Comparative Core-Genomic and Pan-Genomic Analysis

The comparative core-genomic and pan-genomic analysis was conducted to investigate the genetic characteristics among different groups. Increased and decreased core-gene families were extracted and annotated by the KEGG database (database resolution through Python 3.8, based on public information from the KEGG database).Two different classification methods counted results of “Gene function” and “Pathway” and shown in a bar chart. Based on gene data above, Relative Enrichment Ratio (RER) was introduced to describe the correlation between gene enrichment and pathway (Xu and Yuan, 2022 (link)). The RER was calculated using the formula: RER = (number of genes annotated in this pathway)/(total number of genes involved in this pathway) and shown in a line chart; the RER results were screened by 0.1 and 0.2 as the threshold (maximum number of peaks can be retained), and the pathway corresponding to each peak was extracted. All figures were made by GraphPad prism 9.0, R packages, and Adobe Illustrator CS6.

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Yuan C., An T., Li X., Zou J., Lin Z., Gu J., Hu R, & Fang Z. (2024). Genomic analysis of Ralstonia pickettii reveals the genetic features for potential pathogenicity and adaptive evolution in drinking water. Frontiers in Microbiology, 14, 1272636.

Publication 2023

prism 9.0 Illustrator CS6

Corresponding Organization : Tianjin Medical University

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Variable analysis

independent variables

Not explicitly mentioned

dependent variables

Increased and decreased core-gene families
Relative Enrichment Ratio (RER)

control variables

Not explicitly mentioned

controls

The RER was calculated using the formula: RER = (number of genes annotated in this pathway)/(total number of genes involved in this pathway) and shown in a line chart; the RER results were screened by 0.1 and 0.2 as the threshold (maximum number of peaks can be retained), and the pathway corresponding to each peak was extracted.

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