...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>BMC Genomics >A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus
【24h】

A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus

机译：细菌亚种分类的系统生物学方法：脓肿分枝杆菌的概念证明

获取原文
   

获取外文期刊封面封底 >>

       
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Background Mycobacterium abscessus is a rapidly growing mycobacterium that is often associated with human infections. The taxonomy of this species has undergone several revisions and is still being debated. In this study, we sequenced the genomes of 12?M. abscessus strains and used phylogenomic analysis to perform subspecies classification. Results A data mining approach was used to rank and select informative genes based on the relative entropy metric for the construction of a phylogenetic tree. The resulting tree topology was similar to that generated using the concatenation of five classical housekeeping genes: rpoB, hsp65, secA, recA and sodA. Additional support for the reliability of the subspecies classification came from the analysis of erm41 and ITS gene sequences, single nucleotide polymorphisms (SNPs)-based classification and strain clustering demonstrated by a variable number tandem repeat (VNTR) assay and a multilocus sequence analysis (MLSA). We subsequently found that the concatenation of a minimal set of three median-ranked genes: DNA polymerase III subunit alpha (polC), 4-hydroxy-2-ketovalerate aldolase (Hoa) and cell division protein FtsZ (ftsZ), is sufficient to recover the same tree topology. PCR assays designed specifically for these genes showed that all three genes could be amplified in the reference strain of M. abscessus ATCC 19977T. Conclusion This study provides proof of concept that whole-genome sequence-based data mining approach can provide confirmatory evidence of the phylogenetic informativeness of existing markers, as well as lead to the discovery of a more economical and informative set of markers that produces similar subspecies classification in M. abscessus. The systematic procedure used in this study to choose the informative minimal set of gene markers can potentially be applied to species or subspecies classification of other bacteria.
机译：背景脓肿分枝杆菌是一种快速生长的分枝杆菌，通常与人类感染有关。该物种的分类已经过几次修订，目前仍在争论中。在这项研究中，我们对12？M的基因组进行了测序。脓肿菌株，并用植物系统分析进行亚种分类。结果使用数据挖掘方法基于相对熵度量对信息基因进行排序和选择，以构建系统树。最终的树形拓扑类似于使用五个经典管家基因（rpoB，hsp65，secA，recA和sodA）串联生成的树形拓扑。对亚种分类的可靠性的其他支持来自erm41和ITS基因序列的分析，基于单核苷酸多态性（SNPs）的分类以及通过可变数目串联重复（VNTR）分析和多基因座序列分析（MLSA）证明的菌株聚类）。我们随后发现，三个中位基因的最小集合的串联：DNA聚合酶III亚基α（polC），4-羟基-2-酮戊醛酸醛缩酶（Hoa）和细胞分裂蛋白FtsZ（ftsZ），足以恢复相同的树形拓扑。专为这些基因设计的PCR分析表明，这三个基因都可以在脓毒杆菌ATCC 19977 T 的参考菌株中扩增。结论这项研究提供了概念证明，即基于全基因组序列的数据挖掘方法可以为现有标记的系统发育信息学提供验证性证据，并导致发现一组更经济，信息更丰富的标记，从而产生相似的亚种分类。在脓肿。本研究中用于选择信息量最少的基因标记的系统方法可以潜在地应用于其他细菌的物种或亚种分类。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号