TY - JOUR
T1 - The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species
AU - Papanicolaou, Alexie
AU - Schetelig, Marc F.
AU - Arensburger, Peter
AU - Atkinson, Peter W.
AU - Benoit, Joshua B.
AU - Bourtzis, Kostas
AU - Castañera, Pedro
AU - Cavanaugh, John P.
AU - Chao, Hsu
AU - Childers, Christopher
AU - Curril, Ingrid
AU - Dinh, Huyen
AU - Doddapaneni, Harsha Vardhan
AU - Dolan, Amanda
AU - Dugan, Shannon
AU - Friedrich, Markus
AU - Gasperi, Giuliano
AU - Geib, Scott
AU - Georgakilas, Georgios
AU - Gibbs, Richard A.
AU - Giers, Sarah D.
AU - Gomulski, Ludvik M.
AU - González-Guzmán, Miguel
AU - Guillem-Amat, Ana
AU - Han, Yi
AU - Hatzigeorgiou, Artemis G.
AU - Hernández-Crespo, Pedro
AU - Hughes, Daniel S.T.
AU - Jones, Jeffery W.
AU - Karagkouni, Dimitra
AU - Koskinioti, Panagiota
AU - Lee, Sandra L.
AU - Malacrida, Anna R.
AU - Manni, Mosè
AU - Mathiopoulos, Kostas
AU - Meccariello, Angela
AU - Murali, Shwetha C.
AU - Murphy, Terence D.
AU - Muzny, Donna M.
AU - Oberhofer, Georg
AU - Ortego, Félix
AU - Paraskevopoulou, Maria D.
AU - Poelchau, Monica
AU - Qu, Jiaxin
AU - Reczko, Martin
AU - Robertson, Hugh M.
AU - Rosendale, Andrew J.
AU - Rosselot, Andrew E.
AU - Saccone, Giuseppe
AU - Salvemini, Marco
AU - Savini, Grazia
AU - Schreiner, Patrick
AU - Scolari, Francesca
AU - Siciliano, Paolo
AU - Sim, Sheina B.
AU - Tsiamis, George
AU - Ureña, Enric
AU - Vlachos, Ioannis S.
AU - Werren, John H.
AU - Wimmer, Ernst A.
AU - Worley, Kim C.
AU - Zacharopoulou, Antigone
AU - Richards, Stephen
AU - Handler, Alfred M.
N1 - Funding Information:
Support of this project was provided by the U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Animal and Plant Health Inspection Service (APHIS), and National Institute of Food and Agriculture (NIFA)-Biotechnology Risk Assessment Grants Program (grant no. 2011-39211-30769 to AMH) for funding the initial phase of this project, and to the National Institutes of Health (NIH)-National Human Genome Research Institute (NHGRI) for funding the medfly genome sequencing, assembly, and Maker 2.0 automated annotation as part of the i5K 30 genome pilot project (grant no. U54 HG003273 to RAG). The NIH Intramural Research Program, National Library of Medicine funded the NCBI Gnomon annotation and the USDA-National Agricultural Library (NAL) provided support for the WebApollo curation website. Support was provided for: toxin metabolism and insecticide resistance gene studies from MINECO, Spain (AGL2013-42632-R to FO and PH-C); microRNAs, horizontal gene transfer, and bacterial contaminant studies from the European Social Fund and National Strategic Reference Framework‐THALES (MIS375869 to KB, GT, AGH, and KM) and the U.S. National Science Foundation (DEB 1257053 to JHW); cuticle protein gene studies from USDA-NIFA (grant no. 2016-67012-24652 to AJR); sex-determination studies from L.R. Campania (grant 5/02, 2008 to GS); male reproduction and sexual differentiation studies from the FAO/IAEA (Technical Contract No.: 16966 to GGa) and Cariplo IMPROVE (to FS); and programmed cell death gene studies and genomic data analysis (to MFS) from the Emmy Noether program, DFG (SCHE 1833/1-1) and the LOEWE Center for Insect Biotechnology & Bioresources grant of the Hessen State Ministry of Higher Education, Research and the Arts (HMWK), Germany and from the USDA-NIFA-Biotechnology Risk Assessment Grants Program (grant no. 2015-33522-24094 to AMH).
Publisher Copyright:
© 2016 The Author(s).
PY - 2016/9/22
Y1 - 2016/9/22
N2 - Background: The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control. Results: The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT. Conclusions: The medfly genome sequence provides critical insights into the biology of one of the most serious and widespread agricultural pests. This knowledge should significantly advance the means of controlling the size and invasive potential of medfly populations. Its close relationship to Drosophila, and other insect species important to agriculture and human health, will further comparative functional and structural studies of insect genomes that should broaden our understanding of gene family evolution.
AB - Background: The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control. Results: The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT. Conclusions: The medfly genome sequence provides critical insights into the biology of one of the most serious and widespread agricultural pests. This knowledge should significantly advance the means of controlling the size and invasive potential of medfly populations. Its close relationship to Drosophila, and other insect species important to agriculture and human health, will further comparative functional and structural studies of insect genomes that should broaden our understanding of gene family evolution.
KW - Chromosomal synteny
KW - Gene family evolution
KW - Insect adaptation
KW - Insect invasiveness
KW - Insect orthology
KW - Medfly genome
KW - Medfly integrated pest management (IPM)
KW - Tephritid genomics
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U2 - 10.1186/s13059-016-1049-2
DO - 10.1186/s13059-016-1049-2
M3 - Article
C2 - 27659211
AN - SCOPUS:84992521834
VL - 17
JO - Genome Biology
JF - Genome Biology
SN - 1465-6906
IS - 1
M1 - 192
ER -