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

Authors

Brad S. Coates, USDA-ARS, Ames, Iowa and Iowa State UniversityFollow
Analiza P. Alves, University of Nebraska-Lincoln
Haichuan Wang, University of Nebraska-LincolnFollow
Kimberly K. O. Walden, University of Illinois, Champaign-Urbana
B. Wade French, USDA-ARS, Brookings, South DakotaFollow
Nicholas J. Miller, University of Nebraska-LincolnFollow
Craig A. Abel, USDA-ARS, Ames, IowaFollow
Hugh M. Robertson, University of Illinois, Champaign-UrbanaFollow
Thomas W. Sappington, USDA-ARS, Ames, Iowa and Iowa State UniversityFollow
Blair D. Siegfried, University of Nebraska-LincolnFollow

Document Type

Article

Date of this Version

2012

Citation

Journal of Biomedicine and Biotechnology 2012, Article ID 604076, 9 pp.

doi: 10.1155/2012/604076

Comments

This document is a US government work and is not subject to copyright in the United States.

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 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 1.17Mb 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.