1
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Pope NS, Singh A, Childers AK, Kapheim KM, Evans JD, López-Uribe MM. The expansion of agriculture has shaped the recent evolutionary history of a specialized squash pollinator. Proc Natl Acad Sci U S A 2023; 120:e2208116120. [PMID: 37011184 PMCID: PMC10104555 DOI: 10.1073/pnas.2208116120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
The expansion of agriculture is responsible for the mass conversion of biologically diverse natural environments into managed agroecosystems dominated by a handful of genetically homogeneous crop species. Agricultural ecosystems typically have very different abiotic and ecological conditions from those they replaced and create potential niches for those species that are able to exploit the abundant resources offered by crop plants. While there are well-studied examples of crop pests that have adapted into novel agricultural niches, the impact of agricultural intensification on the evolution of crop mutualists such as pollinators is poorly understood. We combined genealogical inference from genomic data with archaeological records to demonstrate that the Holocene demographic history of a wild specialist pollinator of Cucurbita (pumpkins, squashes, and gourds) has been profoundly impacted by the history of agricultural expansion in North America. Populations of the squash bee Eucera pruinosa experienced rapid growth in areas where agriculture intensified within the past 1,000 y, suggesting that the cultivation of Cucurbita in North America has increased the amount of floral resources available to these bees. In addition, we found that roughly 20% of this bee species' genome shows signatures of recent selective sweeps. These signatures are overwhelmingly concentrated in populations from eastern North America where squash bees were historically able to colonize novel environments due to human cultivation of Cucurbita pepo and now exclusively inhabit agricultural niches. These results suggest that the widespread cultivation of crops can prompt adaptation in wild pollinators through the distinct ecological conditions imposed by agricultural environments.
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Affiliation(s)
- Nathaniel S Pope
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403
| | - Avehi Singh
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
| | - Anna K Childers
- Bee Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705
| | - Karen M Kapheim
- Department of Biology, Utah State University, Logan, UT 84322
| | - Jay D Evans
- Bee Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705
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2
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Chang J, Stahlke AR, Chudalayandi S, Rosen BD, Childers AK, Severin AJ. polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies. Genome Biol Evol 2023; 15:7040681. [PMID: 36792366 PMCID: PMC9985148 DOI: 10.1093/gbe/evad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) continuous long reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies made from CLR data. PolishCLR can be initiated from several input options that extend best practices to suboptimal cases. It also provides re-entry points throughout several key processes, including identifying duplicate haplotypes in purge_dups, allowing a break for scaffolding if data are available, and throughout multiple rounds of polishing and evaluation with Arrow and FreeBayes. PolishCLR is containerized and publicly available for the greater assembly community as a tool to complete assemblies from existing, error-prone long-read data.
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Affiliation(s)
- Jennifer Chang
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee.,Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames
| | - Amanda R Stahlke
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, Beltsville Maryland
| | | | - Benjamin D Rosen
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Beltsville, Maryland
| | - Anna K Childers
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, Beltsville Maryland
| | - Andrew J Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames
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3
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Stahlke AR, Chang J, Tembrock LR, Sim SB, Chudalayandi S, Geib SM, Scheffler BE, Perera OP, Gilligan TM, Childers AK, Hackett KJ, Coates BS. A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein. Genome Biol Evol 2023; 15:evac131. [PMID: 35959935 PMCID: PMC9990077 DOI: 10.1093/gbe/evac131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/14/2022] Open
Abstract
Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.
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Affiliation(s)
- Amanda R Stahlke
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland 20705
| | - Jennifer Chang
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, Mississippi 38776
- USDOE, Oak Ridge Institute for Science and Education, P.O. Box 117, Oak Ridge, Tennessee 37831
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50010
| | - Luke R Tembrock
- USDA, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Identification Technology Program, 2301 Research Boulevard, Fort Collins, Colorado 80526
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Sheina B Sim
- USDA, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Crop and Commodity Protection Research Unit, 64 Nowelo Street, Hilo, Hawaii 96720
| | - Sivanandan Chudalayandi
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50010
| | - Scott M Geib
- USDA, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Crop and Commodity Protection Research Unit, 64 Nowelo Street, Hilo, Hawaii 96720
| | - Brian E Scheffler
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, Mississippi 38776
| | - Omaththage P Perera
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Southern Insect Management Research Unit, 141 Experiment Station Road, Stoneville, Mississippi 38776
| | - Todd M Gilligan
- USDA, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Identification Technology Program, 2301 Research Boulevard, Fort Collins, Colorado 80526
| | - Anna K Childers
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland 20705
| | - Kevin J Hackett
- USDA, Agricultural Research Service, Office of National Programs, Crop Production and Protection, 5601 Sunnyside Avenue, Beltsville, Maryland 20705
| | - Brad S Coates
- USDA, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, Iowa 50011
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4
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Stahlke AR, Chang J, Chudalayandi S, Heu CC, Geib SM, Scheffler BE, Childers AK, Fabrick JA. Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton. G3 (Bethesda) 2023; 13:7040364. [PMID: 36790801 PMCID: PMC10085786 DOI: 10.1093/g3journal/jkad040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/30/2023] [Accepted: 02/04/2023] [Indexed: 02/16/2023]
Abstract
The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae), is a major global pest of cotton. Current management practices include chemical insecticides, cultural strategies, sterile insect releases, and transgenic cotton producing crystalline (Cry) protein toxins of the bacterium Bacillus thuringiensis (Bt). These strategies have contributed to eradication of P. gossypiella from the cotton growing areas of the United States and northern Mexico. However, this pest has evolved resistance to Bt cotton in Asia, where it remains a critical pest, and the benefits of using transgenic Bt crops have been lost. A complete annotated reference genome is needed to improve global Bt resistance management of the pink bollworm. We generated the first chromosome-level genome assembly for pink bollworm from a Bt-susceptible laboratory strain (APHIS-S) using PacBio continuous long reads for contig generation, Illumina Hi-C for scaffolding, and Illumina whole-genome re-sequencing for error-correction. The psuedohaploid assembly consists of 29 autosomes and the Z sex chromosome. The assembly exceeds the minimum Earth BioGenome Project quality standards, has a low error-rate, is highly contiguous at both the contig and scaffold level (L/N50 of 18/8.26 MB and 14/16.44 MB, respectively), and complete, with 98.6% of lepidopteran single-copy orthologs represented without duplication. The genome was annotated with 50% repeat content and 14,107 protein-coding genes, further assigned to 41,666 functional annotations. This assembly represents the first publicly available complete annotated genome of pink bollworm and will serve as the foundation for advancing molecular genetics of this important pest species.
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Affiliation(s)
- Amanda R Stahlke
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Jennifer Chang
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, MS 38776, USA.,Oak Ridge Institute for Science and Education, P.O. Box 117, Oak Ridge, TN 37831, USA.,Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50010, USA
| | - Sivanandan Chudalayandi
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50010, USA
| | - Chan C Heu
- Oak Ridge Institute for Science and Education, P.O. Box 117, Oak Ridge, TN 37831, USA.,USDA, Agricultural Research Service, U.S. Arid Land Agricultural Research Center, 21881 N. Cardon Lane, Maricopa, AZ 85138, USA
| | - Scott M Geib
- USDA, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, 64 Nowelo Street, Hilo, HI 96720, USA
| | - Brian E Scheffler
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, MS 38776, USA
| | - Anna K Childers
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Jeffrey A Fabrick
- USDA, Agricultural Research Service, U.S. Arid Land Agricultural Research Center, 21881 N. Cardon Lane, Maricopa, AZ 85138, USA
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5
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Cohen ZP, Perkin LC, Sim SB, Stahlke AR, Geib SM, Childers AK, Smith TPL, Suh C. Insight into weevil biology from a reference quality genome of the boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae). G3 (Bethesda) 2023; 13:jkac309. [PMID: 36454104 PMCID: PMC9911062 DOI: 10.1093/g3journal/jkac309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 12/03/2022]
Abstract
The boll weevil, Anthonomus grandis grandis Boheman, is one of the most historically impactful insects due to its near destruction of the US cotton industry in the early 20th century. Contemporary efforts to manage this insect primarily use pheromone baited traps for detection and organophosphate insecticides for control, but this strategy is not sustainable due to financial and environmental costs. We present a high-quality boll weevil genome assembly, consisting of 306 scaffolds with approximately 24,000 annotated genes, as a first step in the identification of gene targets for novel pest control. Gene content and transposable element distribution are similar to those found in other Curculionidae genomes; however, this is the most contiguous and only assembly reported to date for a member in the species-rich genus Anthonomus. Transcriptome profiles across larval, pupal, and adult life stages led to identification of several genes and gene families that could present targets for novel control strategies.
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Affiliation(s)
- Zachary P Cohen
- Insect Control and Cotton Disease Research Unit, Southern Plains Agricultural Research Center, USDA, Agricultural Research Service, 2771 F and B Road, College Station, TX 77845, USA
| | - Lindsey C Perkin
- Insect Control and Cotton Disease Research Unit, Southern Plains Agricultural Research Center, USDA, Agricultural Research Service, 2771 F and B Road, College Station, TX 77845, USA
| | - Sheina B Sim
- Tropical Crop and Commodity Protection Research Unit, U.S. Pacific Basin Agricultural Research Center, USDA, Agricultural Research Service, 64 Nowelo Street, Hilo, HI 96720, USA
| | - Amanda R Stahlke
- Bee Research Laboratory, Beltsville Agricultural Research Center, USDA, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Scott M Geib
- Tropical Crop and Commodity Protection Research Unit, U.S. Pacific Basin Agricultural Research Center, USDA, Agricultural Research Service, 64 Nowelo Street, Hilo, HI 96720, USA
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, USDA, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Timothy P L Smith
- Genetics and Breeding Research Unit, U.S. Meat Animal Research Center, USDA, Agricultural Research Service, State Spur 18D, Clay Center, NE 68933, USA
| | - Charles Suh
- Insect Control and Cotton Disease Research Unit, Southern Plains Agricultural Research Center, USDA, Agricultural Research Service, 2771 F and B Road, College Station, TX 77845, USA
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6
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Lawniczak MKN, Durbin R, Flicek P, Lindblad-Toh K, Wei X, Archibald JM, Baker WJ, Belov K, Blaxter ML, Marques Bonet T, Childers AK, Coddington JA, Crandall KA, Crawford AJ, Davey RP, Di Palma F, Fang Q, Haerty W, Hall N, Hoff KJ, Howe K, Jarvis ED, Johnson WE, Johnson RN, Kersey PJ, Liu X, Lopez JV, Myers EW, Pettersson OV, Phillippy AM, Poelchau MF, Pruitt KD, Rhie A, Castilla-Rubio JC, Sahu SK, Salmon NA, Soltis PS, Swarbreck D, Thibaud-Nissen F, Wang S, Wegrzyn JL, Zhang G, Zhang H, Lewin HA, Richards S. Standards recommendations for the Earth BioGenome Project. Proc Natl Acad Sci U S A 2022; 119:e2115639118. [PMID: 35042802 PMCID: PMC8795494 DOI: 10.1073/pnas.2115639118] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
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Affiliation(s)
- Mara K N Lawniczak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Richard Durbin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB3 0DH, United Kingdom
| | - Paul Flicek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University 751 23 Uppsala, Sweden
| | | | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - William J Baker
- Department of Accelerated Taxonomy, Royal Botanic Gardens, Kew, Surrey TW9 3AE, United Kingdom
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark L Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Tomas Marques Bonet
- Institute of Evolutionary Biology, Consejo Superior de Investigaciones Científicas-Universitat Pompeau Fabra, Parc de Rechercha Biomédica Barcelona 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies 08010 Barcelona, Spain
- Centre Nacional d'Anàlisi Geonòmica - Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona 08193 Barcelona, Spain
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
| | - Jonathan A Coddington
- Smithsonian Institution, National Museum of Natural History, Washington, DC 20560-0105
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes 111711 Bogotá, Colombia
| | - Robert P Davey
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | | | - Qi Fang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Neil Hall
- Genome British Columbia, Vancouver, BC V5Z 0C4, Canada
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Katharina J Hoff
- Institute of Mathematics and Computer Science, Center for Functional Genomics of Microbes, University of Greifswald 17489 Greifswald, Germany
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Erich D Jarvis
- Vertebrate Genomes Lab, The Rockefeller University, New York, NY 10065
- HHMI, Chevy Chase, MD 20815
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD 20746-2863
| | - Rebecca N Johnson
- Smithsonian Institution, National Museum of Natural History, Washington, DC 20560-0105
| | - Paul J Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom
| | - Xin Liu
- China National GeneBank, Shenzhen 518120, China
| | - Jose Victor Lopez
- Halmos College of Arts and Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Dania Beach, FL 33004
| | - Eugene W Myers
- Department of Systems Biology, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | | | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20894
| | - Monica F Poelchau
- National Agricultural Library, USDA Agricultural Research Service, Beltsville, MD 20705
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20894
| | | | - Sunil Kumar Sahu
- China National GeneBank, Shenzhen 518120, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Nicholas A Salmon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894
| | - Sibo Wang
- China National GeneBank, Shenzhen 518120, China
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269
- Institute for Systems Genomics, Computational Biology Core, University of Connecticut, Storrs, CT 06269
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen 1165 Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen 518083 Shenzhen, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences 650223 Kunming, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen 266555 Qingdao, China
| | - Harris A Lewin
- University of California Davis Genome Center, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
| | - Stephen Richards
- University of California Davis Genome Center, University of California, Davis, CA 95616;
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7
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Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK, Kress WJ, Kuraku S, Lawniczak MKN, Lindblad-Toh K, Lopez JV, Moran NA, Robinson GE, Ryder OA, Shapiro B, Soltis PS, Warnow T, Zhang G, Lewin HA. Why sequence all eukaryotes? Proc Natl Acad Sci U S A 2022; 119:e2115636118. [PMID: 35042801 PMCID: PMC8795522 DOI: 10.1073/pnas.2115636118] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
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Affiliation(s)
- Mark Blaxter
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Anna K Childers
- Bee Research Laboratory, Agricultural Research Service, US Department of Agriculture (USDA), Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC 20052
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC 20013
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Richard Durbin
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Jennifer A M Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 751 23, Australia
- University of Canberra, Bruce, ACT 2617, Australia
| | - Kevin J Hackett
- Crop Production and Protection, Office of National Programs, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich, Norfolk NR4 7UZ, United Kingdom
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - W John Kress
- Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | | | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Nancy A Moran
- Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Oliver A Ryder
- Conservation Genetics, Division of Biology, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Department of Evolution, Behavior and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61301
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- China National Genebank, Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
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8
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Lewin HA, Richards S, Lieberman Aiden E, Allende ML, Archibald JM, Bálint M, Barker KB, Baumgartner B, Belov K, Bertorelle G, Blaxter ML, Cai J, Caperello ND, Carlson K, Castilla-Rubio JC, Chaw SM, Chen L, Childers AK, Coddington JA, Conde DA, Corominas M, Crandall KA, Crawford AJ, DiPalma F, Durbin R, Ebenezer TE, Edwards SV, Fedrigo O, Flicek P, Formenti G, Gibbs RA, Gilbert MTP, Goldstein MM, Graves JM, Greely HT, Grigoriev IV, Hackett KJ, Hall N, Haussler D, Helgen KM, Hogg CJ, Isobe S, Jakobsen KS, Janke A, Jarvis ED, Johnson WE, Jones SJM, Karlsson EK, Kersey PJ, Kim JH, Kress WJ, Kuraku S, Lawniczak MKN, Leebens-Mack JH, Li X, Lindblad-Toh K, Liu X, Lopez JV, Marques-Bonet T, Mazard S, Mazet JAK, Mazzoni CJ, Myers EW, O'Neill RJ, Paez S, Park H, Robinson GE, Roquet C, Ryder OA, Sabir JSM, Shaffer HB, Shank TM, Sherkow JS, Soltis PS, Tang B, Tedersoo L, Uliano-Silva M, Wang K, Wei X, Wetzer R, Wilson JL, Xu X, Yang H, Yoder AD, Zhang G. The Earth BioGenome Project 2020: Starting the clock. Proc Natl Acad Sci U S A 2022; 119:e2115635118. [PMID: 35042800 PMCID: PMC8795548 DOI: 10.1073/pnas.2115635118] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616;
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
| | - Stephen Richards
- University of California Davis Genome Center, University of California, Davis, CA 95616
| | - Erez Lieberman Aiden
- DNA Zoo and The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030
| | - Miguel L Allende
- Center for Genome Regulation, Universidad de Chile 3425 Santiago, Chile
- Facultad de Ciencias, Universidad de Chile 3425 Santiago, Chile
| | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Miklós Bálint
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany
- Institute for Insect Biotechnology, Justus-Liebig University 35392 Giessen, Germany
| | - Katharine B Barker
- Global Genome Biodiversity Network Secretariat, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | | | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara 44121 Ferrara, Italy
| | - Mark L Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Nicolette D Caperello
- University of California Davis Genome Center, University of California, Davis, CA 95616
| | - Keith Carlson
- The Novim Group, University of California, Santa Barbara, CA 93106
| | | | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica 11529 Taipei, Taiwan
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Dalia A Conde
- Conservation Science, Species360 Conservation Science Alliance, Bloomington, MN 55425
- Department of Biology, University of Southern Denmark 5230 Odense M, Denmark
| | - Montserrat Corominas
- Department of Genetics, Microbiology, and Statistics, Universitat de Barcelona 08028 Barcelona, Spain
- Catalan Society for Biology, Institute for Catalan Studies 08001 Barcelona, Spain
| | - Keith A Crandall
- Department of Biostatistics & Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC 20052
- Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes 111711 Bogotá, Colombia
| | | | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - ThankGod E Ebenezer
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Olivier Fedrigo
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
| | - Paul Flicek
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030
| | - M Thomas P Gilbert
- GLOBE Institute, University of Copenhagen 1350 Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology 7491 Trondheim, Norway
| | - Melissa M Goldstein
- Department of Health Policy and Management, George Washington University, Washington, DC 20052
| | - Jennifer Marshall Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Henry T Greely
- Stanford Law School, Stanford University, Stanford, CA 94305
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Kevin J Hackett
- Office of National Programs, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - David Haussler
- Genome Institute, University of California, Santa Cruz, CA 95060
- HHMI, Chevy Chase, MD 20815
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2000, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | | | - Axel Janke
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- HHMI, Chevy Chase, MD 20815
| | - Warren E Johnson
- Walter Reed Biosystematics Unit, Smithsonian Institution, Suitland, MD 20746
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | - Jin-Hyoung Kim
- Division of Life Sciences, Korea Polar Research Institute 21990 Incheon, South Korea
| | - W John Kress
- Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics 411-8540 Shizuoka, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research 650-0047 Hyogo, Japan
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | | | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University 752 36 Uppsala, Sweden
| | - Xin Liu
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, Pompeu Fabra University, Consejo Superior de Investigaciones Cientificas, Parc de Recerca Biomedica de Barcelona 08003 Barcelona, Spain
- Catalan Institute of Research and Advanced Studies 08010 Barcelona, Spain
- Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona 08193 Barcelona, Spain
| | - Sophie Mazard
- Bioplatforms Australia, Macquarie University, Sydney, NSW 2109, Australia
| | - Jonna A K Mazet
- One Health Institute, University of California Davis, CA 95616
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research 14195 Berlin, Germany
- Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research 10315 Berlin, Germany
| | - Eugene W Myers
- Max Planck Institute for Molecular Cell Biology and Genetics 01307 Dresden, Germany
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Sadye Paez
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
| | - Hyun Park
- Division of Biotechnology, Korea University 02841 Seoul, Korea
| | - Gene E Robinson
- Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants Associated Unit to Consejo Superior de Investigaciones Cientificas, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona 08193 Bellaterra, Spain
- Laboratoire d'Ecologie Alpine, University Grenoble Alpes, University Savoie Mont Blanc, CNRS 38000 Grenoble, France
| | - Oliver A Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Division of Biology, Department of Evolution, Behavior, and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Jamal S M Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University 21589 Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University 21589 Jeddah, Saudi Arabia
| | - H Bradley Shaffer
- La Kretz Center for California Conservation Science, Institute of Environment and Sustainability, University of California, Los Angeles, CA 90024
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - Timothy M Shank
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Jacob S Sherkow
- Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- College of Law, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University 224002 Yancheng, China
| | - Leho Tedersoo
- Center of Mycology and Microbiology, University of Tartu 50411 Tartu, Estonia
- College of Science, King Saud University 11451 Riyadh, Saudi Arabia
| | | | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Xiaofeng Wei
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, CA 90007
- Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Julia L Wilson
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Xun Xu
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Huanming Yang
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen 2100 Copenhagen, Denmark
- China National Genebank, Beijing Genomics Institute 51803 Shenzhen, China
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9
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de Miranda JR, Brettell LE, Chejanovsky N, Childers AK, Dalmon A, Deboutte W, de Graaf DC, Doublet V, Gebremedhn H, Genersch E, Gisder S, Granberg F, Haddad NJ, Kaden R, Manley R, Matthijnssens J, Meeus I, Migdadi H, Milbrath MO, Mondet F, Remnant EJ, Roberts JMK, Ryabov EV, Sela N, Smagghe G, Somanathan H, Wilfert L, Wright ON, Martin SJ, Ball BV. Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970's Egypt. Virol J 2022; 19:12. [PMID: 35033134 PMCID: PMC8760790 DOI: 10.1186/s12985-022-01740-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/31/2021] [Indexed: 01/11/2023] Open
Abstract
In 1977, a sample of diseased adult honeybees (Apis mellifera) from Egypt was found to contain large amounts of a previously unknown virus, Egypt bee virus, which was subsequently shown to be serologically related to deformed wing virus (DWV). By sequencing the original isolate, we demonstrate that Egypt bee virus is in fact a fourth unique, major variant of DWV (DWV-D): more closely related to DWV-C than to either DWV-A or DWV-B. DWV-A and DWV-B are the most common DWV variants worldwide due to their close relationship and transmission by Varroa destructor. However, we could not find any trace of DWV-D in several hundred RNA sequencing libraries from a worldwide selection of honeybee, varroa and bumblebee samples. This means that DWV-D has either become extinct, been replaced by other DWV variants better adapted to varroa-mediated transmission, or persists only in a narrow geographic or host range, isolated from common bee and beekeeping trade routes.
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Affiliation(s)
- Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden.
| | - Laura E Brettell
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Renrith, NSW, 2751, Australia.,School of Environment and Life Sciences, University of Salford, Manchester, M5 4WT, UK.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Nor Chejanovsky
- Institute of Plant Protection, The Volcani Center, PO Box 15159, 7528809, Rishon Lezion, Israel
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Anne Dalmon
- Abeilles et Environnement, INRAE, 84914, Avignon, France
| | - Ward Deboutte
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, University of Leuven, 3000, Leuven, Belgium.,Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Dirk C de Graaf
- Laboratory of Molecular Entomology and Bee Pathology, Ghent University, 9000, Ghent, Belgium
| | - Vincent Doublet
- College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK.,Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Haftom Gebremedhn
- Laboratory of Molecular Entomology and Bee Pathology, Ghent University, 9000, Ghent, Belgium.,Tigray Agricultural Research Institute, P.O. Box 492, Mekelle, Ethiopia
| | - Elke Genersch
- Institut Für Mikrobiologie Und Tierseuchen, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Germany.,Department of Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Sebastian Gisder
- Department of Molecular Microbiology and Bee Diseases, Institute for Bee Research, Hohen Neuendorf, Germany
| | - Fredrik Granberg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden
| | - Nizar J Haddad
- Bee Research Department, National Agricultural Research Center, Baq'a, Jordan
| | - Rene Kaden
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden.,Clinical Microbiology, Department of Medical Sciences, Uppsala University, 753 09, Uppsala, Sweden
| | - Robyn Manley
- College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK
| | - Jelle Matthijnssens
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, University of Leuven, 3000, Leuven, Belgium
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Hussein Migdadi
- Bee Research Department, National Agricultural Research Center, Baq'a, Jordan
| | - Meghan O Milbrath
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07, Uppsala, Sweden
| | - Fanny Mondet
- Abeilles et Environnement, INRAE, 84914, Avignon, France
| | - Emily J Remnant
- Behaviour, Ecology and Evolution (BEE) Lab, School of Life and Environmental Sciences, The University of Sydney, Camperdown, 2006, Australia
| | - John M K Roberts
- Commonwealth Scientific and Industrial Research Organisation, Canberra, 2601, Australia
| | - Eugene V Ryabov
- Bee Research Laboratory, Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Noa Sela
- Institute of Plant Protection, The Volcani Center, PO Box 15159, 7528809, Rishon Lezion, Israel
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Hema Somanathan
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, 695551, India
| | - Lena Wilfert
- College of Life and Environmental Sciences, University of Exeter, Penryn, TR10 9FE, UK.,Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Owen N Wright
- Centre for Research in Animal Behaviour, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QG, UK
| | - Stephen J Martin
- School of Environment and Life Sciences, University of Salford, Manchester, M5 4WT, UK.,Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Brenda V Ball
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
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10
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Saha S, Cooksey AM, Childers AK, Poelchau MF, McCarthy FM. Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes. Insects 2021; 12:748. [PMID: 34442314 PMCID: PMC8397112 DOI: 10.3390/insects12080748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 08/11/2021] [Indexed: 12/03/2022]
Abstract
Genome sequencing of a diverse array of arthropod genomes is already underway, and these genomes will be used to study human health, agriculture, biodiversity, and ecology. These new genomes are intended to serve as community resources and provide the foundational information required to apply 'omics technologies to a more diverse set of species. However, biologists require genome annotation to use these genomes and derive a better understanding of complex biological systems. Genome annotation incorporates two related, but distinct, processes: Demarcating genes and other elements present in genome sequences (structural annotation); and associating a function with genetic elements (functional annotation). While there are well-established and freely available workflows for structural annotation of gene identification in newly assembled genomes, workflows for providing the functional annotation required to support functional genomics studies are less well understood. Genome-scale functional annotation is required for functional modeling (enrichment, networks, etc.). A first-pass genome-wide functional annotation effort can rapidly identify under-represented gene sets for focused community annotation efforts. We present an open-source, open access, and containerized pipeline for genome-scale functional annotation of insect proteomes and apply it to various arthropod species. We show that the performance of the predictions is consistent across a set of arthropod genomes with varying assembly and annotation quality.
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Affiliation(s)
- Surya Saha
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA;
- School of Animal and Comparative Biomedical Sciences, University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA;
| | - Amanda M. Cooksey
- School of Animal and Comparative Biomedical Sciences, University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA;
- CyVerse, BioScience Research Laboratories, University of Arizona, 1230 N. Cherry Ave., Tucson, AZ 85721, USA
| | - Anna K. Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, 10300 Baltimore Ave., Beltsville, MD 20705, USA;
| | - Monica F. Poelchau
- National Agricultural Library, Agricultural Research Service, USDA, 10301 Baltimore Ave., Beltsville, MD 20705, USA;
| | - Fiona M. McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA;
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11
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Ryabov EV, Childers AK, Lopez D, Grubbs K, Posada-Florez F, Weaver D, Girten W, vanEngelsdorp D, Chen Y, Evans JD. Dynamic evolution in the key honey bee pathogen deformed wing virus: Novel insights into virulence and competition using reverse genetics. PLoS Biol 2019; 17:e3000502. [PMID: 31600204 PMCID: PMC6805011 DOI: 10.1371/journal.pbio.3000502] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/22/2019] [Accepted: 09/20/2019] [Indexed: 12/23/2022] Open
Abstract
The impacts of invertebrate RNA virus population dynamics on virulence and infection outcomes are poorly understood. Deformed wing virus (DWV), the main viral pathogen of honey bees, negatively impacts bee health, which can lead to colony death. Despite previous reports on the reduction of DWV diversity following the arrival of the parasitic mite Varroa destructor, the key DWV vector, we found high genetic diversity of DWV in infested United States honey bee colonies. Phylogenetic analysis showed that divergent US DWV genotypes are of monophyletic origin and were likely generated as a result of diversification after a genetic bottleneck. To investigate the population dynamics of this divergent DWV, we designed a series of novel infectious cDNA clones corresponding to coexisting DWV genotypes, thereby devising a reverse-genetics system for an invertebrate RNA virus quasispecies. Equal replication rates were observed for all clone-derived DWV variants in single infections. Surprisingly, individual clones replicated to the same high levels as their mixtures and even the parental highly diverse natural DWV population, suggesting that complementation between genotypes was not required to replicate to high levels. Mixed clone–derived infections showed a lack of strong competitive exclusion, suggesting that the DWV genotypes were adapted to coexist. Mutational and recombination events were observed across clone progeny, providing new insights into the forces that drive and constrain virus diversification. Accordingly, our results suggest that Varroa influences DWV dynamics by causing an initial selective sweep, which is followed by virus diversification fueled by negative frequency-dependent selection for new genotypes. We suggest that this selection might reflect the ability of rare lineages to evade host defenses, specifically antiviral RNA interference (RNAi). In support of this hypothesis, we show that RNAi induced against one DWV strain is less effective against an alternate strain from the same population. Deformed wing virus, a key pathogen of honey bees, shows rapid diversification after genetic bottlenecks; a novel reverse-genetic system provides insights into the forces that shape virus diversity, suggesting that virus quasi-species diversification may be driven by selection of genotypes capable of evading host RNAi defences.
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Affiliation(s)
- Eugene V. Ryabov
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
- * E-mail: ,
| | - Anna K. Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Dawn Lopez
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Kyle Grubbs
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Francisco Posada-Florez
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Daniel Weaver
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
- Beeweaver Apiaries, Navasota, Texas, United States of America
| | - William Girten
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
- Department of Chemistry, Fort Lewis College, Durango, Colorado, United States of America
| | - Dennis vanEngelsdorp
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| | - Yanping Chen
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Jay D. Evans
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
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12
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Kingan SB, Urban J, Lambert CC, Baybayan P, Childers AK, Coates B, Scheffler B, Hackett K, Korlach J, Geib SM. A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system. Gigascience 2019; 8:giz122. [PMID: 31609423 PMCID: PMC6791401 DOI: 10.1093/gigascience/giz122] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens to damage economically important crop plants in the region. RESULTS The DNA from 1 individual was used to make 1 standard, size-selected library with an average DNA fragment size of ∼20 kb. The library was run on 1 Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing ∼36× coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Furthermore, it was possible to segregate more than half of the diploid genome into the 2 separate haplotypes. The assembly also recovered 2 microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. CONCLUSIONS We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.
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Affiliation(s)
- Sarah B Kingan
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Julie Urban
- Department of Entomology, 501 ASI Building, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Primo Baybayan
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Anna K Childers
- USDA-ARS, Bee Research Laboratory, 10300 Baltimore Avenue, Building 306, Room 315, BARC-East, Beltsville, MD 20705, USA
| | - Brad Coates
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, 2333 Genetics Laboratory, 819 Wallace Road, Ames, IA 50011, USA
| | - Brian Scheffler
- USDA-ARS, Genomics and Bioinformatics Research, 141 Experiment Station Road, Stoneville, MS 38776, USA
| | - Kevin Hackett
- USDA-ARS, Office of National Programs, George Washington Carver Center, 5601 Sunnyside Avenue, Beltsville, MD 20705, USA
| | - Jonas Korlach
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Scott M Geib
- USDA-ARS, Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, 64 Nowelo St., Hilo, HI 96720, USA
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13
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Techer MA, Rane RV, Grau ML, Roberts JMK, Sullivan ST, Liachko I, Childers AK, Evans JD, Mikheyev AS. Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites. Commun Biol 2019; 2:357. [PMID: 31583288 PMCID: PMC6773775 DOI: 10.1038/s42003-019-0606-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 09/10/2019] [Indexed: 01/28/2023] Open
Abstract
Multispecies host-parasite evolution is common, but how parasites evolve after speciating remains poorly understood. Shared evolutionary history and physiology may propel species along similar evolutionary trajectories whereas pursuing different strategies can reduce competition. We test these scenarios in the economically important association between honey bees and ectoparasitic mites by sequencing the genomes of the sister mite species Varroa destructor and Varroa jacobsoni. These genomes were closely related, with 99.7% sequence identity. Among the 9,628 orthologous genes, 4.8% showed signs of positive selection in at least one species. Divergent selective trajectories were discovered in conserved chemosensory gene families (IGR, SNMP), and Halloween genes (CYP) involved in moulting and reproduction. However, there was little overlap in these gene sets and associated GO terms, indicating different selective regimes operating on each of the parasites. Based on our findings, we suggest that species-specific strategies may be needed to combat evolving parasite communities.
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Affiliation(s)
- Maeva A. Techer
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, 904-0495 Okinawa, Japan
| | - Rahul V. Rane
- Commonwealth Scientific and Industrial Research Organisation, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601 Australia
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Road, Parkville, VIC 3010 Australia
| | - Miguel L. Grau
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, 904-0495 Okinawa, Japan
| | - John M. K. Roberts
- Commonwealth Scientific and Industrial Research Organisation, Clunies Ross St, (GPO Box 1700), Acton, ACT 2601 Australia
| | | | | | | | | | - Alexander S. Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, 904-0495 Okinawa, Japan
- Australian National University, Canberra, ACT 2600 Australia
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14
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Posada-Florez F, Childers AK, Heerman MC, Egekwu NI, Cook SC, Chen Y, Evans JD, Ryabov EV. Deformed wing virus type A, a major honey bee pathogen, is vectored by the mite Varroa destructor in a non-propagative manner. Sci Rep 2019; 9:12445. [PMID: 31455863 PMCID: PMC6712216 DOI: 10.1038/s41598-019-47447-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/09/2019] [Indexed: 12/22/2022] Open
Abstract
Honey bees, the primary managed insect pollinator, suffer considerable losses due to Deformed wing virus (DWV), an RNA virus vectored by the mite Varroa destructor. Mite vectoring has resulted in the emergence of virulent DWV variants. The basis for such changes in DWV is poorly understood. Most importantly, it remains unclear whether replication of DWV occurs in the mite. In this study, we exposed Varroa mites to DWV type A via feeding on artificially infected honey bees. A significant, 357-fold increase in DWV load was observed in these mites after 2 days. However, after 8 additional days of passage on honey bee pupae with low viral loads, the DWV load dropped by 29-fold. This decrease significantly reduced the mites’ ability to transmit DWV to honey bees. Notably, negative-strand DWV RNA, which could indicate viral replication, was detected only in mites collected from pupae with high DWV levels but not in the passaged mites. We also found that Varroa mites contain honey bee mRNAs, consistent with the acquisition of honey bee cells which would additionally contain DWV replication complexes with negative-strand DWV RNA. We propose that transmission of DWV type A by Varroa mites occurs in a non-propagative manner.
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Affiliation(s)
| | - Anna K Childers
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA
| | - Matthew C Heerman
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA
| | - Noble I Egekwu
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA
| | - Steven C Cook
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA
| | - Yanping Chen
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA
| | - Jay D Evans
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA
| | - Eugene V Ryabov
- USDA, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA.
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15
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Carson RP, Bird L, Childers AK, Wheeler F, Duis J. Preserved expressive language as a phenotypic determinant of Mosaic Angelman Syndrome. Mol Genet Genomic Med 2019; 7:e837. [PMID: 31400086 PMCID: PMC6732290 DOI: 10.1002/mgg3.837] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/19/2022] Open
Abstract
Background Angelman Syndrome (AS) is a neurodevelopmental disorder with core features of intellectual disability, speech impairment, movement disorders, and a unique behavioral profile. Typically, AS results from absent maternal expression of UBE3A, but some individuals have imprinting defects in a portion of their cells. These individuals are mosaic for normal and defective UBE3A expression, resulting in mosaic AS (mAS) with a partial loss of gene expression. Methods This study aims to contrast the mAS phenotype to that of AS. Clinical characteristics of mAS were obtained from a parental survey of 22 mAS patients and from the Angelman Natural History study. These were contrasted with those of AS using historical data. Results Developmental delay was present in nearly all mAS patients, whereas the core features of AS were reported in less than 40%. While language and ability to manage activities of daily living were markedly improved over that expected in AS, mAS patients demonstrated a high incidence of behavioral challenges. Conclusion Clinical work‐up of an individual with developmental delay, hyperactivity, anxiety, and an uncharacteristically happy demeanor should prompt methylation studies to rule out mAS. We expand the phenotypic spectrum of AS to include features that overlap with Prader‐Willi such as hyperphagia.
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Affiliation(s)
- Robert P Carson
- Divisions of Child Neurology and Epilepsy, Department of Pediatrics, Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Pharmacology, Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lynne Bird
- Division of Genetics/Dysmorphology, Department of Pediatrics, Rady Children's Hospital, University of California San Diego, San Diego, California
| | - Anna K Childers
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ferrin Wheeler
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jessica Duis
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
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16
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Wallberg A, Bunikis I, Pettersson OV, Mosbech MB, Childers AK, Evans JD, Mikheyev AS, Robertson HM, Robinson GE, Webster MT. A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds. BMC Genomics 2019; 20:275. [PMID: 30961563 PMCID: PMC6454739 DOI: 10.1186/s12864-019-5642-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/24/2019] [Indexed: 01/27/2023] Open
Abstract
Background The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map. Results Each of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor > 98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features. Conclusions The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics. Electronic supplementary material The online version of this article (10.1186/s12864-019-5642-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mai-Britt Mosbech
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna K Childers
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA.,USDA-ARS Bee Research Lab, Beltsville, MD, USA
| | - Jay D Evans
- USDA-ARS Bee Research Lab, Beltsville, MD, USA
| | | | - Hugh M Robertson
- Department of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gene E Robinson
- Department of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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17
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Branstetter MG, Childers AK, Cox-Foster D, Hopper KR, Kapheim KM, Toth AL, Worley KC. Genomes of the Hymenoptera. Curr Opin Insect Sci 2018; 25:65-75. [PMID: 29602364 PMCID: PMC5993429 DOI: 10.1016/j.cois.2017.11.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/16/2017] [Indexed: 05/06/2023]
Abstract
Hymenoptera is the second-most sequenced arthropod order, with 52 publically archived genomes (71 with ants, reviewed elsewhere), however these genomes do not capture the breadth of this very diverse order (Figure 1, Table 1). These sequenced genomes represent only 15 of the 97 extant families. Although at least 55 other genomes are in progress in an additional 11 families (see Table 2), stinging wasps represent 35 (67%) of the available and 42 (76%) of the in progress genomes. A more comprehensive catalog of hymenopteran genomes is needed for research into the evolutionary processes underlying the expansive diversity in terms of ecology, behavior, and physiological traits within this group. Additional sequencing is needed to generate an assembly for even 0.05% of the estimated 1 million hymenopteran species, and we recommend premier level assemblies for at least 0.1% of the >150,000 named species dispersed across the order. Given the haplodiploid sex determination in Hymenoptera, haploid male sequencing will help minimize genome assembly issues to enable higher quality genome assemblies.
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Affiliation(s)
- Michael G Branstetter
- Pollinating Insect-biology, Management, Systematics Research Unit, USDA-ARS, Logan, UT 84322, United States
| | - Anna K Childers
- Bee Research Laboratory, USDA-ARS, Beltsville, MD 20705, United States
| | - Diana Cox-Foster
- Pollinating Insect-biology, Management, Systematics Research Unit, USDA-ARS, Logan, UT 84322, United States
| | - Keith R Hopper
- Beneficial Insects Introduction Research Unit, USDA-ARS, Newark, DE 19713, United States
| | - Karen M Kapheim
- Utah State University, Department of Biology, Logan, UT 84322, United States
| | - Amy L Toth
- Iowa State University, Department of Ecology, Evolution, and Organismal Biology and Department of Entomology, Ames, IA 50011, United States
| | - Kim C Worley
- Human Genome Sequencing Center, and Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
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18
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Schoville SD, Chen YH, Andersson MN, Benoit JB, Bhandari A, Bowsher JH, Brevik K, Cappelle K, Chen MJM, Childers AK, Childers C, Christiaens O, Clements J, Didion EM, Elpidina EN, Engsontia P, Friedrich M, García-Robles I, Gibbs RA, Goswami C, Grapputo A, Gruden K, Grynberg M, Henrissat B, Jennings EC, Jones JW, Kalsi M, Khan SA, Kumar A, Li F, Lombard V, Ma X, Martynov A, Miller NJ, Mitchell RF, Munoz-Torres M, Muszewska A, Oppert B, Palli SR, Panfilio KA, Pauchet Y, Perkin LC, Petek M, Poelchau MF, Record É, Rinehart JP, Robertson HM, Rosendale AJ, Ruiz-Arroyo VM, Smagghe G, Szendrei Z, Thomas GWC, Torson AS, Vargas Jentzsch IM, Weirauch MT, Yates AD, Yocum GD, Yoon JS, Richards S. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Sci Rep 2018; 8:1931. [PMID: 29386578 PMCID: PMC5792627 DOI: 10.1038/s41598-018-20154-1] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/13/2018] [Indexed: 01/04/2023] Open
Abstract
The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.
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Affiliation(s)
- Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, USA.
| | - Yolanda H Chen
- Department of Plant and Soil Sciences, University of Vermont, Burlington, USA
| | | | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Anita Bhandari
- Department of Molecular Physiology, Christian-Albrechts-University at Kiel, Kiel, Germany
| | - Julia H Bowsher
- Department of Biological Sciences, North Dakota State University, Fargo, USA
| | - Kristian Brevik
- Department of Plant and Soil Sciences, University of Vermont, Burlington, USA
| | - Kaat Cappelle
- Department of Crop Protection, Ghent University, Ghent, Belgium
| | - Mei-Ju M Chen
- USDA-ARS National Agricultural Library, Beltsville, MD, USA
| | - Anna K Childers
- USDA-ARS Bee Research Lab, Beltsville, MD, USA
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | | | | | - Justin Clements
- Department of Entomology, University of Wisconsin-Madison, Madison, USA
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moskva, Russia
| | - Patamarerk Engsontia
- Department of Biology, Faculty of Science, Prince of Songkla University, Amphoe Hat Yai, Thailand
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, USA
| | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Chandan Goswami
- National Institute of Science Education and Research, Bhubaneswar, India
| | | | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288, Marseille, France
- INRA, USC 1408 AFMB, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, King Abdulaziz, Saudi Arabia
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, USA
| | - Megha Kalsi
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Sher A Khan
- Department of Entomology, Texas A&M University, College Station, USA
| | - Abhishek Kumar
- Department of Genetics & Molecular Biology in Botany, Christian-Albrechts-University at Kiel, Kiel, Germany
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Fei Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288, Marseille, France
- INRA, USC 1408 AFMB, F-13288, Marseille, France
| | - Xingzhou Ma
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Alexander Martynov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Nicholas J Miller
- Department of Biology, Illinois Institute of Technology, Chicago, USA
| | - Robert F Mitchell
- Department of Biology, University of Wisconsin-Oshkosh, Oshkosh, USA
| | - Monica Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Brenda Oppert
- USDA-ARS Center for Grain and Animal Health Research, New York, USA
| | | | - Kristen A Panfilio
- Institute for Developmental Biology, University of Cologne, Köln, Germany
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, England, UK
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Lindsey C Perkin
- USDA-ARS Center for Grain and Animal Health Research, New York, USA
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Éric Record
- INRA, Aix-Marseille Université, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Joseph P Rinehart
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | | | - Guy Smagghe
- Department of Crop Protection, Ghent University, Ghent, Belgium
| | - Zsofia Szendrei
- Department of Entomology, Michigan State University, East Lansing, USA
| | - Gregg W C Thomas
- Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, USA
| | - Alex S Torson
- Department of Biological Sciences, North Dakota State University, Fargo, USA
| | | | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | - Ashley D Yates
- Department of Entomology, The Ohio State University, Columbus, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, USA
| | - George D Yocum
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | - June-Sun Yoon
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Stephen Richards
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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19
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Yocum GD, Childers AK, Rinehart JP, Rajamohan A, Pitts-Singer TL, Greenlee KJ, Bowsher JH. Environmental history impacts gene expression during diapause development in the alfalfa leafcutting bee, Megachile rotundata. J Exp Biol 2018; 221:jeb.173443. [DOI: 10.1242/jeb.173443] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 05/04/2018] [Indexed: 12/13/2022]
Abstract
Our understanding of the mechanisms controlling insect diapause has increased dramatically with the introduction of global gene expression techniques, such as RNA-seq. However, little attention has been given to how ecologically relevant field conditions may affect gene expression during diapause development because previous studies have focused on laboratory reared and maintained insects. To determine whether gene expression differs between laboratory and field conditions, prepupae of the alfalfa leafcutting bee, Megachile rotundata, entering diapause early or late in the growing season were collected. These two groups were further subdivided in early autumn into laboratory and field maintained groups, resulting in four experimental treatments of diapausing prepupae: early and late field, and early and late laboratory. RNA-seq and differential expression analyses were performed on bees from the four treatment groups in November, January, March and May. The number of treatment-specific differentially expressed genes (97 to 1249) outnumbered the number of differentially regulated genes common to all four treatments (14 to 229), indicating that exposure to laboratory or field conditions had a major impact on gene expression during diapause development. Principle component analysis and hierarchical cluster analysis yielded similar grouping of treatments, confirming that the treatments form distinct clusters. Our results support the conclusion that gene expression during the course of diapause development is not a simple ordered sequence, but rather a highly plastic response determined primarily by the environmental history of the individual insect.
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Affiliation(s)
- George D. Yocum
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | - Anna K. Childers
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
- USDA-ARS Bee Research Lab, Beltsville, MD, USA
| | | | - Arun Rajamohan
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | | | | | - Julia H. Bowsher
- Biological Sciences, North Dakota State University, Fargo, ND, USA
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Ryabov EV, Childers AK, Chen Y, Madella S, Nessa A, vanEngelsdorp D, Evans JD. Recent spread of Varroa destructor virus-1, a honey bee pathogen, in the United States. Sci Rep 2017; 7:17447. [PMID: 29234127 PMCID: PMC5727227 DOI: 10.1038/s41598-017-17802-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/30/2017] [Indexed: 11/09/2022] Open
Abstract
RNA viruses impact honey bee health and contribute to elevated colony loss rates worldwide. Deformed wing virus (DWV) and the closely related Varroa destructor virus-1 (VDV1), are the most widespread honey bee viruses. VDV1 is known to cause high rates of overwintering colony losses in Europe, however it was unknown in the United States (US). Using next generation sequencing, we identified VDV1 in honey bee pupae in the US. We tested 603 apiaries the US in 2016 and found that VDV1 was present in 66.0% of them, making it the second most prevalent virus after DWV, which was present in 89.4% of the colonies. VDV1 had the highest load in infected bees (7.45*1012 ± 1.62*1012 average copy number ± standard error) compared to other tested viruses, with DWV second (1.04*1012 ± 0.53*1012). Analysis of 75 colonies sourced in 2010 revealed that VDV1 was present in only 2 colonies (2.7%), suggesting its recent spread. We also detected newly emerged recombinants between the US strains of VDV1 and DWV. The presence of these recombinants poses additional risk, because similar VDV1-DWV recombinants constitute the most virulent honeybee viruses in the UK.
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Affiliation(s)
- Eugene V Ryabov
- US Department of Agriculture, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA.
| | - Anna K Childers
- US Department of Agriculture, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA
| | - Yanping Chen
- US Department of Agriculture, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA
| | - Shayne Madella
- US Department of Agriculture, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA
| | - Ashrafun Nessa
- University of Maryland, Department of Entomology, College Park, MD, USA
| | | | - Jay D Evans
- US Department of Agriculture, Agricultural Research Service, Bee Research Lab, Beltsville, MD, USA.
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McKenna DD, Scully ED, Pauchet Y, Hoover K, Kirsch R, Geib SM, Mitchell RF, Waterhouse RM, Ahn SJ, Arsala D, Benoit JB, Blackmon H, Bledsoe T, Bowsher JH, Busch A, Calla B, Chao H, Childers AK, Childers C, Clarke DJ, Cohen L, Demuth JP, Dinh H, Doddapaneni H, Dolan A, Duan JJ, Dugan S, Friedrich M, Glastad KM, Goodisman MAD, Haddad S, Han Y, Hughes DST, Ioannidis P, Johnston JS, Jones JW, Kuhn LA, Lance DR, Lee CY, Lee SL, Lin H, Lynch JA, Moczek AP, Murali SC, Muzny DM, Nelson DR, Palli SR, Panfilio KA, Pers D, Poelchau MF, Quan H, Qu J, Ray AM, Rinehart JP, Robertson HM, Roehrdanz R, Rosendale AJ, Shin S, Silva C, Torson AS, Jentzsch IMV, Werren JH, Worley KC, Yocum G, Zdobnov EM, Gibbs RA, Richards S. Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface. Genome Biol 2016; 17:227. [PMID: 27832824 PMCID: PMC5105290 DOI: 10.1186/s13059-016-1088-8] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/19/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species. Complementary studies of genes encoding enzymes involved in digestion of woody plant tissues or detoxification of plant allelochemicals were undertaken with the genomes of 14 additional insects, including the newly sequenced emerald ash borer and bull-headed dung beetle. RESULTS The Asian longhorned beetle genome encodes a uniquely diverse arsenal of enzymes that can degrade the main polysaccharide networks in plant cell walls, detoxify plant allelochemicals, and otherwise facilitate feeding on woody plants. It has the metabolic plasticity needed to feed on diverse plant species, contributing to its highly invasive nature. Large expansions of chemosensory genes involved in the reception of pheromones and plant kairomones are consistent with the complexity of chemical cues it uses to find host plants and mates. CONCLUSIONS Amplification and functional divergence of genes associated with specialized feeding on plants, including genes originally obtained via horizontal gene transfer from fungi and bacteria, contributed to the addition, expansion, and enhancement of the metabolic repertoire of the Asian longhorned beetle, certain other phytophagous beetles, and to a lesser degree, other phytophagous insects. Our results thus begin to establish a genomic basis for the evolutionary success of beetles on plants.
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Affiliation(s)
- Duane D. McKenna
- Department of Biological Sciences, University of Memphis, 3700 Walker Ave., Memphis, TN 38152 USA
- Feinstone Center for Genomic Research, University of Memphis, Memphis, TN 38152 USA
| | - Erin D. Scully
- USDA, Agricultural Research Service, Center for Grain and Animal Health, Stored Product Insect and Engineering Research Unit, Manhattan, KS 66502 USA
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Kelli Hoover
- Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, University Park, PA 16802 USA
| | - Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Scott M. Geib
- USDA, Agricultural Research Service, Daniel K Inouye US Pacific Basin Agricultural Research Center, Tropical Crop and Commodity Protection Research Unit, Hilo, HI 96720 USA
| | - Robert F. Mitchell
- Center for Insect Science and Department of Neuroscience, University of Arizona, Tucson, AZ 85721 USA
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI 54901 USA
| | - Robert M. Waterhouse
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, Geneva, 1211 Switzerland
- The Massachusetts Institute of Technology and The Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Seung-Joon Ahn
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Deanna Arsala
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221 USA
| | - Heath Blackmon
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019 USA
| | - Tiffany Bledsoe
- Center for Insect Science and Department of Neuroscience, University of Arizona, Tucson, AZ 85721 USA
| | - Julia H. Bowsher
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58108 USA
| | - André Busch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Bernarda Calla
- USDA, Agricultural Research Service, Daniel K Inouye US Pacific Basin Agricultural Research Center, Tropical Crop and Commodity Protection Research Unit, Hilo, HI 96720 USA
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Anna K. Childers
- USDA, Agricultural Research Service, Red River Valley Agricultural Research Center, Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - Christopher Childers
- USDA, Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705 USA
| | - Dave J. Clarke
- Department of Biological Sciences, University of Memphis, 3700 Walker Ave., Memphis, TN 38152 USA
| | - Lorna Cohen
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Jeffery P. Demuth
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019 USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Amanda Dolan
- Department of Biology, University of Rochester, Rochester, NY 14627 USA
| | - Jian J. Duan
- USDA, Agricultural Research Service, Beneficial Insects Introduction Research, Newark, DE 19713 USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202 USA
| | - Karl M. Glastad
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | | | - Stephanie Haddad
- Department of Biological Sciences, University of Memphis, 3700 Walker Ave., Memphis, TN 38152 USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Daniel S. T. Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, Geneva, 1211 Switzerland
| | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843 USA
| | - Jeffery W. Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202 USA
| | - Leslie A. Kuhn
- Department of Biochemistry and Molecular Biology, Department of Computers Science and Engineering, and Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824 USA
| | - David R. Lance
- USDA, Animal and Plant Health Inspection Service, Plant Pest and Quarantine, Center for Plant Health Science and Technology, Otis Laboratory, Buzzards Bay, MA 02542 USA
| | - Chien-Yueh Lee
- USDA, Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705 USA
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617 Taiwan
| | - Sandra L. Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Han Lin
- USDA, Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705 USA
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617 Taiwan
| | - Jeremy A. Lynch
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Armin P. Moczek
- Department of Biology, Indiana University, Blomington, IN 47405 USA
| | - Shwetha C. Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - David R. Nelson
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163 USA
| | - Subba R. Palli
- Department of Entomology, University of Kentucky, Lexington, KY 40546 USA
| | - Kristen A. Panfilio
- Institute for Developmental Biology, University of Cologne, Cologne, 50674 Germany
| | - Dan Pers
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Monica F. Poelchau
- USDA, Agricultural Research Service, National Agricultural Library, Beltsville, MD 20705 USA
| | - Honghu Quan
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Ann M. Ray
- Department of Biology, Xavier University, Cincinnati, OH 45207 USA
| | - Joseph P. Rinehart
- USDA, Agricultural Research Service, Red River Valley Agricultural Research Center, Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - Hugh M. Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Richard Roehrdanz
- USDA, Agricultural Research Service, Red River Valley Agricultural Research Center, Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - Andrew J. Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221 USA
| | - Seunggwan Shin
- Department of Biological Sciences, University of Memphis, 3700 Walker Ave., Memphis, TN 38152 USA
| | - Christian Silva
- Department of Biology, University of Rochester, Rochester, NY 14627 USA
| | - Alex S. Torson
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58108 USA
| | | | - John H. Werren
- Department of Biology, University of Rochester, Rochester, NY 14627 USA
| | - Kim C. Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - George Yocum
- USDA, Agricultural Research Service, Red River Valley Agricultural Research Center, Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - Evgeny M. Zdobnov
- Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, Geneva, 1211 Switzerland
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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