Location: Genomics and Bioinformatics Research
Project Number: 6066-21310-006-003-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 15, 2019
End Date: Sep 14, 2024
Objective:
ARS has initiated a nationwide program on developing genomes of agriculturally important insects called Ag100Pests. Under this program, high quality genomes will be developed for ~100 important insects. In addition, ARS has started a new research program on pollinators. These programs anticipate using the latest advances of DNA sequencing technology for the rapid development of quality genomes so that other researchers can use this information to develop DNA markers, understand population dynamics and gene flow, follow the spread and origin of insect infestations, and develop new control methods or in the case of pollinators develop new perseveration methods. However, developing these genomes present novel challenges. The genome size of insects is very broad from something like a mosquito at ~200,000,000 base pairs to a grasshopper which ~7,000,000,000 base pairs. Insect size also varies from the microscopic to inches long. There is limited correlation of genome size to the physical size of the genome. Thus small insects like ticks have genomes ranging from ~1,000,000,000-4,500,000,000 base pairs and honey bees have a genome of ~300,000,000. Under the Ag100Pest program, a leading objective is to derive a genome from one insect individual, however that will not be possible in all instances. The various genome sizes, the level of heterozygosity, and the low amount of input DNA represent significant challenges to creating high quality reference genomes.
Approach:
Next Generation Sequencing technologies will be used to generate data to develop high quality de novo genomes for pollinators and agriculturally important insects. The foundation of the genome assembly will use long read sequence technology and RnaSeq technology to provide data for genome annotation. When possible, a scaffolding technology and whole genome sequencing for error correction will also be utilized. Different strategies will be utilized to assemble the genomes and the cooperating institutes will share sequencing and genome assemblies knowledge to so high quality reference genomes can be produced.
