Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution
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. Mul...
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Frontiers Media S.A.
2025-06-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1537826/full |
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| author | Khandker Shahed Sk Injamamul Islam Papungkorn Sangsawad Won-Kyo Jung Patima Permpoonpattana Nguyen Vu Linh |
| author_facet | Khandker Shahed Sk Injamamul Islam Papungkorn Sangsawad Won-Kyo Jung Patima Permpoonpattana Nguyen Vu Linh |
| author_sort | Khandker Shahed |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-20cb27d4278447cbb0cd17cd2f043b25 |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj-art-20cb27d4278447cbb0cd17cd2f043b252025-08-20T03:31:23ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-06-011610.3389/fmicb.2025.15378261537826Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolutionKhandker Shahed0Sk Injamamul Islam1Papungkorn Sangsawad2Won-Kyo Jung3Patima Permpoonpattana4Nguyen Vu Linh5BioMac Lab, Dhaka, BangladeshBioMac Lab, Dhaka, BangladeshSchool of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, ThailandSchool of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, ThailandDepartment of Agricultural Science and Technology, Faculty of Innovative Agriculture, Fisheries and Food, Prince of Songkla University, Surat Thani Campus, Surat Thani, ThailandDepartment of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, ThailandHorizontal 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.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1537826/fullbenchmarkpathogensgenomealternatives to antibioticSNPs |
| spellingShingle | Khandker Shahed Sk Injamamul Islam Papungkorn Sangsawad Won-Kyo Jung Patima Permpoonpattana Nguyen Vu Linh Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution Frontiers in Microbiology benchmark pathogens genome alternatives to antibiotic SNPs |
| title | Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution |
| title_full | Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution |
| title_fullStr | Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution |
| title_full_unstemmed | Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution |
| title_short | Benchmarking pangenome dynamics and horizontal gene transfer in Mycobacterium marinum evolution |
| title_sort | benchmarking pangenome dynamics and horizontal gene transfer in mycobacterium marinum evolution |
| topic | benchmark pathogens genome alternatives to antibiotic SNPs |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1537826/full |
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