Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element.
Abstract
The discordance between genome size and the complexity of eukaryotes can partly be
attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the
smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in D. ananassae To identify the major contributors to the expansion of the F element and to assess
their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb
region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons
(particularly LTR and LINE retrotransposons) are major contributors to this expansion
(78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but
these differences are exaggerated in D. ananassae Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection.
The 5' ends of F-element genes in both species are enriched in dimethylation of lysine
4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite
differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic
domains. This study improves our understanding of how transposons can affect genome
size and how genes can function within highly repetitive domains.
Type
Journal articleSubject
ChromosomesAnimals
Drosophila
Wolbachia
Histones
Retroelements
Codon
Gene Expression Profiling
Protein Processing, Post-Translational
Base Composition
Base Sequence
Genes, Insect
Female
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https://hdl.handle.net/10161/23708Published Version (Please cite this version)
10.1534/g3.117.040907Publication Info
Leung, Wilson; Shaffer, Christopher D; Chen, Elizabeth J; Quisenberry, Thomas J; Ko,
Kevin; Braverman, John M; ... Elgin, Sarah CR (2017). Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element. G3 (Bethesda, Md.), 7(8). pp. 2439-2460. 10.1534/g3.117.040907. Retrieved from https://hdl.handle.net/10161/23708.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
Alexis Ceasrine
Affiliate
Eric P. Spana
Associate Professor of the Practice of Biology
Leah Esther Waldman
Assistant Professor in the Department of Radiology
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