The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedmann), reveals insights into the biology and adaptive evolution of a highly invasive pest species

Authors: PAPANICOLAOU, ALEXIE - Western Sydney University; SCHETELIG, MARC - Justus-Liebig University; ARENSBURGER, PETER - California Polytechnic State University; ATKINSON, PETER - California State University; BENOIT, JOSHUA - University Of Cincinnati; BOURTZIS, KOSTAS - International Atomic Energy Agency (IAEA); CASTANERA, PEDRO - Centro De Investigacions Biologicas, Cib, (CSIC); CAVANAUGH, JOHN - University Of Cincinnati; CHAO, HSU - Baylor College Of Medicine; Childers, Christopher; CURRIL, INGRID - Georg August University; DINH, HUYEN - Baylor College Of Medicine; DODDAAPANELI, HARSHA - Baylor College Of Medicine; DOLAN, AMANDA - University Of Rochester; DUGAN, SHANNON - Baylor College Of Medicine; FRIEDRICH, MARKUS - Wayne State University; GASPERI, GIULIANO - University Of Pavia; Geib, Scott; GEORGAKILAS, GEORGIOS - University Of Thessaly; GIBBS, RICHARD - Baylor College Of Medicine; GIERS, SARAH - University Of Illinois; GOMULSKI, LUDVIK - University Of Pavia; GONZALEZ-GUZMAN, MIGUEL - Centro De Investigacions Biologicas, Cib, (CSIC); GUILLEM-AMAT, ANA - Centro De Investigacions Biologicas, Cib, (CSIC); HAN, YI - Baylor College Of Medicine; HATZIGEORGIOU, ARTEMIS - University Of Thessaly; HERNANDEZ-CRESPO, PEDRO - Centro De Investigacions Biologicas, Cib, (CSIC); HUGHES, DANIEL - Baylor College Of Medicine; JONES, JEFFERY - Oakland University; KARAGKOUNI, DIMITRA - University Of Thessaly; KOSKINIOTI, PANAGIOTA - University Of Thessaly; LEE, SANDRA - Baylor College Of Medicine; MALACRIDA, ANNA - University Of Pavia; MANNI, MOSE - University Of Pavia; MATHIOPOULOS, KOSTAS - University Of Thessaly; MURALI, SHWETHA - Baylor College Of Medicine; MURPHY, TERENCE - National Institutes Of Health (NIH); MUZNY, DONNA - Baylor College Of Medicine; OBERHOFER, GEORGE - Georg August University; ORTEGO, FELIX - Centro De Investigacions Biologicas, Cib, (CSIC); PARASKEVOPOULOU, MARIA - University Of Thessaly; Poelchau, Monica; QU, JIAXIN - Baylor College Of Medicine; RECZKO, MARTIN - Biomedical Sciences Research Center (BSRC) "alexander Fleming"; ROBERTSON, HUGH - University Of Illinois; ROSENDALE, ANDREW - University Of Cincinnati; ROSSELOT, ANDREW - University Of Cincinnati; SACCONE, GIUSEPPE - The University Of Naples Federico Ii; SALVEMINI, MARCO - The University Of Naples Federico Ii; SAVINI, GRAZIA - University Of Pavia; SCHREINER, PATRICK - University Of California; SCOLARI, FRANCESCA - University Of Pavia; SICILIANO, PAOLO - University Of Pavia; SIM, SHEINA - University Of Hawaii; TSIAMIS, GEORGE - University Of Patras; URENA, ENRIC - Centro De Investigacions Biologicas, Cib, (CSIC); VLACHOS, IOANNIS - University Of Thessaly; WERREN, JOHN - University Of Rochester; WIMMER, ERNST - Georg August University; WORLEY, KIM - Baylor College Of Medicine; ZACHAROPOULOU, ANTIGONE - University Of Patras; RICHARDS, STEPHEN - Baylor College Of Medicine; Handler, Alfred - Al

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/29/2016
Publication Date: 9/22/2016
Citation: Papanicolaou, A., Schetelig, M.F., Arensburger, P., Atkinson, P.W., Benoit, J.B., Bourtzis, K., Castanera, P., Cavanaugh, J.P., Chao, H., Childers, C., Curril, I., Dinh, H., Doddaapaneli, H.V., Dolan, A., Dugan, S., Friedrich, M., Gasperi, G., Geib, S.M., Georgakilas, G., Gibbs, R.A., Giers, S.D., Gomulski, L.M., Gonzalez-Guzman, M., Guillem-Amat, A., Han, Y., Hatzigeorgiou, A.G., Hernandez-Crespo, P., Hughes, D.S., Jones, J.W., Karagkouni, D., Koskinioti, P., Lee, S.L., Malacrida, A.R., Manni, M., Mathiopoulos, K., Murali, S.C., Murphy, T.D., Muzny, D.M., Oberhofer, G., Ortego, F., Paraskevopoulou, M.D., Poelchau, M.F., Qu, J., Reczko, M., Robertson, H.M., Rosendale, A.J., Rosselot, A.E., Saccone, G., Salvemini, M., Savini, G., Schreiner, P., Scolari, F., Siciliano, P., Sim, S.B., Tsiamis, G., Urena, E., Vlachos, I.S., Werren, J.H., Wimmer, E.A., Worley, K.C., Zacharopoulou, A., Richards, S., Handler, A.M. 2016. The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedmann), reveals insights into the biology and adaptive evolution of a highly invasive pest species. Genome Biology. 17:192. https://doi.org/10.1186/s13059-016-1049-2.
DOI: https://doi.org/10.1186/s13059-016-1049-2

Interpretive Summary: The Mediterranean fruit fly (Ceratitis capitata, Diptera: Tephritidae) is one of the most destructive agricultural pests throughout the world due to its broad host plant range that includes more than 260 different fruits, flowers, vegetables, and nuts. Host preferences vary in different regions of the world, which can be associated with its ability to invade and adapt to ecological niches throughout tropical and subtropical regions. To further our understanding of this critical agricultural pest and to develop genetic strategies to control its population size, scientists at the USDA Agriculture Research Service, Center for Medical, Agricultural and Veterinary Entomology, Gainesville, Florida, initiated the Mediterranean fruit fly whole genome sequencing (WGS) project. This represented the first of 30 insect genomes to be sequenced as part of pilot project for the i5K arthropod project at the Baylor College of Medicine Human Genome Sequencing Center (HGSC). A thorough automated structural annotation of the genome was conducted, aided by RNA-Seq data, which allowed a curation community of 20 groups to make key sequence assignments related to genome structure, orthology, and genetic regulation. Manual annotations were also performed for key gene families related to invasiveness, adaptation, insecticide resistance and detoxification, and aspects of sex-determination, reproduction and cell death related to population control strategies. This resource should provide a foundation for continued research on fundamental and comparative studies of insect genomes and gene family evolution, and to the improvement of biologically-based programs having the goal of controlling medfly, in addition to related insect pest populations.

Technical Abstract: The Mediterranean fruit fly is one of the most destructive agricultural pests throughout the world due to its broad host plant range that includes more than 260 different fruits, flowers, vegetables, and nuts. Host preferences vary in different regions of the world, which can be associated with its ability to invade and adapt to ecological niches throughout tropical and subtropical regions. To further our understanding of this critical agricultural pest and to facilitate development of genetic strategies to control its population size, scientists at the USDA, Agriculture Research Service, Center for Medical, Agricultural and Veterinary Entomology, Gainesville, Florida, initiated the Mediterranean fruit fly whole genome sequencing (WGS) project. This species represented the first of 30 insect genomes to be sequenced as part of pilot project for the i5K arthropod project at the Baylor College of Medicine Human Genome Sequencing Center (HGSC). A thorough automated structural annotation of the genome was conducted, aided by RNA-Seq data, which allowed a curation community of 20 groups to make key sequence assignments related to genome structure, orthology, and genetic regulation. Manual annotations were also performed for key gene families related to invasiveness, adaptation, insecticide resistance and detoxification, and aspects of sex-determination, reproduction and cell death related to population control strategies. This resource should provide a foundation for continued research on fundamental and comparative studies of insect genomes and gene family evolution, and to the improvement of biologically-based programs having the goal of controlling medfly, in addition to related insect pest populations.