State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
PLoS One. 2012;7(12):e51769. doi: 10.1371/journal.pone.0051769. Epub 2012 Dec 13.
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.
假基因（Ψs），包括加工和非加工的 Ψs，是普遍存在的遗传元件，源自所有三个生命王国中研究的所有基因组中最初具有功能的基因。然而，利用一个物种内的多个样本的基因组信息对非加工的 Ψs 进行系统调查仍然很少见。在这里，对 80 个完全重测序的拟南芥品系中的 Ψs 进行了系统的比较分析，发现 7546 个基因（约占基因组注释开放阅读框（ORFs）的 28%）在至少一个品系中发生了破坏性突变。这些 Ψs 在染色体上的分布显示 Ψs/ORFs 与它们的局部基因密度之间存在显著的负相关，表明在基因荒漠区域（例如靠近着丝粒）有更高比例的 Ψs。另一方面，与非 Ψ 基因座相比，即使在 Ψ 基因座中的完整编码序列（CDS）也被发现具有更短的 CDS 长度、更少的外显子数和更低的 GC 含量。此外，在所报告的主要参与环境刺激和生物胁迫反应的 Ψs 中，检测到对无效假设的显著功能偏差，这表明它们可能通过假基因化来积累连续突变，对快速变化的环境的适应性进化很重要。
