Distribution of genes and repetitive elements in the Diabrotica virgifera virgifera genome estimated using BAC sequencing.
Feeding damage caused by the western corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with 104 ± 34.5 kb inserts was created, which has an ~4.56X genome coverage based upon a 2.58 Gb (2.80 pg) flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17 Mb of data (~0.05% genome coverage) and indicated ~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs). Sequencing genes within BAC full inserts demonstrated that TE densities are high within intergenic and intron regions and contribute to the increased gene size. Comparison of homologous genome regions cloned within different BAC clones indicated that TE movement may cause haplotype variation within the inbred strain. The data presented here indicate that the D. virgifera virgifera genome is large in size and contains a high proportion of repetitive sequence. These BAC sequencing methods that are applicable for characterization of genomes prior to sequencing may likely be valuable resources for genome annotation as well as scaffolding.
Corn Insects and Crop Genetics Research Unit, ARS, USDA, Ames, IA 50011, USA. brad.coates@ars.usda.gov
Brad S
BS
Coates
Analiza P
AP
Alves
Haichuan
H
Wang
Kimberly K O
KK
Walden
B Wade
BW
French
Nicholas J
NJ
Miller
Craig A
CA
Abel
Hugh M
HM
Robertson
Thomas W
TW
Sappington
Blair D
BD
Siegfried
D000818:Animals; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D001517:Coleoptera / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D004587:Electrophoresis, Agar Gel; D005434:Flow Cytometry; D015723:Gene Library; D017344:Genes, Insect / Q000235:genetics*; D059646:Genome Size; D023281:Genomics; D006239:Haplotypes / Q000235:genetics; D058977:Molecular Sequence Annotation; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
D004251:DNA Transposable Elements