Chrysodeixis includens isolate:SIMRU Inbred Laboratory Colony Genome sequencing and assembly

The soybean looper, Chrysodeixis includens (Walker) (Lepidoptera: Noctuidae) is a ubiquitous pest species distributed across most parts of North and South America. This species has high population densities in southern and eastern USA where it is considered a serious pest causing heavy losses in field crops such as soybeans and some vegetable crops. Soybean loopers are polyphagous and known to feed on 174 plant species across 39 families. A large number of soybean looper host plants are in the families Amaranthaceae, Asteraceae, Brassicaceae, Euphorbiaceae, Fabaceae, Lamiaceae, Malvaceae, Poaceae, and Solanaceae. Soybean is one of the most preferred hosts of this insect providing optimum conditions for feeding and oviposition.Development of insecticide resistance in soybean looper is a major concern for farmers in devising management tactics for this pest. Soybean looper has already developed resistance to almost all classes of insecticides that include carbamates, cyclodienes, organochlorines (DDT), organophosphates, and pyrethroids. The carbohydrazide insecticide methoxyfenozide (an insect growth regulator) was the recommended insecticide for the soybean looper in Mississippi prior to approval of diamide insecticides such as flubendiamide and chlorantraniliprole. Failures in controlling soybean looper with methoxyfenozide were reported in some areas in mid-South in 2009 and 2010. Sporadic control failures with diamide insecticides have been reported for soybean looper. Control failures may indicate low frequencies of mutations conferring resistance in the diamide target, the ryanodine receptor. Although field failures of diamides in controlling soybean looper were reported in North Carolina, Georgia, Florida, and Puerto Rico in 2014, no confirmation or published reports are available to date. However, this does not indicate absence of alleles in field populations that may give rise to resistance in the future. Our goals in this study are to 1) sequence and assembled the soybean looper genome to develop genomic and transcriptomic resources, 2) develop and validate a genetic marker set to conduct population genetic studies and to estimate frequencies of alleles linked to genetic loci conferring resistance to major insecticides (e.g. voltage-gated sodium channel, ryanodine receptor, cytochrome P450 genes, glutathione transferases, nicotinic acetylcholinesterase (nACh) receptor), and 3) conduct field surveys to establish baseline population genetic data for soybean looper.