Population diversity of ORFan genes in Escherichia coli.
Population diversity of ORFan genes in Escherichia coli.
复制标题
大肠杆菌中Orfan基因的种群多样性。
DOI：
10.1093/gbe/evs081
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发表时间：
2012
影响因子：
3.3
通讯作者：
Stoltzfus A
中科院分区：
文献类型：
--
作者：
Yu G;Stoltzfus A
“ORFans”(没有已知亲属的可疑基因)的起源和进化仍不清楚。在这里，我们利用一个独特的机会来研究数千个ORFan的种群多样性，基于35个完整的大肠杆菌和志贺氏菌分离株基因组的收集(这是包括在大肠杆菌系统发育中的)。正如之前的研究所预期的那样，ORFan比非ORFan更短，AT更丰富。我们发现ORFan的分布通常非常狭窄：最常见的模式是只在一个基因组中发现一个ORFan。我们比较了ORFan基因与两个非ORFan基因对照组的种内群体多样性。群体变异模式表明，大多数ORFan不是人工产物，而是编码真正的基因，其蛋白质编码能力是保守的，反映了针对非同义突变的选择。然而，非同义核苷酸多样性高于非ORFAN，而同义多样性大致相同。特别是，与对照相比，在最高十分之一的多样性中，ORFan的数量超过了几倍，这可能是由于较弱的净化选择、正选择或正在腐烂的ORFan的一个亚类。
The origin and evolution of “ORFans” (suspected genes without known relatives) remain unclear. Here, we take advantage of a unique opportunity to examine the population diversity of thousands of ORFans, based on a collection of 35 complete genomes of isolates of Escherichia coli and Shigella (which is included phylogenetically within E. coli). As expected from previous studies, ORFans are shorter and AT-richer in sequence than non-ORFans. We find that ORFans often are very narrowly distributed: the most common pattern is for an ORFan to be found in only one genome. We compared within-species population diversity of ORFan genes with those of two control groups of non-ORFan genes. Patterns of population variation suggest that most ORFans are not artifacts, but encode real genes whose protein-coding capacity is conserved, reflecting selection against nonsynonymous mutations. Nevertheless, nonsynonymous nucleotide diversity is higher than for non-ORFans, whereas synonymous diversity is roughly the same. In particular, there is a several-fold excess of ORFans in the highest decile of diversity relative to controls, which might be due to weaker purifying selection, positive selection, or a subclass of ORFans that are decaying.
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影响因子：
14.9
作者：
Klimke W;Agarwala R;Badretdin A;Chetvernin S;Ciufo S;Fedorov B;Kiryutin B;O'Neill K;Resch W;Resenchuk S;Schafer S;Tolstoy I;Tatusova T
通讯作者：
Tatusova T
影响因子：
7
作者：
Knowles, David G.;McLysaght, Aoife
通讯作者：
McLysaght, Aoife
影响因子：
1.5
作者：
Long, MY;Deutsch, M;Zhang, JM
通讯作者：
Zhang, JM
影响因子：
3.9
作者：
Lawrence, JG;Ochman, H
通讯作者：
Ochman, H
影响因子：
12.3
作者：
Daubin V;Lerat E;Perrière G
通讯作者：
Perrière G