Location: Corn Insects and Crop Genetics Research
Title: Proliferation and copy number variation of BEL-like long terminal repeat retrotransposons within the Diabrotica virgifera virgifera genome Authors
Submitted to: Gene
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 26, 2013
Publication Date: January 25, 2014
Citation: Coates, B.S., Fraser, L.M., French, B.W., Sappington, T.W. 2014. Proliferation and copy number variation of BEL-like long terminal repeat retrotransposons within the Diabrotica virgifera virgifera genome. Gene. 534:362-370. Interpretive Summary: Western corn rootworm (WCR) is a serious insect pest of corn throughout most of the United States. Damage and control costs for this insect are greater than one billion annual for a crop valued at more than 22 billion in the United States. There is an important need to understand this insect at the genetic and genomic level. Previous work by ARS scientists showed that the genome of WCR is large and contains a high proportion of mobile DNA elements called transposons. 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. Using a partial genome sequencing approach, we classified the type and number of transposons within the WCR genome, and showed that transposons are actively moving and creating variation within the WCR genome. This information will be important for describing transposons in the WCR whole genome sequence, and may increase understanding of genetic variation within this species.
Technical Abstract: The proliferation of retrotransposons within a genome can contribute to increased sizes and affect the function of eukaryotic genes. BEL/Pao-like long-terminal repeat (LTR) retrotransposons were annotated from the highly adaptable insect species Diabrotica virgifera virgifera, the western corn rootworm, using survey sequences from bacterial artificial chromosome (BAC) inserts and contigs derived from a low coverage next-generation sequence assembly of the genome. Eleven unique D. v. virgifera BEL elements were identified that contained gag-pol coding sequences, whereas 88 partial coding regions were also characterized from diverged elements. Phylogenetic analysis of RT domains of the pol gene indicated several ancestral BEL element lineages are present in the D. v. virgifera genome. The copy numbers of 99 unique full and partial BEL element sequences were estimated at 8.3 to 1,581.6 using normalized depth of coverage (DOC) among Illumina HiSeq reads that were aligned to each contig (total genome copy number ~8,821). BEL element copy number was highly correlated between different populations of D. v. virgifera (R2 = 0.9846), but individual element number varied as much as 1.68-fold between population samples. These data indicate that the prevalence and proliferation of BEL elements contribute to high genome size and genetic diversity among D. v. virgifera.