Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions.
Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions.
复制标题
对 80 个完全重测序的拟南芥种质中的假基因进行全基因组调查
DOI：
10.1371/journal.pone.0051769
复制
发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Yang S
中科院分区：
文献类型：
--
作者：
Wang L;Si W;Yao Y;Tian D;Araki H;Yang S
假基因（Ψs），包括加工过的和未加工过的Ψs，是源自生命三个王国中所有研究的基因组中原始功能基因的普遍存在的遗传元件。然而，利用一个物种内多个样本的基因组信息对未经处理的 Ψ 进行系统调查仍然很少。这里对 80 个完全重新测序的拟南芥种质内的 Ψ 进行了系统的比较分析，发现至少一个种质中存在破坏性突变的 7546 个基因，代表了约 28% 的基因组注释开放阅读框 (ORF)。这些 Ψ 在染色体上的分布显示 Ψ/ORF 与其局部基因密度之间呈显着负相关，这表明 Ψ 在基因沙漠区域中所占的比例较高，例如靠近着丝粒。另一方面，与非Ψ位点相比，即使是Ψ位点中的完整编码序列（CDS）也被发现具有更短的CDS长度、更少的外显子数量和更低的GC含量。此外，在主要参与对环境刺激和生物胁迫的反应的Ψ中检测到了针对零假设的显着功能偏差，这表明它们可能对于通过假发生积累连续突变来适应快速变化的环境的进化很重要。
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.
登录
查看更多内容
伪施加机制与基因序列长度之间的密切关联。
影响因子：
5.5
作者：
Khachane AN;Harrison PM
通讯作者：
Harrison PM
影响因子：
3.7
作者：
Sangster TA;Bahrami A;Wilczek A;Watanabe E;Schellenberg K;McLellan C;Kelley A;Kong SW;Queitsch C;Lindquist S
通讯作者：
Lindquist S
影响因子：
64.8
作者：
Gan X;Stegle O;Behr J;Steffen JG;Drewe P;Hildebrand KL;Lyngsoe R;Schultheiss SJ;Osborne EJ;Sreedharan VT;Kahles A;Bohnert R;Jean G;Derwent P;Kersey P;Belfield EJ;Harberd NP;Kemen E;Toomajian C;Kover PX;Clark RM;Rätsch G;Mott R
通讯作者：
Mott R
影响因子：
3.3
作者：
Schmid, KJ;Ramos-Onsins, S;Mitchell-Olds, T
通讯作者：
Mitchell-Olds, T
影响因子：
3.3
作者：
Coop, Graham;Witonsky, David;Pritchard, Jonathan K.
通讯作者：
Pritchard, Jonathan K.