CpG Distribution in HKU3-1: A Genomic Perspective on Bat SARS-like Coronavirus (2005)

This project analyzes the distribution of CpG sites in the intergenic regions of HKU3-1, a bat-derived coronavirus from 2005 that is closely related to SARS-CoV and SARS-CoV-2. Understanding the CpG dynamics of HKU3-1 provides insights into the evolutionary patterns of coronaviruses.Key findings include the identification of one intergenic region with a significantly high CpG count, which may indicate a functional or structural role. Most other intergenic regions show low or negligible CpG content, consistent with the widespread CpG depletion observed in coronaviruses. The analysis also reveals patterns of both enrichment and depletion in observed/expected CpG ratios, reflecting evolutionary pressures such as immune evasion and mutational biases.The dataset includes a tab-delimited file named HKU3_1_cpg_analysis.txt, which contains CpG counts and observed/expected ratios for each intergenic region. Visualizations are provided in the form of a bar chart showing CpG counts across regions and a line plot illustrating observed/expected ratios. Additional files include Python scripts used for extracting intergenic regions, calculating CpG metrics, and generating plots, as well as the input genome file DQ022305.gb and the extracted intergenic regions file HKU3_1_intergenic_regions.fasta.The analysis was performed in three main steps. First, intergenic regions were extracted from the HKU3-1 genome using Biopython. Next, CpG counts and observed/expected ratios were calculated for each region. Finally, visualizations were generated using Python libraries such as Pandas and Matplotlib.This work contributes to a better understanding of the genomic architecture of HKU3-1 and its evolutionary strategies. The findings align with broader trends observed in coronaviruses, highlighting shared mechanisms of CpG dynamics.Published on Figshare: 10.6084/m9.figshare.28705403<br><br>