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Journal of Biomedicine and Biotechnology
Volume 2012 (2012), Article ID 604076, 9 pages
http://dx.doi.org/10.1155/2012/604076
Research Article

Distribution of Genes and Repetitive Elements in the Diabrotica virgifera virgifera Genome Estimated Using BAC Sequencing

1Corn Insects and Crop Genetics Research Unit, ARS, USDA, Ames, IA 50011, USA
2Department of Entomology, Iowa State University, Ames, IA 50011, USA
3Department of Entomology, University of Nebraska, Lincoln, NE 68583, USA
4University of Illinois, Champaign-Urbana, IL 61801, USA
5North Central Agricultural Research Laboratory, Brookings, ARS, USDA, SD 57006, USA

Received 29 February 2012; Accepted 16 May 2012

Academic Editor: Yong Lim

Copyright © 2012 Brad S. Coates et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

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 1 0 4 ± 3 4 . 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.