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

Abstract

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 nextgeneration 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 (R 2 = 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.

A novel duplex ddPCR assay for the diagnosis of schistosomiasis japonica: proof of concept in an experimental mouse model

“…This inconsistency may be due to the variable nature of retrotransposons within the genome. In particular, the capacity of retrotransposons to proliferate within the genome allows for a higher chances of variable copy numbers (Laha et al 2002; Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium, 2009; Han, 2010; Finnegan, 2012; Coates et al 2013). However, the details on the amounts and the exact mechanisms involved in the regulation of genome retrotransposon copy number is intricate and, as yet, unclear.…”

Genome size evolution in the beetle genusDiabrotica

“…The copyright holder for this preprint this version posted September 6, 2021. ; https://doi.org/10.1101/2021.09.04.458993 doi: bioRxiv preprint considered appropriate for accurate genome size estimates (Dolezel et al, 2007;Tomaszewska et al, 2021) undecimpunctata ( n = 50) were collected from maize fields near Ames, Iowa, and Monmouth, Illinois, respectively. Each sample was pooled by species, flash-frozen in liquid nitrogen and ground in liquid nitrogen, and then DNA extracted from ~3.0 mg of tissue using the Qiagen DNeasy Blood and Tissue Extraction kit, with modifications as described (Coates et al, 2014).…”

“…The known genome size of the standard barberi (n = 71) and D. undecimpunctata (n = 50) were collected from maize fields near Ames, Iowa, and Monmouth, Illinois, respectively. Each sample was pooled by species, flash-frozen in liquid nitrogen and ground in liquid nitrogen, and then DNA extracted from ~3.0 mg of tissue using the Qiagen DNeasy Blood and Tissue Extraction kit, with modifications as described (Coates et al, 2014). Two micrograms of extracted DNA was submitted to the Iowa State University DNA Facility (Ames, IA, USA) from which ~500bp insert indexed sequencing libraries were generated using the Illumina TruSeq…”

“…Studies also suggest that the D. v. virgifera genome contains a high proportion of repetitive elements (Coates et al, 2012(Coates et al, , 2014. The cadherin gene of D. v. virgifera is approximately 13.3 fold larger than the Tribolium castaneum ortholog due to much larger introns.…”

“…The presence of numerous MITE-like elements within the cadherin gene of D. v. virgifera indicates that the difference in the gene size is due to the insertion of transposable elements in the D. v. virgifera introns (Coates et al, 2012). Class I BEL-like long terminal repeat (LTR) retrotransposons have been also found in the D. v. virgifera genome (Coates et al, 2014).…”