BMC Bioinformatics (Aug 2024)
HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations
- Ravikiran Donthu,
- Jose A. P. Marcelino,
- Rosanna Giordano,
- Yudong Tao,
- Everett Weber,
- Arian Avalos,
- Mark Band,
- Tatsiana Akraiko,
- Shu-Ching Chen,
- Maria P. Reyes,
- Haiping Hao,
- Yarira Ortiz-Alvarado,
- Charles A. Cuff,
- Eddie Pérez Claudio,
- Felipe Soto-Adames,
- Allan H. Smith-Pardo,
- William G. Meikle,
- Jay D. Evans,
- Tugrul Giray,
- Faten B. Abdelkader,
- Mike Allsopp,
- Daniel Ball,
- Susana B. Morgado,
- Shalva Barjadze,
- Adriana Correa-Benitez,
- Amina Chakir,
- David R. Báez,
- Nabor H. M. Chavez,
- Anne Dalmon,
- Adrian B. Douglas,
- Carmen Fraccica,
- Hermógenes Fernández-Marín,
- Alberto Galindo-Cardona,
- Ernesto Guzman-Novoa,
- Robert Horsburgh,
- Meral Kence,
- Joseph Kilonzo,
- Mert Kükrer,
- Yves Le Conte,
- Gaetana Mazzeo,
- Fernando Mota,
- Elliud Muli,
- Devrim Oskay,
- José A. Ruiz-Martínez,
- Eugenia Oliveri,
- Igor Pichkhaia,
- Abderrahmane Romane,
- Cesar Guillen Sanchez,
- Evans Sikombwa,
- Alberto Satta,
- Alejandra A. Scannapieco,
- Brandi Stanford,
- Victoria Soroker,
- Rodrigo A. Velarde,
- Monica Vercelli,
- Zachary Huang
Affiliations
- Ravikiran Donthu
- Puerto Rico Science, Technology and Research Trust
- Jose A. P. Marcelino
- Puerto Rico Science, Technology and Research Trust
- Rosanna Giordano
- Puerto Rico Science, Technology and Research Trust
- Yudong Tao
- Department of Electrical and Computer Engineering, University of Miami
- Everett Weber
- Office of Institutional Research, Dartmouth College
- Arian Avalos
- USDA-ARS, Honey Bee Breeding, Genetics and Physiology Research
- Mark Band
- Roy J. Carver Biotechnology Center, University of Illinois
- Tatsiana Akraiko
- Roy J. Carver Biotechnology Center, University of Illinois
- Shu-Ching Chen
- Data Science and Analytics Innovation Center (dSAIC), University of Missouri-Kansas City
- Maria P. Reyes
- Knight Foundation School of Computing and Information Sciences, Florida International University
- Haiping Hao
- Johns Hopkins University School of Medicine
- Yarira Ortiz-Alvarado
- Department of Biology, University of Puerto Rico
- Charles A. Cuff
- Department of Biology, University of Puerto Rico
- Eddie Pérez Claudio
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh
- Felipe Soto-Adames
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry
- Allan H. Smith-Pardo
- USDA-APHIS-PPQ, Science and Technology (S&T)
- William G. Meikle
- USDA-ARS, Carl Hayden Bee Research Center
- Jay D. Evans
- USDA-ARS, Bee Research Laboratory
- Tugrul Giray
- Department of Biology, University of Puerto Rico
- Faten B. Abdelkader
- University of Carthage, National Agronomic Institute of Tunisia
- Mike Allsopp
- Honey Bee Research Section, ARC-Plant Protection & Health
- Daniel Ball
- Forest Fruits Ltd
- Susana B. Morgado
- Meltagus, Associação de Apicultores do Parque Natural do Tejo Internacional
- Shalva Barjadze
- Institute of Zoology, Ilia State University
- Adriana Correa-Benitez
- Facultad de MedicinaVeterinaria y Zootecnia, Departamento de Medicina y Zootecnia de Abejas, Conejos y Organismos Aquáticos (DMZ:ACyOA), Universidad Nacional Autónoma de México
- Amina Chakir
- Applied Chemistry Laboratory, Semlalia Faculty of Sciences, University Cadi Ayyad
- David R. Báez
- Amateur Beekeeper
- Nabor H. M. Chavez
- Cochabamba Beekeepers Federation (FEDAC)
- Anne Dalmon
- INRAE, French National Research Institute for Agriculture, Food and Environment. UR Abeilles et Environment
- Adrian B. Douglas
- Institute of Earth Systems, Rural Sciences Farmhouse, University of Malta
- Carmen Fraccica
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry
- Hermógenes Fernández-Marín
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP)
- Alberto Galindo-Cardona
- Instituto de Ecología Regional (IER), Universidad Nacional de Tucumán (UNT) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Yerba Buena
- Ernesto Guzman-Novoa
- School of Environmental Sciences, University of Guelph
- Robert Horsburgh
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry
- Meral Kence
- Biology Department, Middle East Technical University
- Joseph Kilonzo
- International Centre of Insect Physiology and Ecology
- Mert Kükrer
- Biology Department, Middle East Technical University
- Yves Le Conte
- INRAE, French National Research Institute for Agriculture, Food and Environment. UR Abeilles et Environment
- Gaetana Mazzeo
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università Degli Studi Di Catania
- Fernando Mota
- Independent Beekeeper
- Elliud Muli
- International Centre of Insect Physiology and Ecology
- Devrim Oskay
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University
- José A. Ruiz-Martínez
- Professional Training in Livestock and Animal Health, High School Lope de Vega
- Eugenia Oliveri
- Istituto Zooprofilattico Sperimentale della Sicilia
- Igor Pichkhaia
- Chkhorotsku Local Historical Museum
- Abderrahmane Romane
- Applied Chemistry Laboratory, Semlalia Faculty of Sciences, University Cadi Ayyad
- Cesar Guillen Sanchez
- Escuela de Agronomía, Sede del Atlántico, University of Costa Rica
- Evans Sikombwa
- Forest Fruits Ltd
- Alberto Satta
- Department of Agricultural Sciences, University of Sassari
- Alejandra A. Scannapieco
- Instituto de Genética Gv IABIMO, INTA-CONICET
- Brandi Stanford
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry
- Victoria Soroker
- Agricultural Research Organization, The Volcani Center, Institute of Plant Protection, Department of Entomology
- Rodrigo A. Velarde
- Bolivian Apiculture Institute (IAB), PROMIEL-SEDEM
- Monica Vercelli
- Monica Vercelli Independent Researcher
- Zachary Huang
- Department of Entomology, MSU Apiculture Lab, Michigan State University
- DOI
- https://doi.org/10.1186/s12859-024-05776-9
- Journal volume & issue
-
Vol. 25,
no. 1
pp. 1 – 33
Abstract
Abstract Background Honey bees are the principal commercial pollinators. Along with other arthropods, they are increasingly under threat from anthropogenic factors such as the incursion of invasive honey bee subspecies, pathogens and parasites. Better tools are needed to identify bee subspecies. Genomic data for economic and ecologically important organisms is increasing, but in its basic form its practical application to address ecological problems is limited. Results We introduce HBeeID a means to identify honey bees. The tool utilizes a knowledge-based network and diagnostic SNPs identified by discriminant analysis of principle components and hierarchical agglomerative clustering. Tests of HBeeID showed that it identifies African, Americas-Africanized, Asian, and European honey bees with a high degree of certainty even when samples lack the full 272 SNPs of HBeeID. Its prediction capacity decreases with highly admixed samples. Conclusion HBeeID is a high-resolution genomic, SNP based tool, that can be used to identify honey bees and screen species that are invasive. Its flexible design allows for future improvements via sample data additions from other localities.
Keywords
