Article

High intrinsic: Rate of DNA loss in Drosophila

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
Nature (Impact Factor: 42.35). 12/1996; 384(6607):346-9. DOI: 10.1038/384346a0
Source: PubMed

ABSTRACT Pseudogenes are common in mammals but virtually absent in Drosophila. All putative Drosophila pseudogenes show patterns of molecular evolution that are inconsistent with the lack of functional constraints. The absence of bona fide pseudogenes is not only puzzling, it also hampers attempts to estimate rates and patterns of neutral DNA change. The estimation problem is especially acute in the case of deletions and insertions, which are likely to have large effects when they occur in functional genes and are therefore subject to strong purifying selection. We propose a solution to this problem by taking advantage of the propensity of retrotransposable elements without long terminal repeats (non-LTR) to create non-functional, 'dead-on-arrival' copies of themselves as a common by-product of their transpositional cycle. Phylogenetic analysis of a non-LTR element, Helena, demonstrates that copies lose DNA at an unusually high rate, suggesting that lack of pseudogenes in Drosophila is the product of rampant deletion of DNA in unconstrained regions. This finding has important implications for the study of genome evolution in general and the 'C-value paradox' in particular.

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    • "In Cryptobranchus, as in plethodontid salamanders, slower rates of DNA loss reflect fewer and smaller deletion events per substitution than are found in other vertebrate taxa (Sun, Arriaza, et al. 2012). Indels 30 bp in length have long been attributed to uncharacterized errors in DNA replication and/or recombination (Petrov et al. 1996; Kvikstad et al. 2007). Recently, comparative genomic analyses have begun to leverage natural variation in indel dynamics, across both genomes and lineages , to reveal the specific mechanisms of indel formation (Kvikstad et al. 2007, 2009; Hu et al. 2011; Nam and Ellegren 2012). "
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    • "It is possible that a mutator allele may have become fixed in the inbred ancestor of these lines. We also detected small deletion events only (i.e., no small insertions), consistent with the deletion bias that has been observed among small indel events in Drosophila (Petrov et al. 1996; Haag-Liautard et al. 2007). "
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    • "Earlier, it was thought that retrogenes are usually processed pseudogenes (Jeffs & Ashburner, 1991; Petrov et al., 1996). But during the late 1980s, abundant retrogenes having intriguing novel functions have been reported (McCarrey & Thomas, 1987). "
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