Paul Sandip, Bhardwaj Archana, Bag Sumit K, Sokurenko Evgeni V, Chattopadhyay Sujay
Department of Microbiology, University of Washington, Seattle, WA 98195 USA.
CSIR - National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India.
Genomics. 2015 Dec;106(6):367-72. doi: 10.1016/j.ygeno.2015.10.001. Epub 2015 Oct 9.
A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing the pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen - a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for a species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars - Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study.
大量的基因组数据，尤其是来自单一物种多个分离株的数据，为微生物基因组学分析开辟了新的视野。分析微生物物种的泛基因组（即基因库总和）对于理解分子进化动态至关重要，其中毒力进化是主要关注点。在此，我们展示了PanCoreGen——一种用于微生物蛋白质编码基因泛基因组和核心基因组分析的独立应用程序。PanCoreGen克服了现有泛基因组分析工具的关键局限性，并为特定物种的泛基因组图谱开发了一种集成注释结构。它为注释草图基因组/重叠群以及检测注释基因组中的未知基因提供了重要的新功能。它还能在泛基因组中生成用户定义的特定群体数据集。有趣的是，通过分析一组沙门氏菌基因组实例，我们在两种人类限制性致病血清型——伤寒杆菌和甲型副伤寒杆菌中检测到水平转移基因适应性趋同的潜在痕迹。总体而言，PanCoreGen是微生物系统发育基因组学和病原基因组学研究的一种先进工具。
