Location: Corn Insects and Crop Genetics ResearchTitle: Estimation of long terminal repeat element content in the Helicoverpa zea genome from high-throughput sequencing of bacterial artificial chromosome pools
Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/26/2016
Publication Date: 11/15/2016
Citation: Coates, B.S., Abel, C.A., Perera, O.P. 2016. Estimation of long terminal repeat element content in the Helicoverpa zea genome from high-throughput sequencing of bacterial artificial chromosome pools. Genome. 60(4):310-324. doi:10.1139/gen-2016-0067.
Interpretive Summary: The corn earworm (CEW) is an insect pest of corn through most of the United States, and can cause severe damage to corn kernels. This damage provides entry points for plant pathogens and fungi that produce mytotoxins that are harmful to human and animal health, which is becoming more prevalent as transgenic corn hybrids that express Bacillus thuringiensis (Bt) toxins become less effective at controlling CEW. Efforts to understand how corn insect pests evolve resistance to Bt are hindered by a general lack of genetic and genomic research tools. To address these gaps, ARS researchers provided the first estimate of the CEW genome size, and constructed a genomic resource consisting of large genomic fragments cloned within bacteria. These genomic resources allowed description of the number and distribution of mobile DNA elements called transposons within the CEW genome. This information will be important for describing transposons in the eventual CEW whole genome sequence, isolating genome regions involved in insecticide resistance traits, and may increase scientific understanding of genetic variation within this species.
Technical Abstract: The lepidopteran pest insect, Helicoverpa zea, feeds on cultivated corn and cotton crops in North America where control remains challenging due to evolution of resistance to chemical and transgenic insecticidal toxins, yet few genomic resources are available for this species. A bacterial artificial chromosome (BAC) library, SIMRU-BAC, containing 36,864 clones with a mean genomic insert size of 145±20 kb was created from a laboratory strain of H. zea, and based on a flow cytometry estimated H. zea haploid genome size of 362.8±8.8 Mb (0.39 pg), has a ~12.9X genome coverage. Assembly of read data generated from all SIMRU-BAC clones partitioned into 14 reduced representation libraries (= 2,688 BAC clones per pool) resulted in 165,485 genomic contigs (N50 = 3,262 bp; 324.6 Mbp total). Retrotransposon and DNA-based transposons were annotated from assembled contigs, in which long terminal repeat protein coding regions were described from 181 contigs (30 Ty1/copia, 78 Ty3/gypsy, and 73 Bel/Pau; N50 = 6487), of which 60 (33.1%) encoded all five functional polyprotein (pol) domains. DNA-seq of individual LTR elements predicted that ~14% are distributed non-randomly across reduced representation BAC pools and suggesting that LTR integrations may be clustered within the genome.