Resolving the structural features of genomic islands: A machine learning approach
Resolving the structural features of genomic islands: A machine learning approach
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DOI：
10.1101/gr.7004508
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发表时间：
2008-02-01
期刊：
影响因子：
7
通讯作者：
Parkhill, Julian
中科院分区：
文献类型：
--
作者：
Vernikos, Georgios S.;Parkhill, Julian
大插入水平获得的DNA，包含功能相关的基因有限的系统发育分布通常被称为基因组岛（GI），和这些岛的结构定义，基于共同的特点，已经提出。尽管大量的移动的元素完全符合地理信息系统的定义，但对地理信息系统的结构共识存在几个问题：目前的GI定义是10年前提出的，当时只有12个完整的细菌基因组，大量GI偏离了该定义，并且假设完全/部分GI结构模型的计算机模拟预测使GI结构空间的采样偏向于“结构良好的”GI。在这项研究中，基因组区域的结构特征通过无假设的自下而上的搜索进行采样，并在机器学习方法中利用这些特征，目的是明确量化和建模每个特征对GI结构的贡献。在三个不同属的37个菌株和12个外群基因组之间进行基于全基因组的比较分析，对668个基因组区域进行采样并用于训练结构GI模型。数据显示，总体而言，地理标志从三个不同的属属于不同的，属特定的结构家庭。然而，通过研究不同属边界的GI结构，降低分类单元分辨率，提供了收敛于相当相似的GI结构的模型，进一步表明GI可以被视为具有核心和可变结构特征的移动的元素的超家族，而不是定义明确的家族。
Large inserts of horizontally acquired DNA that contain functionally related genes with limited phylogenetic distribution are often referred to as genomic islands (GIs), and structural definitions of these islands, based on common features, have been proposed. Although a large number of mobile elements fall well within the GI definition, there are several concerns about the structural consensus for GIs: The current GI definition was put forward 10 yr ago when only 12 complete bacterial genomes were available, a large number of GIs deviate from that definition, and in silico predictions assuming a full/partial GI structural model bias the sampling of the GI structural space toward "well-structured" GIs. In this study, the structural features of genomic regions are sampled by a hypothesis-free, bottom-up search, and these are exploited in a machine learning approach with the aim of explicitly quantifying and modeling the contribution of each feature to the GI structure. Performing a whole-genome-based comparative analysis between 37 strains of three different genera and 12 outgroup genomes, 668 genomic regions were sampled and used to train structural GI models. The data show that, overall, GIs from the three different genera fall into distinct, genus-specific structural families. However, decreasing the taxa resolution, by studying GI structures across different genus boundaries, provides models that converge on a fairly similar GI structure, further suggesting that GIs can be seen as a superfamily of mobile elements, with core and variable structural features, rather than a well-defined family.