Quantifying homologous replacement of loci between haloarchaeal species.
Quantifying homologous replacement of loci between haloarchaeal species.
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DOI：
10.1093/gbe/evs098
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发表时间：
2012
影响因子：
3.3
通讯作者：
Papke RT
中科院分区：
文献类型：
--
作者：
Williams D;Gogarten JP;Papke RT
在体外研究的haloarchaeal属Haloferax已经证明了他们的能力，经常交换物种之间的DNA，而同源重组率估计从自然种群中的Halorubrum是足够高，以保持随机关联的等位基因之间的5个位点。为了量化基因转移和重组的共同持有（放松核心）的基因在类盐细菌（盐古菌）的进化过程中的影响，我们重建了代表所有主要群体的21个基因组的历史。使用一种新的算法和一个串联的核糖体蛋白基因组作为参考，我们创建了一个定向水平遗传转移（HGT）网络的当代和祖先的基因组。基因顺序分析表明，90%的可测HGT是通过直接同源替换，而不是非同源整合后丢失。网络分析揭示了HGT频率和核糖体蛋白进化距离之间的逆对数线性关系，保持在最深的分歧在盐细菌。我们使用这种数学关系来估计每个基因组中HGT传递的总转移和氨基酸替换，提供嵌合体的测量。对于每个基因组的松弛核心基因，我们保守地估计，它们11-20%的进化发生在其他盐古菌中。我们的研究结果是出乎意料的，因为转移和同源重组类盐细菌的成员之间的放松的核心基因破坏了基因的共同进化，然而，产生新的组合的分歧，但功能相关的基因可能会导致适应性表型不能通过累积突变和重组在一个单一的人口。
In vitro studies of the haloarchaeal genus Haloferax have demonstrated their ability to frequently exchange DNA between species, whereas rates of homologous recombination estimated from natural populations in the genus Halorubrum are high enough to maintain random association of alleles between five loci. To quantify the effects of gene transfer and recombination of commonly held (relaxed core) genes during the evolution of the class Halobacteria (haloarchaea), we reconstructed the history of 21 genomes representing all major groups. Using a novel algorithm and a concatenated ribosomal protein phylogeny as a reference, we created a directed horizontal genetic transfer (HGT) network of contemporary and ancestral genomes. Gene order analysis revealed that 90% of testable HGTs were by direct homologous replacement, rather than nonhomologous integration followed by a loss. Network analysis revealed an inverse log-linear relationship between HGT frequency and ribosomal protein evolutionary distance that is maintained across the deepest divergences in Halobacteria. We use this mathematical relationship to estimate the total transfers and amino acid substitutions delivered by HGTs in each genome, providing a measure of chimerism. For the relaxed core genes of each genome, we conservatively estimate that 11–20% of their evolution occurred in other haloarchaea. Our findings are unexpected, because the transfer and homologous recombination of relaxed core genes between members of the class Halobacteria disrupts the coevolution of genes; however, the generation of new combinations of divergent but functionally related genes may lead to adaptive phenotypes not available through cumulative mutations and recombination within a single population.
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影响因子：
3.7
作者：
Anderson I;Scheuner C;Göker M;Mavromatis K;Hooper SD;Porat I;Klenk HP;Ivanova N;Kyrpides N
通讯作者：
Kyrpides N
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
10.7
作者：
Cohen, Ofir;Gophna, Uri;Pupko, Tal
通讯作者：
Pupko, Tal
影响因子：
4.4
作者：
Aivaliotis, Michalis;Gevaert, Kris;Oesterhelt, Dieter
通讯作者：
Oesterhelt, Dieter
影响因子：
2.9
作者：
Bardavid, Rahel Elevi;Oren, Aharon
通讯作者：
Oren, Aharon