Genome-Wide Survey of Pseudogenes in 80 Fully Re-sequenced Arabidopsis thaliana Accessions

Wang, Long; Si, Weina; Yao, Yongfang; Tian, Dacheng; Araki, H.; Yang, Sihai (2012). Genome-Wide Survey of Pseudogenes in 80 Fully Re-sequenced Arabidopsis thaliana Accessions. PLoS ONE, 7(12), e51769. Lawrence, Kans.: Public Library of Science 10.1371/journal.pone.0051769

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

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE)

UniBE Contributor:

Araki, Hitoshi

ISSN:

1932-6203

Publisher:

Public Library of Science

Language:

English

Submitter:

Factscience Import

Date Deposited:

04 Oct 2013 14:41

Last Modified:

13 Dec 2014 00:02

Publisher DOI:

10.1371/journal.pone.0051769

Web of Science ID:

000312386600039

BORIS DOI:

10.7892/boris.16600

URI:

https://boris.unibe.ch/id/eprint/16600 (FactScience: 224271)

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