Modification of the genome topology network and its application to the comparison of group B Streptococcus genomes

Xiao Deng,Xuechao Zhao,Liang Zhang,Jianping Jiang,Yuan Liang,Guoping Zhao,Yan Zhou

doi:10.1186/s12864-019-6234-8

Abstract

BackgroundThe genome topology network (GTN) is a new approach for studying the phylogenetics of bacterial genomes by analysing their gene order. The previous GTN tool gives a phylogenetic tree and calculate the different degrees (DD) of various adjacent gene families with complete genome data, but it is limited to the gene family level.ResultIn this study, we collected 51 published complete and draft group B Streptococcus (GBS) genomes from the NCBI database as the case study data. The phylogenetic tree obtained from the GTN method assigned the genomes into six main clades. Compared with single nucleotide polymorphism (SNP)-based method, the GTN method exhibited a higher resolution in two clades. The gene families located at unique node connections in these clades were associated with the clusters of orthologous groups (COG) functional categories of “[G] Carbohydrate transport and metabolism,”, “[L] Replication, recombination, and repair” and “[J] translation, ribosomal structure and biogenesis”. Thus, these genes were the major factors affecting the differentiation of these six clades in the phylogenetic tree obtained from the GTN.ConclusionThe modified GTN analyzes draft genomic data and exhibits greater functionality than the previous version. The gene family clustering algorithm embedded in the GTN tool is optimized by introducing the Markov cluster algorithm (MCL) tool to assign genes to functional gene families. A bootstrap test is performed to verify the credibility of the clades when allowing users to adjust the relationships of the clades accordingly. The GTN tool gives additional evolutionary information that is a useful complement to the SNP-based method. Information on the differences in the connections between a gene and its adjacent genes in species or clades is easily obtained. The modified GTN tool can be downloaded from https://github.com/0232/Genome_topology_network

Highlights

The genome topology network (GTN) is a new approach for studying the phylogenetics of bacterial genomes by analysing their gene order
The gene family clustering algorithm embedded in the GTN tool is optimized by introducing the Markov cluster algorithm (MCL) tool to assign genes to functional gene families
The GTN tool gives additional evolutionary information that is a useful complement to the single nucleotide polymorphism (SNP)-based method

Summary

Introduction

The genome topology network (GTN) is a new approach for studying the phylogenetics of bacterial genomes by analysing their gene order. Gene order can serve as evidence for evolutionary research The development of gene sequencing technology has led to increases in the amount of available genomic sequencing data and the number of evolutionary analysis tools. The majority of the methods for phylogenetic analysis are based on nucleotide sequence alignment and SNP analysis. In addition to SNP-based analysis, gene order conservation is an effective measure for the study of bacterial evolution [11]. The reconstruction of deep evolutionary histories by analysing molecular sequence data is always difficult, but differences in gene order allow the determination of genomic evolutionary events such as gene recombination, indels, and duplications [13]

Methods

Results

Discussion

Conclusion