genome topology network

The genome topology network (GTN) is a computational tool that analyzes the phylogenetics of bacterial genomes based on their gene order. The authors modified the GTN tool to enhance functionality in this study and applied it to a case study of 51 group B Streptococcus (GBS) genomes.

Key points:

1. The modified GTN tool can now completely analyze and draft genomic data.

2. The gene family clustering algorithm in the GTN tool was optimized using the Markov cluster algorithm (MCL) to assign genes to functional gene families.

3. A bootstrap test was introduced to verify the credibility of the clades and allow users to adjust clade relationships accordingly.

4. The GTN method assigned the 51 GBS genomes into six main clades, exhibiting higher resolution in two clades than the single nucleotide polymorphism (SNP)-based method.

5. Gene families at unique node connections in these clades were associated with specific clusters of orthologous groups (COG) functional categories, indicating their role in clade differentiation.

Topic

Mapping;Phylogenetics;Gene and protein families;DNA polymorphism;Carbohydrates

Detail

  • Operation: Phylogenetic tree generation;Clustering;Phylogenetic tree distances calculation;Phylogenetic tree bootstrapping;Phylogenetic tree analysis (shape)

  • Software interface: Command-line interface

  • Language: Perl

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: National Key Research Program of China, Chinese Academy of Sciences, Science and Technology Commission of Shanghai Municipality.

  • Input: -

  • Output: -

  • Contact: Yan Zhou zhouy@fudan.edu.cn

  • Collection: -

  • Maturity: -

Publications

  • Modification of the genome topology network and its application to the comparison of group B Streptococcus genomes.
  • Deng X, et al. Modification of the genome topology network and its application to the comparison of group B Streptococcus genomes. Modification of the genome topology network and its application to the comparison of group B Streptococcus genomes. 2019; 20:886. doi: 10.1186/s12864-019-6234-8
  • https://doi.org/10.1186/S12864-019-6234-8
  • PMID: 31752672
  • PMC: PMC6868693

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