Abstract
BackgroundSince PGAP (pan-genome analysis pipeline) was published in 2012, it has been widely employed in bacterial genomics research. Though PGAP has integrated several modules for pan-genomics analysis, how to properly and effectively interpret and visualize the results data is still a challenge.ResultTo well present bacterial genomic characteristics, a novel cross-platform software was developed, named PGAP-X. Four kinds of data analysis modules were developed and integrated: whole genome sequences alignment, orthologous genes clustering, pan-genome profile analysis, and genetic variants analysis. The results from these analyses can be directly visualized in PGAP-X. The modules for data visualization in PGAP-X include: comparison of genome structure, gene distribution by conservation, pan-genome profile curve and variation on genic and genomic region. Meanwhile, result data produced by other programs with similar function can be imported to be further analyzed and visualized in PGAP-X. To test the performance of PGAP-X, we comprehensively analyzed 14 Streptococcus pneumonia strains and 14 Chlamydia trachomatis. The results show that, S. pneumonia strains have higher diversity on genome structure and gene contents than C. trachomatis strains. In addition, S. pneumonia strains might have suffered many evolutionary events, such genomic rearrangements, frequent horizontal gene transfer, homologous recombination, and other evolutionary process.ConclusionBriefly, PGAP-X directly presents the characteristics of bacterial genomic diversity with different visualization methods, which could help us to intuitively understand dynamics and evolution in bacterial genomes. The source code and the pre-complied executable programs are freely available from http://pgapx.ybzhao.com.
Highlights
Since Pan-genome analysis pipeline (PGAP) was published in 2012, it has been widely employed in bacterial genomics research
Briefly, PGAP-X directly presents the characteristics of bacterial genomic diversity with different visualization methods, which could help us to intuitively understand dynamics and evolution in bacterial genomes
We developed a genomeoriented software, PGAP-X, which will perform pangenome analysis from genome structure sight
Summary
Implementation of PGAP-X Based on C++/Qt, we developed a microbial comparative genomic analysis platform with a user-friendly graphic interface, which could be run on Windows, Linux and Mac OSX platform. To further investigate the diversity in gene content, pangenome profile analysis was performed by PGAP-X, and the result indicates that S. pneumonia owns an open pan-genome (shown as Fig. 5b), and C. trachomatis has relatively close pan-genome (shown as Additional file 9: Figure S6B). Genetic variation on both gene and genome scale Based on whole genome alignment result and orthologous gene clusters, genetic variation analysis was performed on both genome scale and gene scale for S. pneumonia and C. trachomatis. The genomic regions and genes with high substitution rate are presented for S. pneumonia (Fig. 6a and b) and C. trachomatis
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