisas da Amazônia (INPA)ManausAMCEP 69067‐375Brazil
| | - Christopher W. Dick
- Department of Ecology & Evolutionary BiologyUniversity of MichiganAnn ArborMI48109USA
- Smithsonian Tropical Research InstitutePanama CityRepublic of Panama
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14
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Lara-Cabrera SI, Perez-Garcia MDLL, Maya-Lastra CA, Montero-Castro JC, Godden GT, Cibrian-Jaramillo A, Fisher AE, Porter JM. Phylogenomics of Salvia L. subgenus Calosphace (Lamiaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:725900. [PMID: 34721456 PMCID: PMC8554000 DOI: 10.3389/fpls.2021.725900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/07/2021] [Indexed: 05/13/2023]
Abstract
The evolutionary relationships of Salvia have been difficult to estimate. In this study, we used the Next Generation Sequencing method Hyb-Seq to evaluate relationships among 90 Lamiaceae samples, including representatives of Mentheae, Ocimeae, Salvia subgenera Audibertia, Leonia, Salvia, and 69 species of subgenus Calosphace, representing 32 of Epling's sections. A bait set was designed in MarkerMiner using available transcriptome data to enrich 119 variable nuclear loci. Nuclear and chloroplast loci were assembled with hybphylomaker (HPM), followed by coalescent approach analyses for nuclear data (ASTRAL, BEAST) and a concatenated Maximum Likelihood analysis of chloroplast loci. The HPM assembly had an average of 1,314,368 mapped reads for the sample and 527 putative exons. Phylogenetic inferences resolved strongly supported relationships for the deep-level nodes, agreeing with previous hypotheses which assumed that subgenus Audibertia is sister to subgenus Calosphace. Within subgenus Calosphace, we recovered eight monophyletic sections sensu Epling, Cardinalis, Hastatae, Incarnatae, and Uricae in all the analyses (nDNA and cpDNA), Biflorae, Lavanduloideae, and Sigmoideae in nuclear analyses (ASTRAL, BEAST) and Curtiflorae in ASTRAL trees. Network analysis supports deep node relationships, some of the main clades, and recovers reticulation within the core Calosphace. The chloroplast phylogeny resolved deep nodes and four monophyletic Calosphace sections. Placement of S. axillaris is distinct in nuclear evidence and chloroplast, as sister to the rest of the S. subg. Calosphace in chloroplast and a clade with "Hastatae clade" sister to the rest of the subgenus in nuclear evidence. We also tested the monophyly of S. hispanica, S. polystachia, S. purpurea, and S. tiliifolia, including two samples of each, and found that S. hispanica and S. purpurea are monophyletic. Our baits can be used in future studies of Lamiaceae phylogeny to estimate relationships between genera and among species. In this study, we presented a Hyb-Seq phylogeny for complex, recently diverged Salvia, which could be implemented in other Lamiaceae.
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Affiliation(s)
- Sabina Irene Lara-Cabrera
- Laboratorio de Sistemática Molecular de Plantas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Maria de la Luz Perez-Garcia
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Mexico
| | - Carlos Alonso Maya-Lastra
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, United States
| | - Juan Carlos Montero-Castro
- Laboratorio de Sistemática Molecular de Plantas, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Grant T. Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - Angelica Cibrian-Jaramillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del instituto Politécnico Nacional, Irapuato, Mexico
| | - Amanda E. Fisher
- Department of Biological Sciences, California State University, Long Beach, CA, United States
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15
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Escobar S, Helmstetter AJ, Montúfar R, Couvreur TLP, Balslev H. Phylogenomic relationships and historical biogeography in the South American vegetable ivory palms (Phytelepheae). Mol Phylogenet Evol 2021; 166:107314. [PMID: 34592464 DOI: 10.1016/j.ympev.2021.107314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 01/06/2023]
Abstract
The palm tribe Phytelepheae form a clade of three genera and eight species whose phylogenetic relationships and historical biogeography are not fully understood. Based on morphological similarities and phylogenetic relatedness, it has been suggested that Phytelephas seemannii and Phytelephas schottii are synonyms of Phytelephas macrocarpa, implying the existence of only six species within the Phytelepheae. In addition, uncertainty in their phylogenetic relationships in turn results in blurred biogeographic history. We inferred the phylogenomic relationships in the Phytelepheae by target-capturing 176 nuclear genes and estimated divergence times by using four fossils for time calibration. We lastly explored the biogeographic history of the tribe by inferring its ancestral range evolution. Our phylogenomic trees showed that P. seemannii and P. schottii are not closely related with P. macrocarpa, and therefore, support the existence of eight species in the Phytelepheae. The ancestor of the tribe was widely-distributed in the Chocó, Magdalena, and Amazonia during the Miocene at 19.25 Ma. Early diversification in Phytelephas at 5.27 Ma could have occurred by trans-Andean vicariance after the western Andes uplifted rapidly at ∼ 10 Ma. Our results show the utility of phylogenomic approaches to shed light on species relationships and their biogeographic history.
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Affiliation(s)
- Sebastián Escobar
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, DK 8000 Aarhus C, Denmark.
| | | | - Rommel Montúfar
- Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Thomas L P Couvreur
- IRD, UMR DIADE, University of Montpellier, Montpellier, France; Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Henrik Balslev
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, DK 8000 Aarhus C, Denmark
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16
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Abstract
The evolutionary trajectories of insects and angiosperms appear to be intimately interconnected. Increases in the diversity of phytophagous beetles and angiosperms co-occur in the Mesozoic fossil record, and there is fossil evidence of pollinivory and pollination by insects, both in flowering plants and in gymnosperms. The oldest records of angiosperm pollination indicate flies as pollen vectors. A basal group of angiosperms, the order Magnoliales, has retained plesiomorphic characters such as dozens of pistils and stamens spiraling around the receptacle. In a family of this order, Annonaceae, over 90% of species are pollinated by beetles. In many Annonaceae species, flowers display wide spaces, referred to as floral chambers, where beetles can find shelter from weather conditions and predators, food in the form of pollen and tissues, and a mating site. Two basic types of floral chambers can be distinguished: small chambers visited by small beetles (Nitidulidae, Staphylinidae, Chrysomelidae, and Curculionidae) with diurnal and/or nocturnal activity and large and thermogenic floral chambers visited by beetles of the tribe Cyclocephalini (Scarabaeoidea, Melolonthidae). In the latter case, the heat that the flowers produce may serve as a resource for the beetles that visit them, resulting in smaller endothermy costs for the scarabs. This study reviewed the literature including PhD and MSc theses on cantharophilous Annonaceae in the Cerrado. In this biome, both types of associations are found, although cantharophilous Annonaceae represent a small portion of the plant species (<5%). Cantharophilous Annonaceae in the Cerrado share attributes according to the beetles that pollinate them: species pollinated by small beetles, for instance, may flower throughout the year, whereas Annonaceae pollinated by Cyclocephalini normally flower in the beginning of the rainy season (October/November), in synchrony with the phenological patterns of their pollinators. Cantharophilous Annonaceae flowers, regardless of their size, tend to have light colors and sweet and fruity odors. In addition to the lack of studies on the attraction of beetles by these floral characters, the taxonomic composition of the beetles that pollinate Annonaceae in the Cerrado is poorly known. This review attempts to discuss, in light of what has already been published, potential fields of investigation concerning pollinating beetles’ behavior and evolution.
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17
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Hendriks KP, Mandáková T, Hay NM, Ly E, Hooft van Huysduynen A, Tamrakar R, Thomas SK, Toro‐Núñez O, Pires JC, Nikolov LA, Koch MA, Windham MD, Lysak MA, Forest F, Mummenhoff K, Baker WJ, Lens F, Bailey CD. The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311438. [PMID: 34336398 PMCID: PMC8312739 DOI: 10.1002/aps3.11438] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
Abstract
PREMISE Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort. METHODS AND RESULTS Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24-31%) and Brassicaceae (35-59%) targets resulted in a sizable reconstruction of loci for each target set (x̄ ≥ 70%). CONCLUSIONS High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole.
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Affiliation(s)
- Kasper P. Hendriks
- Naturalis Biodiversity CenterResearch Group Functional TraitsP.O. Box 95172300RALeidenThe Netherlands
- Department of Biology/BotanyOsnabrück UniversityOsnabrück49076Germany
| | | | - Nikolai M. Hay
- Department of BiologyDuke UniversityDurhamNorth Carolina27708USA
| | - Elfy Ly
- Naturalis Biodiversity CenterResearch Group Functional TraitsP.O. Box 95172300RALeidenThe Netherlands
| | - Alex Hooft van Huysduynen
- Naturalis Biodiversity CenterResearch Group Functional TraitsP.O. Box 95172300RALeidenThe Netherlands
| | - Rubin Tamrakar
- Department of BiologyNew Mexico State UniversityLas CrucesNew Mexico88001USA
| | - Shawn K. Thomas
- Division of Biological SciencesUniversity of MissouriColumbiaMissouri65211USA
| | - Oscar Toro‐Núñez
- Departamento de BotánicaUniversidad de ConcepciónConcepciónChile
| | - J. Chris Pires
- Division of Biological SciencesUniversity of MissouriColumbiaMissouri65211USA
| | - Lachezar A. Nikolov
- Department of Molecular, Cell and Developmental BiologyUniversity of California Los AngelesLos AngelesCalifornia90095USA
| | - Marcus A. Koch
- Centre for Organismal Studies COS, Biodiversity and Plant SystematicsHeidelberg University69120HeidelbergGermany
| | | | | | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Klaus Mummenhoff
- Department of Biology/BotanyOsnabrück UniversityOsnabrück49076Germany
| | | | - Frederic Lens
- Naturalis Biodiversity CenterResearch Group Functional TraitsP.O. Box 95172300RALeidenThe Netherlands
- Institute of Biology LeidenPlant SciencesLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - C. Donovan Bailey
- Department of BiologyNew Mexico State UniversityLas CrucesNew Mexico88001USA
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18
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McLay TGB, Birch JL, Gunn BF, Ning W, Tate JA, Nauheimer L, Joyce EM, Simpson L, Schmidt‐Lebuhn AN, Baker WJ, Forest F, Jackson CJ. New targets acquired: Improving locus recovery from the Angiosperms353 probe set. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311420. [PMID: 34336399 PMCID: PMC8312740 DOI: 10.1002/aps3.11420] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/15/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6-18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, and reducing locus recovery. METHODS We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a 'mega353' target file, with each locus represented by 17-373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene data sets. RESULTS Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%. DISCUSSION Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets.
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Affiliation(s)
- Todd G. B. McLay
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
- Centre for Australian National Biodiversity ResearchCSIROCanberraAustralia
| | - Joanne L. Birch
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
| | - Bee F. Gunn
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
| | - Weixuan Ning
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Jennifer A. Tate
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Lars Nauheimer
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | - Elizabeth M. Joyce
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | - Lalita Simpson
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | | | | | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Chris J. Jackson
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
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19
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Strijk JS, Hinsinger DD, Roeder MM, Chatrou LW, Couvreur TLP, Erkens RHJ, Sauquet H, Pirie MD, Thomas DC, Cao K. Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology. Mol Ecol Resour 2021; 21:1608-1619. [PMID: 33569882 PMCID: PMC8251617 DOI: 10.1111/1755-0998.13353] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 11/27/2022]
Abstract
The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome-level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676× sequencing depth) from PacBio and Illumina short-reads, in combination with 10× Genomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo-chromosomes using Hi-C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size showed a slow continuous contraction, probably related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.
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Affiliation(s)
- Joeri S. Strijk
- Institute for Biodiversity and Environmental ResearchUniversiti Brunei DarussalamJalan Tungku LinkBrunei Darussalam
- Alliance for Conservation Tree GenomicsPha Tad Ke Botanical GardenLuang PrabangLaos
- Guangxi Key Laboratory of Forest Ecology and ConservationBiodiversity Genomics TeamNanningGuangxiChina
| | - Damien D. Hinsinger
- Alliance for Conservation Tree GenomicsPha Tad Ke Botanical GardenLuang PrabangLaos
- Génomique Métabolique, GenoscopeInstitut de Biologie François JacobCommissariat à l′Énergie Atomique (CEA), CNRSUniversité ÉvryUniversité Paris‐SaclayÉvryFrance
| | - Mareike M. Roeder
- Community Ecology and Conservation GroupXishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglun, MenglaYunnanChina
- AueninstitutInstitute for Geography and GeoecologyKarlsruhe Institute of TechnologyRastattGermany
| | - Lars W. Chatrou
- Systematic and Evolutionary Botany LaboratoryGhent UniversityGhentBelgium
| | | | - Roy H. J. Erkens
- Maastricht Science ProgrammeMaastricht UniversityMaastrichtThe Netherlands
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW)Royal Botanic Gardens and Domain TrustSydneyNSWAustralia
| | - Michael D. Pirie
- Department of Natural HistoryUniversity MuseumUniversity of BergenBergenNorway
| | | | - Kunfang Cao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresourcesGuangxi UniversityNanningGuangxiChina
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20
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Shah T, Schneider JV, Zizka G, Maurin O, Baker W, Forest F, Brewer GE, Savolainen V, Darbyshire I, Larridon I. Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits. AMERICAN JOURNAL OF BOTANY 2021; 108:1201-1216. [PMID: 34180046 DOI: 10.1002/ajb2.1682] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/23/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. METHODS We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. RESULTS For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. CONCLUSIONS The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.
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Affiliation(s)
- Toral Shah
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | - Julio V Schneider
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - William Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | | | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L., Ledeganckstraat 35, Gent, 9000, Belgium
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21
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Ren C, Wang L, Nie ZL, Johnson G, Yang QE, Wen J. Development and phylogenetic utilities of a new set of single-/low-copy nuclear genes in Senecioneae (Asteraceae), with new insights into the tribal position and the relationships within subtribe Tussilagininae. Mol Phylogenet Evol 2021; 162:107202. [PMID: 33992786 DOI: 10.1016/j.ympev.2021.107202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/13/2021] [Accepted: 05/06/2021] [Indexed: 11/26/2022]
Abstract
The tribe Senecioneae is one of the largest tribes in Asteraceae, with a nearly cosmopolitan distribution. Despite great efforts devoted to elucidate the evolution of Senecioneae, many questions still remain concerning the systematics of this group, from the tribal circumscription and position to species relationships in many genera. The hybridization-based target enrichment method of next-generation sequencing has been accepted as a promising approach to resolve phylogenetic problems. We herein develop a set of single-/low-copy genes for Senecioneae, and test their phylogenetic utilities. Our results demonstrate that these genes work highly efficiently for Senecioneae, with a high average gene recovery of 98.8% across the tribe and recovering robust phylogenetic hypotheses at different levels. In particular, the delimitation of the Senecioneae has been confirmed to include Abrotanella and exclude Doronicum, with the former sister to core Senecioneae and the latter shown to be more closely related to Calenduleae. Moreover, Doronicum and Calenduleae are inferred to be the closest relatives of Senecioneae, which is a new hypothesis well supported by statistical topology tests, morphological evidence, and the profile of pyrrolizidine alkaloids, a special kind of chemical characters generally used to define Senecioneae. Furthermore, this study suggests a complex reticulation history in the diversification of Senecioneae, accounting for the prevalence of polyploid groups in the tribe. With subtribe Tussilagininae s.str. as a case study showing a more evident pattern of gene duplication, we further explored reconstructing the phylogeny in the groups with high ploidy levels. Our results also demonstrate that tree topologies based on sorted paralogous copies are stable across different methods of phylogenetic inference, and more congruent with the morphological evidence and the results of previous phylogenetic studies.
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Affiliation(s)
- Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Long Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Qin-Er Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Key Laboratory of Digital Botanical Garden of Guangdong Province, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China.
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
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22
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Baker WJ, Bailey P, Barber V, Barker A, Bellot S, Bishop D, Botigué LR, Brewer G, Carruthers T, Clarkson JJ, Cook J, Cowan RS, Dodsworth S, Epitawalage N, Françoso E, Gallego B, Johnson MG, Kim JT, Leempoel K, Maurin O, McGinnie C, Pokorny L, Roy S, Stone M, Toledo E, Wickett NJ, Zuntini AR, Eiserhardt WL, Kersey PJ, Leitch IJ, Forest F. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life. Syst Biol 2021; 71:301-319. [PMID: 33983440 PMCID: PMC8830076 DOI: 10.1093/sysbio/syab035] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/22/2022] Open
Abstract
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96\documentclass[12pt]{minimal}
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}{}$\%$\end{document}) and 2333 genera (17\documentclass[12pt]{minimal}
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}{}$\%$\end{document}). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]
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Affiliation(s)
- William J Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Vanessa Barber
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Abigail Barker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - David Bishop
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Laura R Botigué
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Grace Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Tom Carruthers
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - James J Clarkson
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Jeffrey Cook
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Robyn S Cowan
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, United Kingdom
| | | | - Elaine Françoso
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Berta Gallego
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jan T Kim
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Computer Science, School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, United Kingdom
| | - Kevin Leempoel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Plant Biotechnology and Genomics (CBGP) UPM-INIA, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Malcolm Stone
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Eduardo Toledo
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA
| | | | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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23
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Ogutcen E, Christe C, Nishii K, Salamin N, Möller M, Perret M. Phylogenomics of Gesneriaceae using targeted capture of nuclear genes. Mol Phylogenet Evol 2021; 157:107068. [PMID: 33422648 DOI: 10.1016/j.ympev.2021.107068] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 01/07/2023]
Abstract
Gesneriaceae (ca. 3400 species) is a pantropical plant family with a wide range of growth form and floral morphology that are associated with repeated adaptations to different environments and pollinators. Although Gesneriaceae systematics has been largely improved by the use of Sanger sequencing data, our understanding of the evolutionary history of the group is still far from complete due to the limited number of informative characters provided by this type of data. To overcome this limitation, we developed here a Gesneriaceae-specific gene capture kit targeting 830 single-copy loci (776,754 bp in total), including 279 genes from the Universal Angiosperms-353 kit. With an average of 557,600 reads and 87.8% gene recovery, our target capture was successful across the family Gesneriaceae and also in other families of Lamiales. From our bait set, we selected the most informative 418 loci to resolve phylogenetic relationships across the entire Gesneriaceae family using maximum likelihood and coalescent-based methods. Upon testing the phylogenetic performance of our baits on 78 taxa representing 20 out of 24 subtribes within the family, we showed that our data provided high support for the phylogenetic relationships among the major lineages, and were able to provide high resolution within more recent radiations. Overall, the molecular resources we developed here open new perspectives for the study of Gesneriaceae phylogeny at different taxonomical levels and the identification of the factors underlying the diversification of this plant group.
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Affiliation(s)
- Ezgi Ogutcen
- Conservatoire et Jardin botaniques de la Ville de Genève and Department of Botany and Plant Biology, University of Geneva, 1292 Chambésy, Switzerland
| | - Camille Christe
- Conservatoire et Jardin botaniques de la Ville de Genève and Department of Botany and Plant Biology, University of Geneva, 1292 Chambésy, Switzerland
| | - Kanae Nishii
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK; Kanagawa University, 2946, Tsuchiya, Hiratsuka-shi, Kanagawa 259-1293, Japan
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Michael Möller
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK
| | - Mathieu Perret
- Conservatoire et Jardin botaniques de la Ville de Genève and Department of Botany and Plant Biology, University of Geneva, 1292 Chambésy, Switzerland.
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24
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Wang Y, Cvetković T, Aritsara ANA, Carrion ADA, Strijk JS. Complete chloroplast sequence of Fenerivia ghesquiereana (Annonaceae): a rare and endemic tree from Madagascar. Mitochondrial DNA B Resour 2021; 6:158-160. [PMID: 33542954 PMCID: PMC7836981 DOI: 10.1080/23802359.2020.1855604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Fenerivia ghesquiereana (Cavaco & Keraudren) R.M.K. Saunders (Annaonaceae) is a rare and endemic tree restricted to the warm tropical forests of Madagascar, a major global hotspot for biodiversity. Species in the genus are mostly restricted to a thin belt along the eastern edge of the island and remain under intense pressure due to deforestation for logging, mining and slash-and-burn agriculture (‘tavy’), despite national pledges to curb biodiversity losses and increase park protection to combat illegal logging and poaching. Here we report the complete chloroplast genome sequence of this species to support ongoing efforts to complete the (sub-)tribal classification of the family. The chloroplast sequence of F. ghesquiereana was 160,194 bp in length, including two inverted repeat regions of 26,093 bp, a large single-copy region of 89,041 bp and a small single-copy region of 18,967 bp. A total of 160 genes were annotated, of which 115 are coding, 37 are tRNA genes, and eight are rRNA genes. The overall GC content was 39%; this was higher in the IRs (43.4%) when compared to the LSC (30.7%) and the SSC (33.9%) regions. A Maximum Likelihood phylogenetic analysis with a selection of other plastomes in Annonaceae placed F. ghesquiereana as sister to Meiogyne hainanensis (Merr.) in subfamily Malmeoideae.
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Affiliation(s)
- Yixi Wang
- Biodiversity Genomics Team, Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi University, Nanning, China
| | - Tijana Cvetković
- Biodiversity Genomics Team, Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi University, Nanning, China
| | - Amy N. A. Aritsara
- Plant Ecophysiology and Evolution Group, College of Forestry, Guangxi University, Nanning, China
- Département Forestière et Environnement, Ecole Supérieure des Sciences Agronomiques, Université d’Antananarivo, Antananarivo, Madagascar
| | - Angelo D. A. Carrion
- Biodiversity Genomics Team, Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi University, Nanning, China
| | - Joeri S. Strijk
- Biodiversity Genomics Team, Guangxi Key Laboratory of Forest Ecology and Conservation, Guangxi University, Nanning, China
- Pha Tad Ke Botanical Garden, Alliance for Conservation Tree Genomics, Luang Prabang, Laos
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25
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Kates HR, Doby JR, Siniscalchi CM, LaFrance R, Soltis DE, Soltis PS, Guralnick RP, Folk RA. The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success. FRONTIERS IN PLANT SCIENCE 2021; 12:669064. [PMID: 34249041 PMCID: PMC8262526 DOI: 10.3389/fpls.2021.669064] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/12/2021] [Indexed: 05/22/2023]
Abstract
Phylogenetic datasets are now commonly generated using short-read sequencing technologies unhampered by degraded DNA, such as that often extracted from herbarium specimens. The compatibility of these methods with herbarium specimens has precipitated an increase in broad sampling of herbarium specimens for inclusion in phylogenetic studies. Understanding which sample characteristics are predictive of sequencing success can guide researchers in the selection of tissues and specimens most likely to yield good results. Multiple recent studies have considered the relationship between sample characteristics and DNA yield and sequence capture success. Here we report an analysis of the relationship between sample characteristics and sequencing success for nearly 8,000 herbarium specimens. This study, the largest of its kind, is also the first to include a measure of specimen quality ("greenness") as a predictor of DNA sequencing success. We found that taxonomic group and source herbarium are strong predictors of both DNA yield and sequencing success and that the most important specimen characteristics for predicting success differ for DNA yield and sequencing: greenness was the strongest predictor of DNA yield, and age was the strongest predictor of proportion-on-target reads recovered. Surprisingly, the relationship between age and proportion-on-target reads is the inverse of expectations; older specimens performed slightly better in our capture-based protocols. We also found that DNA yield itself is not a strong predictor of sequencing success. Most literature on DNA sequencing from herbarium specimens considers specimen selection for optimal DNA extraction success, which we find to be an inappropriate metric for predicting success using next-generation sequencing technologies.
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Affiliation(s)
- Heather R. Kates
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- *Correspondence: Heather R. Kates,
| | - Joshua R. Doby
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - Carol M. Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Raphael LaFrance
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Biodiversity Institute, University of Florida, Gainesville, FL, United States
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
- Biodiversity Institute, University of Florida, Gainesville, FL, United States
| | - Robert P. Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Biodiversity Institute, University of Florida, Gainesville, FL, United States
- Robert P. Guralnick,
| | - Ryan A. Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
- Ryan A. Folk,
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26
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Schneider JV, Paule J, Jungcurt T, Cardoso D, Amorim AM, Berberich T, Zizka G. Resolving Recalcitrant Clades in the Pantropical Ochnaceae: Insights From Comparative Phylogenomics of Plastome and Nuclear Genomic Data Derived From Targeted Sequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:638650. [PMID: 33613613 PMCID: PMC7890083 DOI: 10.3389/fpls.2021.638650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/15/2021] [Indexed: 05/13/2023]
Abstract
Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family's backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family's species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.
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Affiliation(s)
- Julio V. Schneider
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Entomology III, Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Tanja Jungcurt
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Domingos Cardoso
- Instituto de Biologia, Universidade Federal da Bahia (UFBA), Salvador, Brazil
| | - André Márcio Amorim
- Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
- Herbário André Maurício Vieira de Carvalho, CEPEC, CEPLAC, Itabuna, Brazil
| | - Thomas Berberich
- Senckenberg Biodiversity and Climate Research Center, Lab-Center, Frankfurt am Main, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
- *Correspondence: Georg Zizka, ;
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27
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Individualistic evolutionary responses of Central African rain forest plants to Pleistocene climatic fluctuations. Proc Natl Acad Sci U S A 2020; 117:32509-32518. [PMID: 33277432 DOI: 10.1073/pnas.2001018117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Understanding the evolutionary dynamics of genetic diversity is fundamental for species conservation in the face of climate change, particularly in hyper-diverse biomes. Species in a region may respond similarly to climate change, leading to comparable evolutionary dynamics, or individualistically, resulting in dissimilar patterns. The second-largest expanse of continuous tropical rain forest (TRF) in the world is found in Central Africa. Here, present-day patterns of genetic structure are thought to be dictated by repeated expansion and contraction of TRFs into and out of refugia during Pleistocene climatic fluctuations. This refugia model implies a common response to past climate change. However, given the unrivalled diversity of TRFs, species could respond differently because of distinct environmental requirements or ecological characteristics. To test this, we generated genome-wide sequence data for >700 individuals of seven codistributed plants from Lower Guinea in Central Africa. We inferred species' evolutionary and demographic histories within a comparative phylogeographic framework. Levels of genetic structure varied among species and emerged primarily during the Pleistocene, but divergence events were rarely concordant. Demographic trends ranged from repeated contraction and expansion to continuous growth. Furthermore, patterns in genetic variation were linked to disparate environmental factors, including climate, soil, and habitat stability. Using a strict refugia model to explain past TRF dynamics is too simplistic. Instead, individualistic evolutionary responses to Pleistocene climatic fluctuations have shaped patterns in genetic diversity. Predicting the future dynamics of TRFs under climate change will be challenging, and more emphasis is needed on species ecology to better conserve TRFs worldwide.
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28
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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. AMERICAN JOURNAL OF BOTANY 2020; 107:1710-1735. [PMID: 33253423 PMCID: PMC7839790 DOI: 10.1002/ajb2.1568] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [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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29
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Straub SCK, Boutte J, Fishbein M, Livshultz T. Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb-Seq. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11400. [PMID: 33304663 PMCID: PMC7705337 DOI: 10.1002/aps3.11400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/12/2020] [Indexed: 05/07/2023]
Abstract
PREMISE Apocynaceae is the 10th largest flowering plant family and a focus for study of plant-insect interactions, especially as mediated by secondary metabolites. However, it has few genomic resources relative to its size. Target capture sequencing is a powerful approach for genome reduction that facilitates studies requiring data from the nuclear genome in non-model taxa, such as Apocynaceae. METHODS Transcriptomes were used to design probes for targeted sequencing of putatively single-copy nuclear genes across Apocynaceae. The sequences obtained were used to assess the success of the probe design, the intrageneric and intraspecific variation in the targeted genes, and the utility of the genes for inferring phylogeny. RESULTS From 853 candidate nuclear genes, 835 were consistently recovered in single copy and were variable enough for phylogenomics. The inferred gene trees were useful for coalescent-based species tree analysis, which showed all subfamilies of Apocynaceae as monophyletic, while also resolving relationships among species within the genus Apocynum. Intraspecific comparison of Elytropus chilensis individuals revealed numerous single-nucleotide polymorphisms with potential for use in population-level studies. DISCUSSION Community use of this Hyb-Seq probe set will facilitate and promote progress in the study of Apocynaceae across scales from population genomics to phylogenomics.
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Affiliation(s)
- Shannon C. K. Straub
- Department of BiologyHobart and William Smith Colleges300 Pulteney StreetGenevaNew York14456USA
| | - Julien Boutte
- Department of BiologyHobart and William Smith Colleges300 Pulteney StreetGenevaNew York14456USA
| | - Mark Fishbein
- Department of Plant Biology, Ecology, and EvolutionOklahoma State University301 Physical SciencesStillwaterOklahoma74078USA
| | - Tatyana Livshultz
- Department of Biodiversity, Earth, and Environmental Sciences and the Academy of Natural SciencesDrexel University1900 Benjamin Franklin ParkwayPhiladelphiaPennsylvania19103USA
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30
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Maia DS, Lopes CF, Saldanha AA, Silva NL, Sartori ÂLB, Carollo CA, Sobral MG, Alves SN, Silva DB, de Siqueira JM. Larvicidal effect from different Annonaceae species on Culex quinquefasciatus. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:36983-36993. [PMID: 32577964 DOI: 10.1007/s11356-020-08997-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
The recent outbreaks of mosquito-borne diseases highlighted the pivotal importance of mosquito vector control in tropical areas worldwide. Several strategies have been developed to control vector populations and disease transmission in endemic areas. The steps to obtain natural active compounds involve the pre-selection in a biological model and subsequently evaluation on specific models. The present study reports the evaluation of 35 extracts, fractions, and essential oils obtained from five species from the Annonaceae family on Artemia salina and Culex quinquefasciatus. The A. salina results were used as a pre-screening for larvicidal test about mosquitoes. A correlation of biological activity in both bioassays was observed for the hydroethanolic extracts and their respective hexane and chloroform fractions of the leaves of Annona species, except A. nutans. The same correlation was also observed for all tested essential oils and petroleum ether extracts from Duguetia species. It was possible to limit an interval of lethality about A. salina, which has a corresponding range to the larvicidal test against the mosquito. The main components present in D. lanceolata essential oil or enriched fraction were α-selinene, aristolochene, (E)-caryophyllene, and (E)-calamenene. For D. furfuracea, the main components present of the underground parts were (E)-asarone, 2,4,5-trimethoxystyrene, spathulenol, and bicyclogermacrene for aerial parts. The A. salina test could be used as a model for the pre-screening of larvicidal activity.
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Affiliation(s)
- Débora Soares Maia
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João del Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG, 35501-296, Brazil.
| | - Camila Ferreira Lopes
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João del Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG, 35501-296, Brazil
| | - Aline Aparecida Saldanha
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João del Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG, 35501-296, Brazil
| | - Nathália Lucca Silva
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João del Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG, 35501-296, Brazil
| | - Ângela Lúcia Bagnatori Sartori
- Laboratório de Produtos Naturais e Espectrometria de Massas, Faculdade de Ciências Farmacêuticas, Alimentação e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, 79070-900, Brazil
| | - Carlos Alexandre Carollo
- Laboratório de Produtos Naturais e Espectrometria de Massas, Faculdade de Ciências Farmacêuticas, Alimentação e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, 79070-900, Brazil
| | - Marcos Guerra Sobral
- Departamento de Ciências Naturais, Universidade Federal São João Del Rei, São João Del Rei, MG, 36301-160, Brazil
| | - Stênio Nunes Alves
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João del Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG, 35501-296, Brazil
| | - Denise Brentan Silva
- Laboratório de Produtos Naturais e Espectrometria de Massas, Faculdade de Ciências Farmacêuticas, Alimentação e Nutrição, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, 79070-900, Brazil
| | - João Máximo de Siqueira
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João del Rei, Av. Sebastião Gonçalves Coelho, 400, Divinópolis, MG, 35501-296, Brazil
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31
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Ma ZY, Nie ZL, Ren C, Liu XQ, Zimmer EA, Wen J. Phylogenomic relationships and character evolution of the grape family (Vitaceae). Mol Phylogenet Evol 2020; 154:106948. [PMID: 32866616 DOI: 10.1016/j.ympev.2020.106948] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/02/2020] [Accepted: 08/24/2020] [Indexed: 11/30/2022]
Abstract
The grape family consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop - the grape Vitis vinifera. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the family. The five tribes of the grape family, including Ampelopsideae, Cayratieae, Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both nuclear and chloroplast genomic data and the backbone relationships are congruent with previous reports. The cupular floral disc (raised above and free from ovary at the upper part) is an ancestral state of Vitaceae, with the inconspicuous floral disc as derived in the tribe Parthenocisseae, and the state of adnate to the ovary as derived in the tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral in Vitaceae, with the 4-merous flowers evolved at least two times in the family. The compound dichasial cyme (cymose with two secondary axes) is ancestral in Vitaceae and the thyrse inflorescence (a combination of racemose and cymose branching) in tribe Viteae is derived. The ribbon-like trichome only evolved once in Vitaceae, as a synapomorphy for the tribe Viteae.
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Affiliation(s)
- Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C. 20013-7012, USA
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C. 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C. 20013-7012, USA.
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32
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Helmstetter AJ, Amoussou BEN, Bethune K, Kamdem NG, Glèlè Kakaï R, Sonké B, Couvreur TLP. Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species. Mol Ecol 2020; 29:3560-3573. [PMID: 32743910 DOI: 10.1111/mec.15572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 12/23/2022]
Abstract
The world's second largest expanse of tropical rainforest is in Central Africa, and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across Central African rainforest plants. In particular, previous studies have repeatedly demonstrated a north-south genetic discontinuity around the equatorial line, in a continuous expanse of rainforest where a climatic inversion is documented. Here, we took a phylogeographic approach by sequencing 351 nuclear markers in 112 individuals across the distribution of the African rainforest tree species Annickia affinis (Annonaceae). We showed for the first time that the north-south divide is the result of a single, major colonization event across the climatic inversion from an ancestral population located in Gabon. We suggested that differences in ecological niche of populations located on either side of this inversion may have contributed to this phylogenetic discontinuity. We found evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly developed genomic tools can provide invaluable insights into our understanding of tropical rainforest evolutionary dynamics.
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Affiliation(s)
| | - Biowa E N Amoussou
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France.,Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Kevin Bethune
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Narcisse G Kamdem
- Laboratoire de Botanique Systématique et d'Ecologie, Département des Sciences Biologiques, Ecole Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
| | - Romain Glèlè Kakaï
- Laboratoire de Biomathématiques et d'Estimations Forestières, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Ecologie, Département des Sciences Biologiques, Ecole Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
| | - Thomas L P Couvreur
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France.,Laboratoire de Botanique Systématique et d'Ecologie, Département des Sciences Biologiques, Ecole Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
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33
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Strijk JS, Binh HT, Ngoc NV, Pereira JT, Slik JWF, Sukri RS, Suyama Y, Tagane S, Wieringa JJ, Yahara T, Hinsinger DD. Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea. PLoS One 2020; 15:e0232936. [PMID: 32442164 PMCID: PMC7244142 DOI: 10.1371/journal.pone.0232936] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 04/24/2020] [Indexed: 11/21/2022] Open
Abstract
Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile-thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus-a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.
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Affiliation(s)
- Joeri S. Strijk
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
| | | | | | - Joan T. Pereira
- Sabah Forestry Department, Forest Research Centre, Sandakan, Sabah, Malaysia
| | - J. W. Ferry Slik
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Rahayu S. Sukri
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Yoshihisa Suyama
- Kawatabi Field Science Centre, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Shuichiro Tagane
- The Kagoshima University Museum, Kagoshima University, Kagoshima, Japan
| | | | - Tetsukazu Yahara
- Center for Asian Conservation Ecology, Kyushu University, Fukuoka, Japan
| | - Damien D. Hinsinger
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l′Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
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Stull GW, Soltis PS, Soltis DE, Gitzendanner MA, Smith SA. Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages. AMERICAN JOURNAL OF BOTANY 2020; 107:790-805. [PMID: 32406108 DOI: 10.1002/ajb2.1468] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
PREMISE Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well-documented phenomenon at shallow evolutionary levels but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes, but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome. METHODS We present a phylogenomic examination of a major angiosperm clade (Asteridae) based on sequence data from the nuclear, plastid, and mitochondrial genomes as a means of evaluating currently accepted relationships inferred from the plastome and exploring potential sources of genomic conflict in this group. RESULTS We recovered at least five instances of well-supported cytonuclear discordance concerning the placements of major asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis, and Icacinaceae). We attribute this conflict to a combination of incomplete lineage sorting and hybridization, the latter supported in part by previously inferred whole-genome duplications. CONCLUSIONS Our results challenge several long-standing hypotheses of asterid relationships and have implications for morphological character evolution and for the importance of ancient whole-genome duplications in early asterid evolution. These findings also highlight the value of reevaluating broad-scale angiosperm and green-plant phylogeny with nuclear genomic data.
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Affiliation(s)
- Gregory W Stull
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
- Department of Botany, Smithsonian Institution, Washington, D.C., 20013, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
| | | | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
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35
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Helmstetter AJ, Kamga SM, Bethune K, Lautenschläger T, Zizka A, Bacon CD, Wieringa JJ, Stauffer F, Antonelli A, Sonké B, Couvreur TLP. Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae). PLANTS (BASEL, SWITZERLAND) 2020; 9:E549. [PMID: 32340211 PMCID: PMC7238857 DOI: 10.3390/plants9040549] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 03/27/2020] [Accepted: 04/08/2020] [Indexed: 11/16/2022]
Abstract
Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. Raphia is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of Raphia is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. R. regalis is strongly supported as sister to all other Raphia species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species R. taedigera is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the Raphia individuals from Madagascar are potentially a distinct species different from the widely distributed R. farinifera. In conclusion, our results support the infra generic classification of Raphia based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling, and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution, and other eco-evolutionary aspects of this charismatic, socially, and economically important palm genus.
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Affiliation(s)
| | - Suzanne Mogue Kamga
- Laboratoire de Botanique systématique et d’Ecologie, Department of Biological Sciences, University of Yaoundé I, Higher Teacher Training College, Yaoundé B.P. 047, Cameroon; (S.M.K.); (B.S.)
| | - Kevin Bethune
- IRD, DIADE, University Montpellier, 34394 Montpellier, France; (A.J.H.); (K.B.)
| | - Thea Lautenschläger
- Institute of Botany, Department of Biology, Faculty of Science, Technische Universität Dresden, 01062 Dresden, Germany;
| | - Alexander Zizka
- German Center for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, 04103 Leipzig, Germany;
| | - Christine D. Bacon
- Department of Biological and Environmental Sciences and Gothenburg Global Biodiversity Centre, University of Gothenburg, 405 30 Gothenburg, Sweden; (C.D.B.); (A.A.)
- Gothenburg Global Biodiversity Centre, Box 461, SE 40530 Goteborg, Sweden
| | - Jan J. Wieringa
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands;
| | - Fred Stauffer
- Department of Botany and Plant Biology, Conservatory and Botanical Garden of the City of Geneva, University of Geneva, 1205 Geneva, Switzerland;
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences and Gothenburg Global Biodiversity Centre, University of Gothenburg, 405 30 Gothenburg, Sweden; (C.D.B.); (A.A.)
- Gothenburg Global Biodiversity Centre, Box 461, SE 40530 Goteborg, Sweden
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Bonaventure Sonké
- Laboratoire de Botanique systématique et d’Ecologie, Department of Biological Sciences, University of Yaoundé I, Higher Teacher Training College, Yaoundé B.P. 047, Cameroon; (S.M.K.); (B.S.)
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36
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Andermann T, Torres Jiménez MF, Matos-Maraví P, Batista R, Blanco-Pastor JL, Gustafsson ALS, Kistler L, Liberal IM, Oxelman B, Bacon CD, Antonelli A. A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project. Front Genet 2020; 10:1407. [PMID: 32153629 PMCID: PMC7047930 DOI: 10.3389/fgene.2019.01407] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/24/2019] [Indexed: 12/17/2022] Open
Abstract
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.
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Affiliation(s)
- Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Maria Fernanda Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Romina Batista
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, PPG GCBEv–Instituto Nacional de Pesquisas da Amazônia—INPA Campus II, Manaus, Brazil
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - José L. Blanco-Pastor
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | | | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Isabel M. Liberal
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond-Surrey, United Kingdom
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Jones KE, Fér T, Schmickl RE, Dikow RB, Funk VA, Herrando‐Moraira S, Johnston PR, Kilian N, Siniscalchi CM, Susanna A, Slovák M, Thapa R, Watson LE, Mandel JR. An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11295. [PMID: 31667023 PMCID: PMC6814182 DOI: 10.1002/aps3.11295] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/05/2019] [Indexed: 05/23/2023]
Abstract
PREMISE Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. METHODS Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. RESULTS Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DISCUSSION The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.
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Affiliation(s)
- Katy E. Jones
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinKönigin‐Luise‐Str. 6–814195BerlinGermany
| | - Tomáš Fér
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
| | - Roswitha E. Schmickl
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
- Institute of BotanyThe Czech Academy of SciencesZámek 1CZ 25243PrůhoniceCzech Republic
| | - Rebecca B. Dikow
- Data Science LabOffice of the Chief Information OfficerSmithsonian InstitutionWashingtonD.C.20013‐7012USA
| | - Vicki A. Funk
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonD.C.20013‐7012USA
| | | | - Paul R. Johnston
- Freie Universität BerlinEvolutionary BiologyBerlinGermany
- Berlin Center for Genomics in Biodiversity ResearchBerlinGermany
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB)BerlinGermany
| | - Norbert Kilian
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinKönigin‐Luise‐Str. 6–814195BerlinGermany
| | - Carolina M. Siniscalchi
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB‐CSIC‐ICUB)Pg. del Migdia s.n.ES 08038BarcelonaSpain
| | - Marek Slovák
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2CZ 12800PragueCzech Republic
- Plant Science and Biodiversity CentreSlovak Academy of SciencesSK‐84523BratislavaSlovakia
| | - Ramhari Thapa
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
| | - Linda E. Watson
- Department of Plant Biology, Ecology, and EvolutionOklahoma State UniversityStillwaterOklahoma74078USA
| | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
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Brewer GE, Clarkson JJ, Maurin O, Zuntini AR, Barber V, Bellot S, Biggs N, Cowan RS, Davies NMJ, Dodsworth S, Edwards SL, Eiserhardt WL, Epitawalage N, Frisby S, Grall A, Kersey PJ, Pokorny L, Leitch IJ, Forest F, Baker WJ. Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms. FRONTIERS IN PLANT SCIENCE 2019; 10:1102. [PMID: 31620145 PMCID: PMC6759688 DOI: 10.3389/fpls.2019.01102] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/12/2019] [Indexed: 05/03/2023]
Abstract
The world's herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise and capture genomic regions of interest for high-throughput sequencing. In this study on herbariomics, we used this targeted sequencing approach and the Angiosperms353 universal probe set to recover up to 351 nuclear genes from 435 herbarium specimens that are up to 204 years old and span the breadth of angiosperm diversity. We show that on average 207 genes were successfully retrieved from herbarium specimens, although the mean number of genes retrieved and target enrichment efficiency is significantly higher for silica gel-dried specimens. Forty-seven target nuclear genes were recovered from a herbarium specimen of the critically endangered St Helena boxwood, Mellissia begoniifolia, collected in 1815. Herbarium specimens yield significantly less high-molecular-weight DNA than silica gel-dried specimens, and genomic DNA quality declines with sample age, which is negatively correlated with target enrichment efficiency. Climate, taxon-specific traits, and collection strategies additionally impact target sequence recovery. We also detected taxonomic bias in targeted sequencing outcomes for the 10 most numerous angiosperm families that were investigated in depth. We recommend that (1) for species distributed in wet tropical climates, silica gel-dried specimens should be used preferentially; (2) for species distributed in seasonally dry tropical climates, herbarium and silica gel-dried specimens yield similar results, and either collection can be used; (3) taxon-specific traits should be explored and established for effective optimisation of taxon-specific studies using herbarium specimens; (4) all herbarium sheets should, in future, be annotated with details of the preservation method used; (5) long-term storage of herbarium specimens should be in stable, low-humidity, and low-temperature environments; and (6) targeted sequencing with universal probes, such as Angiosperms353, should be investigated closely as a new approach for DNA barcoding that will ensure better exploitation of herbarium specimens than traditional Sanger sequencing approaches.
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Affiliation(s)
- Grace E. Brewer
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - James J. Clarkson
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Olivier Maurin
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Vanessa Barber
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Sidonie Bellot
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Nicola Biggs
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Robyn S. Cowan
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Nina M. J. Davies
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, Luton, BedfordshireUnited Kingdom
| | - Sara L. Edwards
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Wolf L. Eiserhardt
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Bioscience, Aarhus University, Ny Munkegade Aarhus C, Denmark
| | | | - Sue Frisby
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Aurélie Grall
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Paul J. Kersey
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Lisa Pokorny
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), Pozuelo de Alarcón, Madrid, Spain
| | - Ilia J. Leitch
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Félix Forest
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - William J. Baker
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
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Ojeda DI, Koenen E, Cervantes S, de la Estrella M, Banguera-Hinestroza E, Janssens SB, Migliore J, Demenou BB, Bruneau A, Forest F, Hardy OJ. Phylogenomic analyses reveal an exceptionally high number of evolutionary shifts in a florally diverse clade of African legumes. Mol Phylogenet Evol 2019; 137:156-167. [DOI: 10.1016/j.ympev.2019.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 04/26/2019] [Accepted: 05/02/2019] [Indexed: 11/15/2022]
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Larridon I, Villaverde T, Zuntini AR, Pokorny L, Brewer GE, Epitawalage N, Fairlie I, Hahn M, Kim J, Maguilla E, Maurin O, Xanthos M, Hipp AL, Forest F, Baker WJ. Tackling Rapid Radiations With Targeted Sequencing. FRONTIERS IN PLANT SCIENCE 2019; 10:1655. [PMID: 31998342 PMCID: PMC6962237 DOI: 10.3389/fpls.2019.01655] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/22/2019] [Indexed: 05/19/2023]
Abstract
In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. Despite ample taxon sampling, relationships in many genera remain poorly understood, hampered by diversification rates that outpace mutation rates in the loci used. The C4 Cyperus clade of the genus Cyperus has been particularly difficult to resolve. Previous studies based on a limited set of markers resolved relationships among Cyperus species using the C3 photosynthetic pathway, but not among C4 Cyperus clade taxa. We test the ability of two targeted sequencing kits to resolve relationships in the C4 Cyperus clade, the universal Angiosperms-353 kit and a Cyperaceae-specific kit. Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. The power to resolve shallow-level relationships was tested using a summary species tree method and a concatenated maximum likelihood approach. High resolution and support are obtained using both approaches, but high levels of missing data disproportionately impact the latter. Targeted sequencing provides new insights into the evolution of morphology in the C4 Cyperus clade, demonstrating for example that the former segregate genus Alinula is polyphyletic despite its seeming morphological integrity. An unexpected result is that the Cyperus margaritaceus-Cyperus niveus complex comprises a clade separate from and sister to the core C4 Cyperus clade. Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations.
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Affiliation(s)
- Isabel Larridon
- Royal Botanic Gardens, Kew, Surrey, United Kingdom
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, Ghent, Belgium
- *Correspondence: Isabel Larridon, ; Tamara Villaverde,
| | - Tamara Villaverde
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
- The Morton Arboretum, Lisle, IL, United States
- The Field Museum, Chicago, IL, United States
- *Correspondence: Isabel Larridon, ; Tamara Villaverde,
| | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Surrey, United Kingdom
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
- Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), Madrid, Spain
| | | | | | - Isabel Fairlie
- Royal Botanic Gardens, Kew, Surrey, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Jan Kim
- Royal Botanic Gardens, Kew, Surrey, United Kingdom
| | - Enrique Maguilla
- The Morton Arboretum, Lisle, IL, United States
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | | | | | - Andrew L. Hipp
- The Morton Arboretum, Lisle, IL, United States
- The Field Museum, Chicago, IL, United States
| | - Félix Forest
- Royal Botanic Gardens, Kew, Surrey, United Kingdom
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