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Li J, Han G, Tian X, Liang D, Zhang P. UPrimer: A Clade-Specific Primer Design Program Based on Nested-PCR Strategy and Its Applications in Amplicon Capture Phylogenomics. Mol Biol Evol 2023; 40:msad230. [PMID: 37832226 PMCID: PMC10630340 DOI: 10.1093/molbev/msad230] [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: 04/17/2023] [Revised: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023] Open
Abstract
Amplicon capture is a promising target sequence capture approach for phylogenomic analyses, and the design of clade-specific nuclear protein-coding locus (NPCL) amplification primers is crucial for its successful application. In this study, we developed a primer design program called UPrimer that can quickly design clade-specific NPCL amplification primers based on genome data, without requiring manual intervention. Unlike other available primer design programs, UPrimer uses a nested-PCR strategy that greatly improves the amplification success rate of the designed primers. We examined all available metazoan genome data deposited in NCBI and developed NPCL primer sets for 21 metazoan groups with UPrimer, covering a wide range of taxa, including arthropods, mollusks, cnidarians, echinoderms, and vertebrates. On average, each clade-specific NPCL primer set comprises ∼1,000 NPCLs. PCR amplification tests were performed in 6 metazoan groups, and the developed primers showed a PCR success rate exceeding 95%. Furthermore, we demonstrated a phylogenetic case study in Lepidoptera, showing how NPCL primers can be used for phylogenomic analyses with amplicon capture. Our results indicated that using 100 NPCL probes recovered robust high-level phylogenetic relationships among butterflies, highlighting the utility of the newly designed NPCL primer sets for phylogenetic studies. We anticipate that the automated tool UPrimer and the developed NPCL primer sets for 21 metazoan groups will enable researchers to obtain phylogenomic data more efficiently and cost-effectively and accelerate the resolution of various parts of the Tree of Life.
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Affiliation(s)
- JiaXuan Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - GuangCheng Han
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiao Tian
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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Vandepol N, Liber J, Desirò A, Na H, Kennedy M, Barry K, Grigoriev IV, Miller AN, O'Donnell K, Stajich JE, Bonito G. Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. FUNGAL DIVERS 2020; 104:267-289. [PMID: 33364917 PMCID: PMC7751987 DOI: 10.1007/s13225-020-00455-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022]
Abstract
Early efforts to classify Mortierellaceae were based on macro- and micromorphology, but sequencing and phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conflicting taxonomic groupings and polyphyletic genera. Although some taxonomic confusion in the family has been clarified, rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae. In this study, we applied two parallel approaches to resolve the Mortierellaceae phylogeny: low coverage genome (LCG) sequencing and high-throughput, multiplexed targeted amplicon sequencing to generate sequence data for multi-gene phylogenetics. We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic groups led to the definition of 14 genera, 7 of which are newly proposed. Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a well-resolved phylogeny. The multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach, but was unable to resolve higher-level organization of groups. We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity, biology, and evolution.
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Affiliation(s)
- Natalie Vandepol
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing MI 48824, USA
| | - Julian Liber
- Department of Plant Biology, Michigan State University, East Lansing MI 48824, USA
| | - Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
| | - Hyunsoo Na
- Joint Genome Institute, Berkeley, CA 94720, USA
| | | | | | | | - Andrew N Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
| | - Kerry O'Donnell
- United States Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology & Institute for Integrative Genome Biology, University of California-Riverside, Riverside CA 92521, USA
| | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing MI 48824, USA
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing MI 48824, USA
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Almudi I, Martín-Blanco CA, García-Fernandez IM, López-Catalina A, Davie K, Aerts S, Casares F. Establishment of the mayfly Cloeon dipterum as a new model system to investigate insect evolution. EvoDevo 2019; 10:6. [PMID: 30984364 PMCID: PMC6446309 DOI: 10.1186/s13227-019-0120-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/21/2019] [Indexed: 02/07/2023] Open
Abstract
The great capability of insects to adapt to new environments promoted their extraordinary diversification, resulting in the group of Metazoa with the largest number of species distributed worldwide. To understand this enormous diversity, it is essential to investigate lineages that would allow the reconstruction of the early events in the evolution of insects. However, research on insect ecology, physiology, development and evolution has mostly focused on few well-established model species. The key phylogenetic position of mayflies within Paleoptera as the sister group of the rest of winged insects and life history traits of mayflies make them an essential order to understand insect evolution. Here, we describe the establishment of a continuous culture system of the mayfly Cloeon dipterum and a series of experimental protocols and omics resources that allow the study of its development and its great regenerative capability. Thus, the establishment of Cloeon as an experimental platform paves the way to understand genomic and morphogenetic events that occurred at the origin of winged insects.
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Affiliation(s)
- Isabel Almudi
- 1GEM-DMC2 Unit, The CABD (CSIC-UPO-JA), Ctra. de Utrera km 1, 41013 Seville, Spain
| | | | | | | | - Kristofer Davie
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Herestraat 49, 3000 Louvain, Belgium.,3Department of Human Genetics, KU Leuven, Oude Markt 13, 3000 Louvain, Belgium
| | - Stein Aerts
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Herestraat 49, 3000 Louvain, Belgium.,3Department of Human Genetics, KU Leuven, Oude Markt 13, 3000 Louvain, Belgium
| | - Fernando Casares
- 1GEM-DMC2 Unit, The CABD (CSIC-UPO-JA), Ctra. de Utrera km 1, 41013 Seville, Spain
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4
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Abdelkrim J, Aznar-Cormano L, Buge B, Fedosov A, Kantor Y, Zaharias P, Puillandre N. Delimiting species of marine gastropods (Turridae, Conoidea) using RAD sequencing in an integrative taxonomy framework. Mol Ecol 2018; 27:4591-4611. [DOI: 10.1111/mec.14882] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 08/27/2018] [Accepted: 09/04/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Jawad Abdelkrim
- Institut de Systématique Evolution Biodiversité (ISYEB); Muséum National d'Histoire Naturelle; CNRS; Sorbonne Université; EPHE; Paris France
- Service de Systématique Moléculaire SSM- UMS2700 - Muséum National d'Histoire Naturelle; Paris France
| | - Laetitia Aznar-Cormano
- Institut de Systématique Evolution Biodiversité (ISYEB); Muséum National d'Histoire Naturelle; CNRS; Sorbonne Université; EPHE; Paris France
| | - Barbara Buge
- Muséum National d'Histoire Naturelle; Paris France
| | - Alexander Fedosov
- A.N. Severtsov Institute of Ecology and Evolution; Russian Academy of Sciences; Moscow Russia
| | - Yuri Kantor
- A.N. Severtsov Institute of Ecology and Evolution; Russian Academy of Sciences; Moscow Russia
| | - Paul Zaharias
- Institut de Systématique Evolution Biodiversité (ISYEB); Muséum National d'Histoire Naturelle; CNRS; Sorbonne Université; EPHE; Paris France
| | - Nicolas Puillandre
- Institut de Systématique Evolution Biodiversité (ISYEB); Muséum National d'Histoire Naturelle; CNRS; Sorbonne Université; EPHE; Paris France
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Frenken T, Alacid E, Berger SA, Bourne EC, Gerphagnon M, Grossart HP, Gsell AS, Ibelings BW, Kagami M, Küpper FC, Letcher PM, Loyau A, Miki T, Nejstgaard JC, Rasconi S, Reñé A, Rohrlack T, Rojas-Jimenez K, Schmeller DS, Scholz B, Seto K, Sime-Ngando T, Sukenik A, Van de Waal DB, Van den Wyngaert S, Van Donk E, Wolinska J, Wurzbacher C, Agha R. Integrating chytrid fungal parasites into plankton ecology: research gaps and needs. Environ Microbiol 2017; 19:3802-3822. [DOI: 10.1111/1462-2920.13827] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/09/2017] [Accepted: 06/10/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Thijs Frenken
- Department of Aquatic Ecology; Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10; Wageningen PB 6708 The Netherlands
| | - Elisabet Alacid
- Departament de Biologia Marina i Oceanografia; Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49; Barcelona 08003 Spain
| | - Stella A. Berger
- Department of Experimental Limnology; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2; Stechlin D-16775 Germany
| | - Elizabeth C. Bourne
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straβe 6-8; Berlin D-14195 Germany
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301; Berlin 12587 Germany
| | - Mélanie Gerphagnon
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301; Berlin 12587 Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2; Stechlin D-16775 Germany
- Institute for Biochemistry and Biology, Potsdam University, Maulbeerallee 2; Potsdam D-14476 Germany
| | - Alena S. Gsell
- Department of Aquatic Ecology; Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10; Wageningen PB 6708 The Netherlands
| | - Bas W. Ibelings
- Department F.-A. Forel for Environmental and Aquatic Sciences & Institute for Environmental Sciences; University of Geneva, 66 Boulevard Carl Vogt; Geneva 4 CH 1211 Switzerland
| | - Maiko Kagami
- Department of Environmental Sciences, Faculty of Science; Toho University, 2-2-1, Miyama; Funabashi Chiba 274-8510 Japan
| | - Frithjof C. Küpper
- Oceanlab, University of Aberdeen, Main Street; Newburgh Scotland AB41 6AA UK
| | - Peter M. Letcher
- Department of Biological Sciences; The University of Alabama, 300 Hackberry Lane; Tuscaloosa AL 35487 USA
| | - Adeline Loyau
- Department of System Ecotoxicology; Helmholtz Center for Environmental Research - UFZ, Permoserstrasse 15; 04318 Leipzig Germany
- Department of Conservation Biology; Helmholtz Center for Environmental Research - UFZ, Permoserstrasse 15; Leipzig 04318 Germany
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS; Toulouse France
| | - Takeshi Miki
- Institute of Oceanography; National Taiwan University, No.1 Section 4, Roosevelt Road; Taipei 10617 Taiwan
- Research Center for Environmental Changes; Academia Sinica, No.128 Section 2, Academia Road, Nankang; Taipei 11529 Taiwan
| | - Jens C. Nejstgaard
- Department of Experimental Limnology; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2; Stechlin D-16775 Germany
| | - Serena Rasconi
- WasserCluster Lunz - Biological Station; Inter-University Centre for Aquatic Ecosystem Research, A-3293 Lunz am See; Austria
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia; Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49; Barcelona 08003 Spain
| | - Thomas Rohrlack
- Faculty of Environmental Sciences and Natural Resource Management; Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås; Norway
| | - Keilor Rojas-Jimenez
- Department of Experimental Limnology; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2; Stechlin D-16775 Germany
- Universidad Latina de Costa Rica, Campus San Pedro, Apdo; San Jose 10138-1000 Costa Rica
| | - Dirk S. Schmeller
- Department of Conservation Biology; Helmholtz Center for Environmental Research - UFZ, Permoserstrasse 15; Leipzig 04318 Germany
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS; Toulouse France
| | - Bettina Scholz
- BioPol ehf, Einbúastig 2, Skagaströnd 545; Iceland
- Faculty of Natural Resource Sciences; University of Akureyri, Borgir v. Nordurslod; Akureyri IS 600 Iceland
| | - Kensuke Seto
- Department of Environmental Sciences, Faculty of Science; Toho University, 2-2-1, Miyama; Funabashi Chiba 274-8510 Japan
- Sugadaira Montane Research Center; University of Tsukuba, 1278-294, Sugadaira-Kogen; Ueda, Nagano, 386-2204 Japan
| | - Télesphore Sime-Ngando
- Université Clermont Auvergne, UMR CNRS 6023 LMGE, Laboratoire Microorganismes: Génome et Environnement (LMGE); Campus Universitaire des Cézeaux, Impasse Amélie Murat 1, CS 60026, Aubière, 63178 France
| | - Assaf Sukenik
- Kinneret Limnological Laboratory; Israel Oceanographic & Limnological Research, P.O.Box 447; Migdal, 14950 Israel
| | - Dedmer B. Van de Waal
- Department of Aquatic Ecology; Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10; Wageningen PB 6708 The Netherlands
| | - Silke Van den Wyngaert
- Department of Experimental Limnology; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhuette 2; Stechlin D-16775 Germany
| | - Ellen Van Donk
- Department of Aquatic Ecology; Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10; Wageningen PB 6708 The Netherlands
- Department of Biology; University of Utrecht, Padualaan 8; Utrecht TB 3508 The Netherlands
| | - Justyna Wolinska
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301; Berlin 12587 Germany
- Institute of Biology, Freie Universität Berlin, Königin-Luise-Straβe 1-3; Berlin, 14195 Germany
| | - Christian Wurzbacher
- Department of Biological and Environmental Sciences; University of Gothenburg, Box 461; Göteborg, 405 30 Sweden
- Gothenburg Global Biodiversity Centre, Box 461; Göteborg, SE-405 30 Sweden
| | - Ramsy Agha
- Department of Ecosystem Research; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301; Berlin 12587 Germany
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