Processed pseudogenes, processed genes, and spontaneous mutations in the Arabidopsis genome.

Journal of Molecular Evolution
David Benovoy, Guy Drouin

Abstract

We identified 411 processed sequences in the Arabidopsis thaliana genome based on the fact that they have lost their intron(s) and have a length that is at least 95% of the length of the gene that gave rise to them. These sequences were generated by 230 different genes and clearly originated from retrotranspositons events because most of them (91%) have a poly(A)-tail. They are composed of 376 sequences with frame shifts and/or premature stop codons (processed pseudogenes) and 35 sequences without disablements (processed genes). Eleven of these processed genes are likely functional retrotransposed genes because they have low Ka/Ks ratios and high Ks values, and their sequences match numerous Arabidopsis ESTs. Processed sequences are mostly randomly distributed in the Arabidopsis genome and their rate of accumulation has steadily been decreasing since it peaked some 50 MYA. In contrast with the situation observed in mammals, the processed sequences found in the Arabidopsis genome originate from genes with high copy numbers and not from highly expressed genes. The patterns of spontaneous mutations in Arabidopsis are slightly different than those of mammals but are similar to those observed in Drosophila. This suggests that methyl...Continue Reading

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Citations

Aug 19, 2011·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Mateusz JanickiGuojun Yang
Jun 8, 2012·Molecular Biology and Evolution·Kazuhiko Ohshima
Jul 31, 2009·Plant Physiology·Cheng ZouShin-Han Shiu
Mar 16, 2012·Genome Génome / Conseil National De Recherches Canada·Xinyu ZhuBaohua Wang
Jul 18, 2009·BMC Genomics·Françoise Thibaud-NissenC Robin Buell
Mar 15, 2011·RNA·Ryan Charles PinkDavid Raul Francisco Carter
Aug 29, 2013·International Journal of Evolutionary Biology·Kazuhiko Ohshima
Apr 27, 2013·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Wen LiXiu-Jie Wang
May 2, 2007·The Plant Journal : for Cell and Molecular Biology·Hongzhi KongClaude W dePamphilis
Jan 24, 2017·Plant & Cell Physiology·Yi Wang
Apr 14, 2017·Viruses·Magdalena Regina Kubiak, Izabela Makałowska
Oct 10, 2015·BMC Genomics·Owais MahmudiJens Lagergren
Mar 7, 2021·Scientific Reports·Flavia MascagniAndrea Porceddu

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