Shahed Khandker, Islam Sk Injamamul, Sangsawad Papungkorn, Jung Won-Kyo, Permpoonpattana Patima, Linh Nguyen Vu
BioMac Lab, Dhaka, Bangladesh.
School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand.
Front Microbiol. 2025 Jun 17;16:1537826. doi: 10.3389/fmicb.2025.1537826. eCollection 2025.
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 (), a close relative of . 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 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 , and the analytical framework presented here provides a robust approach for future studies aiming to inform therapeutic interventions and vaccine development.
水平基因转移（HGT）是微生物进化的关键驱动因素，促进了遗传多样性并导致了抗生素耐药性的出现。本研究探讨了[]（[]的近亲）的泛基因组动态和HGT。分析了多个泛基因组数据集以量化基因的获得、丢失和泛基因组开放性，利用Panstripe和广义线性模型（GLM）框架评估菌株间基因的存在/缺失情况。此外，使用eggNOG和InterProScan对基因本体（GO）注释进行了比较基准分析，以评估其功能注释的准确性。我们的研究结果表明基因获得和丢失率存在显著差异，这表明注释准确性存在差异以及存在移动遗传元件（MGE）。还鉴定出了单核苷酸多态性（SNP），突出了可能影响致病性和抗生素耐药性等菌株特异性特征的遗传变异性。[]的泛基因组被表征为高度开放，基因含量存在很大变异性，反映了持续的基因交换和适应性。功能注释基准分析表明，eggNOG和InterProScan提供了互补的见解，每个工具在基因功能识别的不同优势方面表现出色。总体而言，这些发现突出了[]中HGT、泛基因组进化和抗生素耐药性之间的复杂相互作用，并且这里提出的分析框架为未来旨在为治疗干预和疫苗开发提供信息的研究提供了一种强大的方法。
