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Title: Distribution of genes and repetitive elements in the Diabrotica virgifera virgifera genome estimated using BAC sequencing

item Coates, Brad
item ALVES, ANA - University Of Nebraska
item WANG, HAICHUAN - University Of Nebraska
item WALDEN, KIMBERLY - University Of Illinois
item French, Bryan
item MILLER, NICHOLAS - University Of Nebraska
item Abel, Craig
item ROBERTSON, HUGH - University Of Illinois
item Sappington, Thomas
item SIEGFRIED, BLAIR - University Of Nebraska

Submitted to: Journal of Biomedicine and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/16/2012
Publication Date: 8/6/2012
Citation: Coates, B.S., Alves, A., Wang, H., Walden, K., French, B.W., Miller, N.M., Abel, C.A., Robertson, H.M., Sappington, T.W., Siegfried, B.D. 2012. Distribution of genes and repetitive elements in the Diabrotica virgifera virgifera genome estimated using BAC sequencing. Journal of Biomedicine and Biotechnology. 2012:1.

Interpretive Summary: Western corn rootworm (WCR) is a serious insect pest of corn in the United States and Europe. Damage and control costs for this insect exceed $1 billion from an annual crop valued at more than $22 billion in the U.S. alone. There is an important need to understand this insect at the genetic and genomic level. The genome of WCR will soon be sequenced using an inbred non-diapausing strain with the goal of devising new tactics for control of this insect. We estimated the size of the WCR genome, and performed partial genome sequencing to describe the frequency of gene and repetitive DNA. This information will be important for developing strategies for the WCR whole genome sequencing project.

Technical Abstract: Feeding damage caused by the corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance traits that allow survival when exposed to chemical and transgenic toxins. Genome sequencing of an inbred non-diapausing strain is soon to be underway with the intent of devising novel tactics for control of this insect. Herein we report the initial characterization of genome size and repetitive DNA composition that will assist in devising a strategy for genome sequencing. A Bacterial Artificial Chromosome (BAC) library, DvvBAC1, containing 109,486 clones with 104.4 plus or minus 34.5 kilobase (kb) genome inserts was created for the flow cytometry estimated 2.56 gigabase (Gb) [2.80 picogram (pg)] haploid genome size that encompassed an approximately 4.56-fold genome coverage. Paired end sequencing of 1037 BAC inserts produced 1.17 megabase (Mb) of sequence data (approximately 0.05-fold genome coverage) and showed that approximately 9.4 and 16.0% of reads respectively correspond to protein coding regions and transposon-derived genes. Full BAC insert and complete gene sequencing demonstrated that transposable element densities are high within intergenic and intron regions, and contribute to the increased gene size. The proliferation of repetitive and transposable element (TE) DNA has led to an increased genome size, where small TEs are distributed throughout and large retroelements appear to be at greatest frequencies between genes. Assembly of the gene space from single-end "next generation" 454 sequencing reads suggests that whole genome sequencing strategies and successful assembly of a highly repetitive genome are possible.