PT - JOURNAL ARTICLE AU - Sean D. Schoville AU - Yolanda H. Chen AU - Martin N. Andersson AU - Joshua B. Benoit AU - Anita Bhandari AU - Julia H. Bowsher AU - Kristian Brevik AU - Kaat Cappelle AU - Mei-Ju M. Chen AU - Anna K. Childers AU - Christopher Childers AU - Olivier Christiaens AU - Justin Clements AU - Elena N. Elpidina AU - Patamarerk Engsontia AU - Markus Friedrich AU - Inmaculada García-Robles AU - Richard A. Gibbs AU - Chandan Goswami AU - Alessandro Grapputo AU - Kristina Gruden AU - Marcin Grynberg AU - Bernard Henrissat AU - Emily C. Jennings AU - Jeffery W. Jones AU - Megha Kalsi AU - Sher A. Khan AU - Abhishek Kumar AU - Fei Li AU - Vincent Lombard AU - Xingzhou Ma AU - Alexander Martynov AU - Nicholas J. Miller AU - Robert F. Mitchell AU - Monica Munoz-Torres AU - Anna Muszewska AU - Brenda Oppert AU - Subba Reddy Palli AU - Kristen A. Panfilio AU - Yannick Pauchet AU - Lindsey C. Perkin AU - Marko Petek AU - Monica F. Poelchau AU - Éric Record AU - Joseph P. Rinehart AU - Hugh M. Robertson AU - Andrew J. Rosendale AU - Victor M. Ruiz-Arroyo AU - Guy Smagghe AU - Zsofia Szendrei AU - Elise M. Szuter AU - Gregg W.C. Thomas AU - Alex S. Torson AU - Iris M. Vargas Jentzsch AU - Matthew T. Weirauch AU - Ashley D. Yates AU - George D. Yocum AU - June-Sun Yoon AU - Stephen Richards TI - A model species for agricultural pest genomics: the genome of the Colorado potato beetle, <em>Leptinotarsa decemlineata</em> (Coleoptera: Chrysomelidae) AID - 10.1101/192641 DP - 2017 Jan 01 TA - bioRxiv PG - 192641 4099 - http://biorxiv.org/content/early/2017/09/25/192641.short 4100 - http://biorxiv.org/content/early/2017/09/25/192641.full AB - Background The Colorado potato beetle, Leptinotarsa decemlineata Say, is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to not only rapidly adapt to a broad range of solanaceaeous plants and variable climates during its global invasion, but, most notably, to rapidly evolve resistance to insecticides (over 50 different compounds in all major classes, in some cases within the first year of use). 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 whole-genome sequencing, transcriptome sequencing, and a large community-driven annotation effort.Results We present a 140x coverage whole genome sequence from a single female L. decemlineata, with a reference gene set of 24,740 genes. Transposable elements comprise at least 17% of the genome, and are heavily represented in an analysis of rapidly evolving gene families compared to other Coleoptera. Population genetic analyses provide evidence of high levels of nucleotide diversity, local geographic structure, and recent population growth in pest populations, pointing to the availability of considerable standing genetic variation. These factors may play an important role in rapid evolutionary change. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes (e.g. cysteine peptidase genes) in gut tissues, as well as expansions of the gustatory receptors for bitter tasting plants in the nightshade family, Solanaceae. Despite its notoriety for adapting to insecticides, L. decemlineata has a similar suite of genes involved in resistance (metabolic detoxification and cuticle penetration) compared to other beetles, although expansions in specific cytochrome P450 subfamilies are known to be associated with insecticide resistance. Finally, this beetle has interesting duplications in RNAi genes that might be linked to its high sensitivity to RNAi and could be important in the future development of gene targeted pesticides.Conclusions As a representative of one of the most evolutionarily diverse lineages, the L. decemlineata genome will undoubtedly provide new opportunities for deeper understanding on the ecology, evolution, and management of this species, as well as new opportunities to leverage genomic technologies to understand the basis of a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.