Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains.
Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains.
复制标题
通过去除混杂菌株获得高质量的枯草芽孢杆菌全基因组景观
DOI：
10.1093/bib/bbaa013
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发表时间：
2020
影响因子：
9.5
通讯作者：
Gao Feng
中科院分区：
文献类型：
--
作者：
Wu Hao;Wang Dan;Gao Feng
Pan-genome analysis is widely used to study the evolution and genetic diversity of species, particularly in bacteria. However, the impact of strain selection on the outcome of pan-genome analysis is poorly understood. Furthermore, a standard protocol to ensure high-quality pan-genome results is lacking. In this study, we carried out a series of pan-genome analyses of different strain sets ofBacillus subtilisto understand the impact of various strains on the performance and output quality of pan-genome analyses. Consequently, we found that the results obtained by pan-genome analyses ofB. subtiliscan be influenced by the inclusion of incorrectly classifiedBacillussubspecies strains, phylogenetically distinct strains, engineered genome-reduced strains, chimeric strains, strains with a large number of unique genes or a large proportion of pseudogenes, and multiple clonal strains. Since the presence of these confounding strains can seriously affect the quality and true landscape of the pan-genome, we should remove these deviations in the process of pan-genome analyses. Our study provides new insights into the removal of biases from confounding strains in pan-genome analyses at the beginning of data processing, which enables the achievement of a closer representation of a high-quality pan-genome landscape ofB. subtilisthat better reflects the performance and credibility of theB. subtilispan-genome. This procedure could be added as an important quality control step in pan-genome analyses for improving the efficiency of analyses, and ultimately contributing to a better understanding of genome function, evolution and genome-reduction strategies forB. subtilisin the future.
