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Mabry ME, Abrahams RS, Al-Shehbaz IA, Baker WJ, Barak S, Barker MS, Barrett RL, Beric A, Bhattacharya S, Carey SB, Conant GC, Conran JG, Dassanayake M, Edger PP, Hall JC, Hao Y, Hendriks KP, Hibberd JM, King GJ, Kliebenstein DJ, Koch MA, Leitch IJ, Lens F, Lysak MA, McAlvay AC, McKibben MTW, Mercati F, Moore RC, Mummenhoff K, Murphy DJ, Nikolov LA, Pisias M, Roalson EH, Schranz ME, Thomas SK, Yu Q, Yocca A, Pires JC, Harkess AE. Complementing model species with model clades. THE PLANT CELL 2024; 36:1205-1226. [PMID: 37824826 PMCID: PMC11062466 DOI: 10.1093/plcell/koad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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Affiliation(s)
- Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - R Shawn Abrahams
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | | | | | - Simon Barak
- Ben-Gurion University of the Negev, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 8499000, Israel
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gavin C Conant
- Department of Biological Sciences, Bioinformatics Research Center, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - John G Conran
- ACEBB and SGC, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | | | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Frederic Lens
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, 2333 BE Leiden, the Netherlands
| | - Martin A Lysak
- CEITEC, and NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, The Bronx, NY 10458, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Francesco Mercati
- National Research Council (CNR), Institute of Biosciences and Bioresource (IBBR), Palermo 90129, Italy
| | | | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
| | | | - Michael Pisias
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO 65211, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Hilo, HI 96720, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Alex E Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Ball LD, Bedoya AM, Taylor CM, Lagomarsino LP. A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11554. [PMID: 38106541 PMCID: PMC10719880 DOI: 10.1002/aps3.11554] [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: 02/16/2023] [Revised: 05/08/2023] [Accepted: 05/13/2023] [Indexed: 12/19/2023]
Abstract
Premise Rubiaceae is among the most species-rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large-scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single-copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae-specific probe set that allows for comparable phylogenetic inference across clades is lacking. Methods Here, we use publicly accessible genomic resources to identify putatively single-copy nuclear loci for target enrichment in two Rubiaceae groups: tribe Hillieae (Cinchonoideae) and tribal complex Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent-aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from 10 different tribes and three subfamilies, and one outgroup in Apocynaceae. Results We recovered an average of 75% and 84% of targeted exons and loci, respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support (≥0.98 local posterior probability) at nearly all nodes and evidence of gene tree discordance. Discussion Our probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.
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Affiliation(s)
- Laymon D Ball
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803 USA
| | - Ana M Bedoya
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803 USA
| | - Charlotte M Taylor
- Missouri Botanical Garden 4344 Shaw Blvd. Saint Louis Missouri 63110 USA
| | - Laura P Lagomarsino
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803 USA
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3
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Hendriks KP, Kiefer C, Al-Shehbaz IA, Bailey CD, Hooft van Huysduynen A, Nikolov LA, Nauheimer L, Zuntini AR, German DA, Franzke A, Koch MA, Lysak MA, Toro-Núñez Ó, Özüdoğru B, Invernón VR, Walden N, Maurin O, Hay NM, Shushkov P, Mandáková T, Schranz ME, Thulin M, Windham MD, Rešetnik I, Španiel S, Ly E, Pires JC, Harkess A, Neuffer B, Vogt R, Bräuchler C, Rainer H, Janssens SB, Schmull M, Forrest A, Guggisberg A, Zmarzty S, Lepschi BJ, Scarlett N, Stauffer FW, Schönberger I, Heenan P, Baker WJ, Forest F, Mummenhoff K, Lens F. Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. Curr Biol 2023; 33:4052-4068.e6. [PMID: 37659415 DOI: 10.1016/j.cub.2023.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/22/2023] [Accepted: 08/08/2023] [Indexed: 09/04/2023]
Abstract
The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To evaluate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moderate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
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Affiliation(s)
- Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany; Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands.
| | - Christiane Kiefer
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | | | - C Donovan Bailey
- Department of Biology, New Mexico State University, PO Box 30001, MSC 3AF, Las Cruces, NM 88003, USA
| | - Alex Hooft van Huysduynen
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Lachezar A Nikolov
- Department of Molecular, Cell and Developmental Biology, University of California, 610 Charles E. Young Dr. S., Los Angeles, CA 90095, USA
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, PO Box 6811, Cairns, QLD 4870, Australia
| | | | - Dmitry A German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Lesosechnaya Ulitsa, 25, Barnaul, Altai Krai, Russia
| | - Andreas Franzke
- Heidelberg Botanic Garden, Heidelberg University, Im Neuenheimer Feld 361, 69120 Heidelberg, Germany
| | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Óscar Toro-Núñez
- Departamento de Botánica, Universidad de Concepción, Barrio Universitario, Concepción, Chile
| | - Barış Özüdoğru
- Department of Biology, Hacettepe University, Beytepe, Ankara 06800, Türkiye
| | - Vanessa R Invernón
- Sorbonne Université, Muséum National d'Histoire Naturelle, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP 39, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Nora Walden
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Nikolai M Hay
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Philip Shushkov
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN 47405, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mats Thulin
- Department of Organismal Biology, Uppsala University, Norbyvägen 18, 752 36 Uppsala, Sweden
| | | | - Ivana Rešetnik
- Department of Biology, University of Zagreb, Marulićev trg 20/II, 10000 Zagreb, Croatia
| | - Stanislav Španiel
- Institute of Botany, Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Dúbravská cesta 9, 845 23 Bratislava, Slovakia
| | - Elfy Ly
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - J Chris Pires
- Soil and Crop Sciences, Colorado State University, 307 University Ave., Fort Collins, CO 80523-1170, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Barbara Neuffer
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Robert Vogt
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Christian Bräuchler
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Heimo Rainer
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Steven B Janssens
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31 - box 2435, 3001 Leuven, Belgium; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Michaela Schmull
- Harvard University Herbaria, 22 Divinity Ave., Cambridge, MA 02138, USA
| | - Alan Forrest
- Centre for Middle Eastern Plants, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Alessia Guggisberg
- ETH Zürich, Institut für Integrative Biologie, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Sue Zmarzty
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Brendan J Lepschi
- Australian National Herbarium, Centre for Australian National Biodiversity Research, Clunies Ross St, Acton, ACT 2601, Australia
| | - Neville Scarlett
- La Trobe University, Plenty Road and Kingsbury Dr., Bundoora, VIC 3086, Australia
| | - Fred W Stauffer
- Conservatory and Botanic Gardens of Geneva, CP 60, Chambésy, 1292 Geneva, Switzerland
| | - Ines Schönberger
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | - Peter Heenan
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Frederic Lens
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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McLay TGB, Fowler RM, Fahey PS, Murphy DJ, Udovicic F, Cantrill DJ, Bayly MJ. Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia. Mol Phylogenet Evol 2023; 187:107869. [PMID: 37423562 DOI: 10.1016/j.ympev.2023.107869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/11/2023]
Abstract
Eucalypts are a large and ecologically important group of plants on the Australian continent, and understanding their evolution is important in understanding evolution of the unique Australian flora. Previous phylogenies using plastome DNA, nuclear-ribosomal DNA, or random genome-wide SNPs, have been confounded by limited genetic sampling or by idiosyncratic biological features of the eucalypts, including widespread plastome introgression. Here we present phylogenetic analyses of Eucalyptus subgenus Eudesmia (22 species from western, northern, central and eastern Australia), in the first study to apply a target-capture sequencing approach using custom, eucalypt-specific baits (of 568 genes) to a lineage of Eucalyptus. Multiple accessions of all species were included, and target-capture data were supplemented by separate analyses of plastome genes (average of 63 genes per sample). Analyses revealed a complex evolutionary history likely shaped by incomplete lineage sorting and hybridization. Gene tree discordance generally increased with phylogenetic depth. Species, or groups of species, toward the tips of the tree are mostly supported, and three major clades are identified, but the branching order of these clades cannot be confirmed with confidence. Multiple approaches to filtering the nuclear dataset, by removing genes or samples, could not reduce gene tree conflict or resolve these relationships. Despite inherent complexities in eucalypt evolution, the custom bait kit devised for this research will be a powerful tool for investigating the evolutionary history of eucalypts more broadly.
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Affiliation(s)
- Todd G B McLay
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia.
| | - Rachael M Fowler
- School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Patrick S Fahey
- Research Centre for Ecosystem Resilience, The Royal Botanic Garden Sydney, Sydney 2000, NSW, Australia; Qld Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia 4072, Qld, Australia
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Frank Udovicic
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia
| | - David J Cantrill
- Royal Botanic Gardens Victoria, Melbourne 3004, Vic, Australia; School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
| | - Michael J Bayly
- School of BioSciences, The University of Melbourne, Parkville 3010, Vic, Australia
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Hay NM, Windham MD, Mandáková T, Lysak MA, Hendriks KP, Mummenhoff K, Lens F, Pryer KM, Bailey CD. A Hyb-Seq phylogeny of Boechera and related genera using a combination of Angiosperms353 and Brassicaceae-specific bait sets. AMERICAN JOURNAL OF BOTANY 2023; 110:e16226. [PMID: 37561651 DOI: 10.1002/ajb2.16226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
PREMISE Although Boechera (Boechereae, Brassicaceae) has become a plant model system for both ecological genomics and evolutionary biology, all previous phylogenetic studies have had limited success in resolving species relationships within the genus. The recent effective application of sequence data from target enrichment approaches to resolve the evolutionary relationships of several other challenging plant groups prompted us to investigate their usefulness in Boechera and Boechereae. METHODS To resolve the phylogeny of Boechera and closely related genera, we utilized the Hybpiper pipeline to analyze two combined bait sets: Angiosperms353, with broad applicability across flowering plants; and a Brassicaceae-specific bait set designed for use in the mustard family. Relationships for 101 samples representing 81 currently recognized species were inferred from a total of 1114 low-copy nuclear genes using both supermatrix and species coalescence methods. RESULTS Our analyses resulted in a well-resolved and highly supported phylogeny of the tribe Boechereae. Boechereae is divided into two major clades, one comprising all western North American species of Boechera, the other encompassing the eight other genera of the tribe. Our understanding of relationships within Boechera is enhanced by the recognition of three core clades that are further subdivided into robust regional species complexes. CONCLUSIONS This study presents the first broadly sampled, well-resolved phylogeny for most known sexual diploid Boechera. This effort provides the foundation for a new phylogenetically informed taxonomy of Boechera that is crucial for its continued use as a model system.
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Affiliation(s)
- Nikolai M Hay
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Michael D Windham
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kasper P Hendriks
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, Osnabrück, D-49076, Germany
| | - Frederic Lens
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, 27708, North Carolina, USA
| | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
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6
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Pezzini FF, Ferrari G, Forrest LL, Hart ML, Nishii K, Kidner CA. Target capture and genome skimming for plant diversity studies. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11537. [PMID: 37601316 PMCID: PMC10439825 DOI: 10.1002/aps3.11537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast-freeze newly collected living samples to conserve high-quality DNA can be complicated when plants are only found in remote areas. Therefore, short-read reduced-genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non-model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best-informed choice regarding reduced genome representation for evolutionary studies of non-model plants in cases where whole-genome sequencing remains impractical.
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Affiliation(s)
| | - Giada Ferrari
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | | | | | - Kanae Nishii
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
| | - Catherine A Kidner
- Royal Botanic Garden Edinburgh Edinburgh United Kingdom
- School of Biological Sciences University of Edinburgh Edinburgh United Kingdom
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7
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Farhat P, Mandáková T, Divíšek J, Kudoh H, German DA, Lysak MA. The evolution of the hypotetraploid Catolobus pendulus genome - the poorly known sister species of Capsella. FRONTIERS IN PLANT SCIENCE 2023; 14:1165140. [PMID: 37223809 PMCID: PMC10200890 DOI: 10.3389/fpls.2023.1165140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/04/2023] [Indexed: 05/25/2023]
Abstract
The establishment of Arabidopsis as the most important plant model has also brought other crucifer species into the spotlight of comparative research. While the genus Capsella has become a prominent crucifer model system, its closest relative has been overlooked. The unispecific genus Catolobus is native to temperate Eurasian woodlands, from eastern Europe to the Russian Far East. Here, we analyzed chromosome number, genome structure, intraspecific genetic variation, and habitat suitability of Catolobus pendulus throughout its range. Unexpectedly, all analyzed populations were hypotetraploid (2n = 30, ~330 Mb). Comparative cytogenomic analysis revealed that the Catolobus genome arose by a whole-genome duplication in a diploid genome resembling Ancestral Crucifer Karyotype (ACK, n = 8). In contrast to the much younger Capsella allotetraploid genomes, the presumably autotetraploid Catolobus genome (2n = 32) arose early after the Catolobus/Capsella divergence. Since its origin, the tetraploid Catolobus genome has undergone chromosomal rediploidization, including a reduction in chromosome number from 2n = 32 to 2n = 30. Diploidization occurred through end-to-end chromosome fusion and other chromosomal rearrangements affecting a total of six of 16 ancestral chromosomes. The hypotetraploid Catolobus cytotype expanded toward its present range, accompanied by some longitudinal genetic differentiation. The sister relationship between Catolobus and Capsella allows comparative studies of tetraploid genomes of contrasting ages and different degrees of genome diploidization.
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Affiliation(s)
- Perla Farhat
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Divíšek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Dmitry A. German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Russia
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czechia
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8
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Ortiz-Sepulveda CM, Genete M, Blassiau C, Godé C, Albrecht C, Vekemans X, Van Bocxlaer B. Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms. Mol Ecol Resour 2023; 23:659-679. [PMID: 36349833 DOI: 10.1111/1755-0998.13735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022]
Abstract
Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here, we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced substantial data sets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in molluscs, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.
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Affiliation(s)
| | - Mathieu Genete
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | | | - Cécile Godé
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Christian Albrecht
- Department of Animal Ecology and Systematics, Justus Liebig University, D-35392 Giessen, Germany.,Department of Biology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Xavier Vekemans
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
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9
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Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ. Phylogenomics and the flowering plant tree of life. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:299-323. [PMID: 36416284 DOI: 10.1111/jipb.13415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
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Affiliation(s)
- Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
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Rushworth CA, Wagner MR, Mitchell-Olds T, Anderson JT. The Boechera model system for evolutionary ecology. AMERICAN JOURNAL OF BOTANY 2022; 109:1939-1961. [PMID: 36371714 DOI: 10.1002/ajb2.16090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.
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Affiliation(s)
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
| | | | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae. Genes (Basel) 2022; 13:genes13040707. [PMID: 35456513 PMCID: PMC9032687 DOI: 10.3390/genes13040707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2022] [Accepted: 04/15/2022] [Indexed: 02/05/2023] Open
Abstract
The molecular phylogenies of Cactaceae have enabled us to better understand their systematics, biogeography, and diversification ages. However, most of the phylogenetic relationships within Cactaceae major groups remain unclear, largely due to the lack of an appropriate set of molecular markers to resolve its contentious relationships. Here, we explored the genome and transcriptome assemblies available for Cactaceae and identified putative orthologous regions shared among lineages of the subfamily Cactoideae. Then we developed a probe set, named Cactaceae591, targeting both coding and noncoding nuclear regions for representatives from the subfamilies Pereskioideae, Opuntioideae, and Cactoideae. We also sampled inter- and intraspecific variation to evaluate the potential of this panel to be used in phylogeographic studies. We retrieved on average of 547 orthologous regions per sample. Targeting noncoding nuclear regions showed to be crucial to resolving inter- and intraspecific relationships. Cactaceae591 covers 13 orthologous genes shared with the Angiosperms353 kit and two plastid regions largely used in Cactaceae studies, enabling the phylogenies generated by our panel to be integrated with angiosperm and Cactaceae phylogenies, using these sequences. We highlighted the importance of using coalescent-based species tree approaches on the Cactaceae591 dataset to infer accurate phylogenetic trees in the presence of extensive incomplete lineage sorting in this family.
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12
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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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13
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Demeulenaere E, Schils T, Burleigh JG, Ringelberg JJ, Koenen EJM, Ickert-Bond SM. Phylogenomic assessment prompts recognition of the Serianthes clade and confirms the monophyly of Serianthes and its relationship with Falcataria and Wallaceodendron in the wider ingoid clade (Leguminosae, Caesalpinioideae). PHYTOKEYS 2022; 205:335-361. [PMID: 36762011 PMCID: PMC9849021 DOI: 10.3897/phytokeys.205.79144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 05/02/2022] [Indexed: 05/03/2023]
Abstract
The Indo-Pacific legume genus Serianthes was recently placed in the Archidendron clade (sensu Koenen et al. 2020), a subclade of the mimosoid clade in subfamily Caesalpinioideae, which also includes Acacia, Archidendron, Archidendropsis, Falcataria, Pararchidendron, Paraserianthes and Wallaceodendron. Serianthes comprises ca. 18 species, five subspecies and two varieties that are characterised by bipinnately compound leaves with alternate sessile leaflets, branched axillary corymbiform panicles and woody indehiscent pods. Generic relationships, as well as species relationships within genera in the Archidendron clade, remain uncertain. While the sister relationship between Serianthes and the genus Falcataria is strongly supported by molecular data, the distinction between Serianthes and the monotypic genus Wallaceodendron has been questioned, based on their similar flower and fruit morphologies. We combined three gene-enriched hybrid capture DNA sequence datasets (generated from the 964 mimobaits v1 probe set, the expanded 997 mimobaits v2 probe set and the GoFlag angiosperm 408 probe set) and used their overlapping markers (77 loci of the target exonic and flanking regions) to test the monophyly of Serianthes and to investigate generic relationships within the Archidendron clade using 55 ingoid plus two outgroup taxa. We show that Serianthes is monophyletic, confirm the Serianthes + Falcataria sister relationship to Wallaceodendron and recognise this combined clade as the Serianthes clade within the Archidendron clade. We also evaluated the use of overlapping loci across datasets in combination with concordance analyses to test generic relationships and further investigate previously unresolved relationships across the wider ingoid clade. Concordance analysis revealed limited gene tree conflicts near the tips of the Archidendron clade, but increased discordance at the base of the clade, which could be attributed to rapid lineage divergence (radiation) and/or incomplete lineage sorting.
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Affiliation(s)
- Else Demeulenaere
- Center for Island Sustainability, University of Guam, UOG Station, Mangilao, 96923, Guam
| | - Tom Schils
- Center for Island Sustainability, University of Guam, UOG Station, Mangilao, 96923, Guam
| | - J. Gordon Burleigh
- Marine Laboratory, University of Guam, UOG Station, Mangilao, 96923, Guam
| | - Jens J. Ringelberg
- Department of Biology, University of Florida, PO Box 118525, Gainesville, FL 32611-8525, USA
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Stefanie M. Ickert-Bond
- Evolutionary Biology & Ecology, Free University of Brussels, Av. F.D. Roosevelt, 50, CP 160/12 - B-1050 Brussels, Belgium
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14
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Ufimov R, Zeisek V, Píšová S, Baker WJ, Fér T, van Loo M, Dobeš C, Schmickl R. Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11442. [PMID: 34336405 PMCID: PMC8312748 DOI: 10.1002/aps3.11442] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/09/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome. METHODS To evaluate the relative performance of these probe sets, we compared the enrichment efficiency, locus recovery, alignment length, proportion of parsimony-informative sites, proportion of potential paralogs, the topology and support of the resulting species trees, and the gene tree discordance. RESULTS Locus recovery was highest for our custom Malinae probe set, and replacing the original Angiosperms353 sequences with a Malus representative improved the locus recovery relative to Angiosperms353. The proportion of parsimony-informative sites was similar between all probe sets, while the gene tree discordance was lower in the case of the custom probes. DISCUSSION A custom probe set benefits from data completeness and can be tailored toward the specificities of the project of choice; however, Angiosperms353 was equally as phylogenetically informative as the custom probes. We therefore recommend using both a custom probe set and Angiosperms353 to facilitate large-scale systematic studies, where financially possible.
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Affiliation(s)
- Roman Ufimov
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsSeckendorff‐Gudent‐Weg 8Vienna1130Austria
- Komarov Botanical InstituteRussian Academy of Sciencesul. Prof. Popova 2St. Petersburg197376Russian Federation
| | - Vojtěch Zeisek
- Institute of BotanyThe Czech Academy of SciencesZámek 1Průhonice252 43Czech Republic
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2Prague128 01Czech Republic
| | - Soňa Píšová
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsSeckendorff‐Gudent‐Weg 8Vienna1130Austria
- Institute of BotanyThe Czech Academy of SciencesZámek 1Průhonice252 43Czech Republic
| | | | - Tomáš Fér
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2Prague128 01Czech Republic
| | - Marcela van Loo
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsSeckendorff‐Gudent‐Weg 8Vienna1130Austria
| | - Christoph Dobeš
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsSeckendorff‐Gudent‐Weg 8Vienna1130Austria
| | - Roswitha Schmickl
- Institute of BotanyThe Czech Academy of SciencesZámek 1Průhonice252 43Czech Republic
- Department of BotanyFaculty of ScienceCharles UniversityBenátská 2Prague128 01Czech Republic
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15
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Baker WJ, Dodsworth S, Forest F, Graham SW, Johnson MG, McDonnell A, Pokorny L, Tate JA, Wicke S, Wickett NJ. Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants. AMERICAN JOURNAL OF BOTANY 2021; 108:1059-1065. [PMID: 34293179 DOI: 10.1002/ajb2.1703] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Affiliation(s)
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Angela McDonnell
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Jennifer A Tate
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Susann Wicke
- Plant Evolutionary Biology, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Plant Systematics and Biodiversity, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
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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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17
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McDonnell AJ, Baker WJ, Dodsworth S, Forest F, Graham SW, Johnson MG, Pokorny L, Tate J, Wicke S, Wickett NJ. Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311443. [PMID: 34336400 PMCID: PMC8312743 DOI: 10.1002/aps3.11443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 05/30/2023]
Affiliation(s)
- Angela J. McDonnell
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60022USA
| | | | - Steven Dodsworth
- School of Life SciencesUniversity of BedfordshireUniversity SquareLutonLU1 3JUUnited Kingdom
| | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Sean W. Graham
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409USA
| | - Lisa Pokorny
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP) UPM‐INIA‐CSIC28223Pozuelo de Alarcón (Madrid)Spain
| | - Jennifer Tate
- School of Fundamental SciencesMassey UniversityPalmerston North4442New Zealand
| | - Susann Wicke
- Plant Evolutionary BiologyInstitute for Evolution and BiodiversityUniversity of MünsterMünsterGermany
- Plant Systematics and BiodiversityInstitute for BiologyHumboldt‐Universität zu BerlinBerlinGermany
| | - Norman J. Wickett
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60022USA
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18
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Siniscalchi CM, Hidalgo O, Palazzesi L, Pellicer J, Pokorny L, Maurin O, Leitch IJ, Forest F, Baker WJ, Mandel JR. Lineage-specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311422. [PMID: 34336403 PMCID: PMC8312747 DOI: 10.1002/aps3.11422] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/15/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family-specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family-specific kit and those obtained with the universal kit can be merged for downstream analyses. METHODS We used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets. RESULTS Our results show that the Compositae1061 kit provides an average of 721 loci, with 9-46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways. DISCUSSION Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community.
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Affiliation(s)
- Carolina M. Siniscalchi
- Department of Biological SciencesMississippi State UniversityMississippi StateMississippi39762USA
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
| | - Oriane Hidalgo
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia s.n.BarcelonaCatalonia08038Spain
| | - Luis Palazzesi
- División PaleobotánicaMuseo Argentino de Ciencias NaturalesCONICETBuenos AiresC1405DJRArgentina
| | - Jaume Pellicer
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)Passeig del Migdia s.n.BarcelonaCatalonia08038Spain
| | - Lisa Pokorny
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Present address:
Centre for Plant Biotechnology and Genomics (CBGP) UPM‐INIAPozuelo de Alarcón (Madrid)28223Spain
| | - Olivier Maurin
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Ilia J. Leitch
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Felix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | | | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of MemphisMemphisTennessee38152USA
- Center for BiodiversityUniversity of MemphisMemphisTennessee38152USA
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19
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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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