open access

https://hdl.handle.net/2115/64500

Genome-wide survey of Pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions

英語

2012-12-13

Public Library of Science

PLoS One

7(12)

e51769

Pseudogenes (Ys), including processed and non-processed Ys, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life. However, systematic surveys of non-processed Ys utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of Ys within 80 fully re-sequenced Arabidopsis thaliana accessions, and 7546 genes, representing ,28% of the genomic annotated open reading frames (ORFs), were found with disruptive mutations in at least one accession. The distribution of these Ys on chromosomes showed a significantly negative correlation between Ys/ORFs and their local gene densities, suggesting a higher proportion of Ys in gene desert regions, e.g. near centromeres. On the other hand, compared with the non-Y loci, even the intact coding sequences (CDSs) in the Y loci were found to have shorter CDS length, fewer exon number and lower GC content. In addition, a significant functional bias against the null hypothesis was detected in the Ys mainly involved in responses to environmental stimuli and biotic stress as reported, suggesting that they are likely important for adaptive evolution to rapidly changing environments by pseudogenization to accumulate successive mutations.

学術雑誌論文

Version of Record

Creative Commons Attribution 4.0 International