ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Aquatic Microbiology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1537826
This article is part of the Research TopicAdvancements in Diversity and Drug Resistance Mechanisms in Mycobacterial DiseasesView all 7 articles
Benchmarking Pangenome Dynamics and Horizontal Gene Transfer in Mycobacterium marinum Evolution
Provisionally accepted
- 1BioMac Lab, Dhaka, Bangladesh
- 2Chiang Mai University, Chiang Mai, Thailand
- 3Prince of Songkla University, Songkhla, Thailand
- 4Jashore University of Science and Technology, Jashore, Bangladesh
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Horizontal gene transfer (HGT) is a key driver of microbial evolution, promoting genetic diversity and contributing to the emergence of antibiotic resistance. This study explores the pangenome dynamics and HGT in Mycobacterium marinum (M. marinum), a close relative of Mycobacterium tuberculosis. Multiple pangenome datasets were analyzed to quantify gene gain, loss, and pangenome openness, utilizing Panstripe and a Generalized Linear Model (GLM) framework to assess gene presence/absence across strains. Additionally, a comparative benchmarking analysis of gene ontology (GO) annotations were conducted using eggNOG and InterProScan to evaluate their functional annotation accuracy. Our findings demonstrated significant differences in gene gain and loss rates, suggesting variations in annotation accuracy and the presence of mobile genetic elements (MGE). Single nucleotide polymorphisms (SNPs) were also identified, highlighting the genetic variability that may impact strain-specific traits such as pathogenicity and antibiotic resistance. Pangenome of M. marinum was characterized as highly open, with substantial variability in gene content, reflecting ongoing genetic exchange and adaptability. Functional annotation benchmarking demonstrated that eggNOG and InterProScan provided complementary insights, with each tool excelling in distinct strengths of gene function identification. Overall, these findings highlight the complex interplay between HGT, pangenome evolution, and antibiotic resistance in M. marinum, and the analytical framework presented here provides a robust approach for future studies aiming to inform therapeutic interventions and vaccine development.
Keywords: Benchmark, pathogens, Genome, Alternatives to antibiotic, snps
Received: 01 Dec 2024; Accepted: 20 May 2025.
Copyright: © 2025 Shahed, Montha, Permpoonpattana, Nguyen Vu and Islam. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Patima Permpoonpattana, Prince of Songkla University, Songkhla, 90110, Thailand
Linh Nguyen Vu, Chiang Mai University, Chiang Mai, 50200, Thailand
Sk Injamamul Islam, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
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