The cobweb of life revealed by genome-scale estimates of horizontal gene transfer.
The cobweb of life revealed by genome-scale estimates of horizontal gene transfer.
复制标题
DOI：
10.1371/journal.pbio.0030316
复制
发表时间：
2005-10
期刊：
影响因子：
9.8
通讯作者：
Kim J
中科院分区：
文献类型：
--
作者：
Ge F;Wang LS;Kim J
随着越来越多的基因组序列的可用性，越来越清楚的是，基因组经历遗传信息的水平转移和整合。然而，这种水平基因转移（HGT）在多大程度上影响了生物体的核心谱系历史仍然存在争议。基于对完整基因组序列的初步分析，HGT被认为是如此广泛，以至于它可能是“遗传学的本质”，并可能使系谱的树状形式受到质疑。另一方面，可能有偏见的估计HGT的程度和连贯的系统发育模式的研究结果表明，生命的系统发育树图是很好的代表。在这里，我们重新审视这个问题，通过评估HGT的程度之间的核心orthopathic基因使用一种新的统计方法的基础上统计比较树的拓扑结构。我们将该方法应用于40个微生物基因组中的集群的Orthopathy组数据库中的一组策划的297个Orthopathy基因簇，我们检测到显着的HGT事件中的33个297个集群在广泛的功能类别。对HGT事件位置的估计表明，在直向同源基因中，HGT的平均基因组特异性率较低（2.0%），这与其他HGT的定量结果基本一致。我们认为，HGT事件，即使在相对普遍的情况下，仍然保持了树状的历史完整的生物，就像蜘蛛网挂在树枝上。应用于40个微生物基因组中的297个直向同源基因簇的统计方法表明，种间基因转移率较低。因此，物种关系可以用树结构来建模。
With the availability of increasing amounts of genomic sequences, it is becoming clear that genomes experience horizontal transfer and incorporation of genetic information. However, to what extent such horizontal gene transfer (HGT) affects the core genealogical history of organisms remains controversial. Based on initial analyses of complete genomic sequences, HGT has been suggested to be so widespread that it might be the “essence of phylogeny” and might leave the treelike form of genealogy in doubt. On the other hand, possible biased estimation of HGT extent and the findings of coherent phylogenetic patterns indicate that phylogeny of life is well represented by tree graphs. Here, we reexamine this question by assessing the extent of HGT among core orthologous genes using a novel statistical method based on statistical comparisons of tree topology. We apply the method to 40 microbial genomes in the Clusters of Orthologous Groups database over a curated set of 297 orthologous gene clusters, and we detect significant HGT events in 33 out of 297 clusters over a wide range of functional categories. Estimates of positions of HGT events suggest a low mean genome-specific rate of HGT (2.0%) among the orthologous genes, which is in general agreement with other quantitative of HGT. We propose that HGT events, even when relatively common, still leave the treelike history of phylogenies intact, much like cobwebs hanging from tree branches. A stastical approach applied to 297 orthologous gene clusters in 40 microbial genomes suggests a low rate of interspecies gene transfer. Species relationships can therefore be modeled with a tree structure.
登录
查看更多内容
影响因子：
12.3
作者：
Brochier C;Forterre P;Gribaldo S
通讯作者：
Gribaldo S
影响因子：
10.7
作者：
Daubin, V;Ochman, H
通讯作者：
Ochman, H
影响因子：
3.9
作者：
Dutilh, BE;Huynen, MA;Snel, B
通讯作者：
Snel, B
影响因子：
3.5
作者：
Iyer, LM;Koonin, EV;Aravind, L
通讯作者：
Aravind, L
影响因子：
64.8
作者：
Huang, CY;Ayliffe, MA;Timmis, JN
通讯作者：
Timmis, JN