Comparing Mycobacterium tuberculosis genomes using genome topology networks

BMC Genomics
Jianping JiangYan Zhou

Abstract

Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. In this work, we introduce a 'Genome Topology Network' (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of 'unfixed ortholog' has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the o...Continue Reading

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Citations

Jun 22, 2018·Tuberculosis and Respiratory Diseases·Sungweon RyooSeung Heon Lee
Mar 23, 2019·Anatomical Sciences Education·Jing-Bao Nie, David Gareth Jones
Aug 9, 2017·Microbial Genomics·Sabine E EckertGraham Speight

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Software Mentioned

PERL
CVTree
DAVID
orthoMCL
MEGA
BLAST

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