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

ABSTRACT: Pseudogenes (?s), including processed and non-processed ?s, 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 ?s utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of ?s 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 ?s on chromosomes showed a significantly negative correlation between ?s/ORFs and their local gene densities, suggesting a higher proportion of ?s in gene desert regions, e.g. near centromeres. On the other hand, compared with the non-? loci, even the intact coding sequences (CDSs) in the ? 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 ?s 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.

SUBMITTER: Wang L 

PROVIDER: S-EPMC3521719 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature