Nullomers: Really a Matter of Natural Selection?
Open Access
- 10 October 2007
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 2 (10) , e1022
- https://doi.org/10.1371/journal.pone.0001022
Abstract
Nullomers are short DNA sequences that are absent from the genomes of humans and other species. Assuming that nullomers are the signatures of natural selection against deleterious sequences in humans, the use of nullomers in drug target identification, pesticide development, environmental monitoring, and forensic applications has been envisioned. Here, we show that the hypermutability of CpG dinucleotides, rather than the natural selection against the nullomer sequences, is likely the reason for the phenomenal event of short sequence motifs becoming nullomers. Furthermore, many reported human nullomers differ by only one nucleotide, which reinforces the role of mutation in the evolution of the constellation of nullomers in populations and species. The known nullomers in chimpanzee, cow, dog, and mouse genomes show patterns that are consistent with those seen in humans. The role of mutations, instead of selection, in generating nullomers cast doubt on the utility of nullomers in many envisioned applications, because of their dependence on the role of lethal selection on the origin of nullomers.Keywords
This publication has 8 references indexed in Scilit:
- ABSENT SEQUENCES: NULLOMERS AND PRIMESPacific Symposium on Biocomputing, 2006
- Genome comparison without alignment using shortest unique substringsBMC Bioinformatics, 2005
- How independent are the appearances of n-mers in different genomes?Bioinformatics, 2004
- Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate GenomesGenome Research, 2003
- Transposable elements and the evolution of genome size in eukaryotesGenetica, 2002
- Genome-Scale Compositional Comparisons in EukaryotesGenome Research, 2001
- The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model.Proceedings of the National Academy of Sciences, 1990
- ENZYMATIC SYNTHESIS OF DEOXYRIBONUCLEIC ACID .8. FREQUENCIES OF NEAREST NEIGHBOR BASE SEQUENCES IN DEOXYRIBONUCLEIC ACID1961