Estimation of long terminal repeat element content in the Helicoverpa zea genome from high-throughput sequencing of bacterial artificial chromosome pools.
The lepidopteran pest insect Helicoverpa zea feeds on cultivated corn and cotton across the Americas where control remains challenging owing to the evolution of resistance to chemical and transgenic insecticidal toxins, yet genomic resources remain scarce for this species. A bacterial artificial chromosome (BAC) library having a mean genomic insert size of 145 ± 20 kbp was created from a laboratory strain of H. zea, which provides ∼12.9-fold coverage of a 362.8 ± 8.8 Mbp (0.37 ± 0.09 pg) flow cytometry estimated haploid genome size. Assembly of Illumina HiSeq 2000 reads generated from 14 pools that encompassed all BAC clones resulted in 165 485 genomic contigs (N50= 3262 bp; 324.6 Mbp total). Long terminal repeat (LTR) protein coding regions annotated from 181 contigs included 30 Ty1/copia, 78 Ty3/gypsy, and 73 BEL/Pao elements, of which 60 (33.1%) encoded all five functional polyprotein (pol) domains. Approximately 14% of LTR elements are distributed non-randomly across pools of BAC clones.
a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA.|b Department of Entomology, Iowa State University, Ames, IA 50011, USA.
Brad S
BS
Coates
a USDA-ARS, Corn Insects & Crop Genetics Research Unit, Genetics Laboratory, Iowa State University, Ames, IA 50011, USA.
Craig A
CA
Abel
c USDA-ARS, Southern Insect Management Research Unit, 141 Experiment Station Road, P.O. Box 346, Stoneville, MS 38776, USA.
Omaththage P
OP
Perera
D000818:Animals; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D019143:Evolution, Molecular; D059646:Genome Size; D049750:Genome, Insect; D015698:Genomic Library; D006238:Haploidy; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D007915:Lepidoptera / Q000235:genetics*; D008297:Male; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D020079:Terminal Repeat Sequences
Helicoverpa; bacterial artificial chromosome; chromosome bactérien artificiel; evolutionary genetics; génétique évolutive; retrotransposon; rétrotransposon