Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints.
Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints.
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DOI：
10.1093/molbev/mst166
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发表时间：
2014-01
影响因子：
10.7
通讯作者：
Urrutia AO
中科院分区：
文献类型：
--
作者：
Bush SJ;Castillo-Morales A;Tovar-Corona JM;Chen L;Kover PX;Urrutia AO
对同一植物物种的多个基因组进行测序揭示了多态性基因和外显子丢失。与抗病性相关的基因在那些表现出结构变异的基因中比例过高，这表明基因和外显子存在-缺失变异（PAV）具有适应性作用。为了阐明多态性编码区丢失的可能功能相关性以及驱动该过程的机制，我们对 17 个完全测序的拟南芥种质中丢失整个外显子或其整个编码区的基因进行了表征。我们发现，尽管观察到与某些功能类别相关的基因显着富集，但 PAV 事件在很大程度上仅限于具有降低重要性特征的基因：PAV 基因往往是基因组中的新添加物、组织特异性和低表达。此外，PAV基因位于基因密度较低和转座元件密度较高的区域。部分编码区PAV事件仅与受影响种质中基因表达水平的轻微降低相关，并且发生在Col-0种质中具有较高水平选择性剪接的基因中。总之，这些结果表明，尽管不能排除自适应场景，但可以在不调用 PAV 事件的情况下解释它们。
The sequencing of multiple genomes of the same plant species has revealed polymorphic gene and exon loss. Genes associated with disease resistance are overrepresented among those showing structural variations, suggesting an adaptive role for gene and exon presence–absence variation (PAV). To shed light on the possible functional relevance of polymorphic coding region loss and the mechanisms driving this process, we characterized genes that have lost entire exons or their whole coding regions in 17 fully sequenced Arabidopsis thaliana accessions. We found that although a significant enrichment in genes associated with certain functional categories is observed, PAV events are largely restricted to genes with signatures of reduced essentiality: PAV genes tend to be newer additions to the genome, tissue specific, and lowly expressed. In addition, PAV genes are located in regions of lower gene density and higher transposable element density. Partial coding region PAV events were associated with only a marginal reduction in gene expression level in the affected accession and occurred in genes with higher levels of alternative splicing in the Col-0 accession. Together, these results suggest that although adaptive scenarios cannot be ruled out, PAV events can be explained without invoking them.
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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：
3.5
作者：
Chen L;Tovar-Corona JM;Urrutia AO
通讯作者：
Urrutia AO
影响因子：
11.4
作者：
Makino, Takashi;Hokamp, Karsten;McLysaght, Aoife
通讯作者：
McLysaght, Aoife
影响因子：
4.9
作者：
Gos, Gesseca;Wright, Stephen I.
通讯作者：
Wright, Stephen I.
影响因子：
9.8
作者：
Johnston, Henry R.;Cutler, David J.
通讯作者：
Cutler, David J.