Deletions in Processed Pseudogenes Accumulate Faster in Rodents Than in Humans
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The relative rates of point nucleotide substitution and accumulation of gap events (deletions and insertions) were calculated for 22 human and 30 rodent processed pseudogenes. Deletion events not only outnumbered insertions (the ratio being 7:1 and 3:1 for human and rodent pseudogenes, respectively), but also the total length of deletions was greater than that of insertions. Compared with their functional homologs, human processed pseudogenes were found to be shorter by about 1.2%, and rodent pseudogenes by about 2.3%. DNA loss from processed pseudogenes through deletion is estimated to be at least seven times faster in rodents than in humans. In comparison with the rate of point substitutions, the abridgment of pseudogenes during evolutionary times is a slow process that probably does not retard the rate of growth of the genome due to the proliferation of processed pseudogenes.
Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.
Redelings B, Holmes I, Lunter G, Pupko T, Anisimova M Mol Biol Evol. 2024; 41(9).
PMID: 39172750 PMC: 11385596. DOI: 10.1093/molbev/msae177.
Loewenthal G, Wygoda E, Nagar N, Glick L, Mayrose I, Pupko T Open Biol. 2022; 12(12):220223.
PMID: 36514983 PMC: 9748784. DOI: 10.1098/rsob.220223.
AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era.
Ly-Trong N, Naser-Khdour S, Lanfear R, Minh B Mol Biol Evol. 2022; 39(5).
PMID: 35511713 PMC: 9113491. DOI: 10.1093/molbev/msac092.
A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions.
Loewenthal G, Rapoport D, Avram O, Moshe A, Wygoda E, Itzkovitch A Mol Biol Evol. 2021; 38(12):5769-5781.
PMID: 34469521 PMC: 8662616. DOI: 10.1093/molbev/msab266.
Causes and Effects of Loss of Classical Nonhomologous End Joining Pathway in Parasitic Eukaryotes.
Nenarokova A, Zahonova K, Krasilnikova M, Gahura O, McCulloch R, Zikova A mBio. 2019; 10(4).
PMID: 31311886 PMC: 6635534. DOI: 10.1128/mBio.01541-19.