Proliferation and copy number variation of BEL-like long terminal repeat retrotransposons within the Diabrotica virgifera virgifera genome

The proliferation of retrotransposons within a genome can contribute to increased size 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 rootwo...

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Bibliographic Details
Published in:Gene 2014-01, Vol.534 (2), p.362-370
Main Authors: Coates, Brad S., Fraser, Lisa M., French, B. Wade, Sappington, Thomas W.
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Animals
Chromosomes, Artificial, Bacterial
Coleoptera - genetics
Corn rootworm
DNA Copy Number Variations
Gene Expression
Genome variation
Genome, Insect
Integration/excision mutation
Molecular Sequence Data
Phylogeny
Retroelements
Sequence Alignment
Terminal Repeat Sequences
Transcription, Genetic
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Summary:The proliferation of retrotransposons within a genome can contribute to increased size 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 genome sequence assembly. Eleven unique D. v. virgifera BEL elements were identified that contained full-length gag–pol coding sequences, whereas 88 different partial coding regions were characterized from partially assembled elements. Estimated genome copy number for full and partial BEL-like elements ranged from ~8 to 1582 among individual contigs using a normalized depth of coverage (DOC) among Illumina HiSeq reads (total genome copy number ~8821). BEL element copy number was correlated among different D. v. virgifera populations (R2=0.9846), but individual element numbers varied ≤1.68-fold and the total number varied by ~527 copies. These data indicate that BEL element proliferation likely contributed to a large genome size, and suggest that differences in copy number are a source of genetic variability among D. v. virgifera. [Display omitted] •BEL retrotransposon proliferation contributes to large D. v. virgifera genome size.•BEL element copy number variation (CNV) exists among D. v. virgifera populations.•CNVs are potential genetic sources for adaptive phenotypic variation.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2013.09.100