Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects
Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects
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DOI：
10.4056/sigs.3446951
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发表时间：
2013-01-01
影响因子：
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通讯作者：
Klenk, Hans-Peter
中科院分区：
文献类型：
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作者：
Goeker, Markus;Klenk, Hans-Peter
尽管基因组测序的成本稳步下降，但在大规模项目中，优先排序生物体仍然很重要。基于系统发育的选择对于识别那些基因组可能与已经测序的生物差异最大的生物是有意义的。在这里，我们描述了一种方法，该方法推断系统发育评分独立于哪一组生物之前已被定位，这是计算简单，易于在实践中应用。评分本身，以及数据的预处理和后处理，用两个现实世界的例子来说明，在这两个例子中，该方法已经应用于选择基因组测序的目标。这些项目包括JGI CSP细菌和古细菌基因组百科全书第一期，目标是1000种类型菌株，以及规模较小的玫瑰杆菌分支的系统基因组学。讨论了该方法的潜在工件，并将其与基于分类学分类的选择方法进行了比较。
Despite the steadily decreasing costs of genome sequencing, prioritizing organisms for sequencing remains important in large-scale projects. Phylogeny-based selection is of interest to identify those organisms whose genomes can be expected to differ most from those that have already been sequenced. Here, we describe a method that infers a phylogenetic scoring independent of which set of organisms has previously been targeted, which is computationally simple and easy to apply in practice. The scoring itself, as well as pre- and post-processing of the data, is illustrated using two real-world examples in which the method has already been applied for selecting targets for genome sequencing. These projects are the JGI CSP Genomic Encyclopedia of Bacteria and Archaea phase I, targeting 1,000 type strains, and, on a smaller-scale, the phylogenomics of the Roseobacter clade. Potential artifacts of the method are discussed and compared to a selection approach based on the taxonomic classification.