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Editorial: Microbial comparative genomics and pangenomics: new tools, approaches and insights into gene and genome evolution
Open accessAbstract
The emergence of Next Generation Sequencing (NGS) technologies was the game changer during the first decade of the 21 st century that led to the development of a new sub-field of Genomics i.e., Pangenomics. The initial concept of Pangenome fulfilled the demand for minimum inclusion of the required number of genomes to achieve good confidence by covering the entire genes of a species (Tettelin et al., 2005). The entire spectrum of genes, gene order, gene content, and their structural variations could be explored to assess the species' phylogenetic relatedness. This gene-oriented branch of genomics categorizes genes into three groups based on their relatedness among various strains of a species. This includes core (shared among 99% of the strains), shell (10-99%), and, cloud (<10% of the strains) genes. The core genes are evolutionarily conserved, while shell and cloud genes constitute This study also confirmed a high genomic diversity present in this human pathogen in this country and showed the prevalence of mixed infections in Ningbo was higher than the ones reported in other regions of China.Looking ahead, the awesome ability of Artificial Intelligence in the recognition of patterns, and the anticipated dissemination of these methodologies to all areas of scientific knowledge combined with the advent of the first commercial generation of quantum computers at the turn of the decade and the corresponding leap in the computational power available to biologists anticipate a new major leap in Comparative Genomics and Pangenomics. The development of new methodologies combining these technological revolutions suggests that soon biologists will be able to directly simulate the phenotype of microbial strains and species from the observed genotypes, leading to the evolution of the current descriptive nature of Comparative Genomics and Pangenomics towards a new one more predictive. The future thus looks bright.
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“Comparative genomics is therefore important because it can resolve evolutionary divergence and strain-level functional variation that may be obscured by genus- or 16S rRNA-based classification, particularly in gut bacteria with high intra-taxon genomic diversity. 26”
From Comparative Genomic Insights into Pangenome Diversity and Functional Adaptation of Akkermansia and Faecalibacterium as Gut-Associated Next-Generation Probiotics: A Systematic Review (2026) · cites this paper as [26]
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Seki, K., & Nagano, Y. (2025) · Scientific Reports · doi:10.1038/s41598-025-29683-y · Cited by 5
Mukharjee, S. K., Hasan, M. F., & Sikdar, B. (2026) · BMC Genomics · doi:10.1186/s12864-026-13081-3 · Cited by 1
Naveed, M., Khan, S. M., Aziz, T., Saleem, A., Siddig, N. H., & Al‐Hoshani, N. (2026) · Current Genomics · doi:10.1016/j.curgen.2026.09.010 · Cited by 1
Arlan, L., Lestari, R. D., Israyusnita, F., Kotala, S., Adi, N. W., Sari, D. F., Hanifah, Z., Rudiansyah, R., Khasanah, F., Tukan, F. F. D. L., et al. (2026) · F1000Research · doi:10.12688/f1000research.186241.1
Ghayas, H., Ejaz, U., Taj, A., Yousuf, S., & Sohail, M. (2025) · Gene Reports · doi:10.1016/j.genrep.2025.102355
García‐Illarramendi, J. M. (2025) · Tesis Doctorals en Xarxa (Consorci de Serveis Universitaris de Catalunya)
Peng, D., Huang, T., & Kang, W. (2026) · Biology · doi:10.3390/biology15100751
Metadata
- Authors
- Verma, D., Satyanarayana, T., & Dias, P. J.
- Affiliations
- Babasaheb Bhimrao Ambedkar University (IN)
- Netaji Subhas University of Technology (IN)
- University of Lisbon (PT)
- Corresponding author
- Verma, Digvijay
- Satyanarayana, Tulasi
- Dias, Paulo Jorge
- Venue
- Frontiers in Genetics
- Publisher
- Frontiers Media SA
- Published
- 2024-10-24
- Volume
- 15
- Pages
- 1490645-1490645
- ISSN
- 1664-8021 (ISSN-L)
- PMC
- PMC11540761
- OpenAlex
- W4403745076
- Cited by
- 5
- References
- 8
- Citations by year
- 2026: 3 · 2025: 2
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- pangenomics, comparative genomics, microbial genomics, gene evolution, genome evolution, genomic diversity, co-infection, human pathogens, artificial intelligence in genomics, quantum computing
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