Hybrid Whole-Genome Assembly Using Oxford Nanopore and Illumina Platforms for Functional Genomics of Streptococcus equi subsp. zooepidemicus MTCC3523 in Optimized Hyaluronic Acid Production

Toosi, Fatemeh Khatami and Naseroleslami, Maryam and Tabatabaei, Seyedeh Zoha (2025) Hybrid Whole-Genome Assembly Using Oxford Nanopore and Illumina Platforms for Functional Genomics of Streptococcus equi subsp. zooepidemicus MTCC3523 in Optimized Hyaluronic Acid Production. International Journal of Science and Research Archive, 14 (3). pp. 565-577. ISSN 2582-8185

Recent advancements in sequencing technologies have transformed bacterial genomics, enabling high-resolution genome characterization. Whole-genome sequencing (WGS) plays a crucial role in bacterial taxonomy, functional genomics, and evolutionary studies. Hybrid sequencing approaches that combine short-read and long-read technologies have significantly improved genome assembly and annotation, particularly for complex and repetitive genomes. This study compares Illumina and Oxford Nanopore sequencing in the WGS of Streptococcus equi subsp. zooepidemicus MTCC 3523. Illumina sequencing, known for its high accuracy, produces short reads, while Nanopore sequencing generates long reads but has higher error rates. By integrating both platforms, a hybrid assembly approach enhances sequencing accuracy, gene prediction, and structural variant detection. Hybrid assembly yielded a 2.1 Mb genome with 11 contigs, improving contiguity and completeness. Gene prediction and functional annotation identified 2,008 coding sequences, which were mapped to key metabolic pathways. Comparative genome analysis showed ~100% similarity with the reference strain S. equi subsp. zooepidemicus NCTC 7023, with six major genomic rearrangements detected. Additionally, this study provides insights into the genetic regulation of hyaluronic acid (HA) biosynthesis, a key biomedical and industrial product. Precise localization of the hyaluronidase gene offers new possibilities for genetic modifications to enhance HA yield. The findings emphasize the complementary strengths of Illumina and Nanopore sequencing in bacterial genomics. This research demonstrates the effectiveness of hybrid approaches in microbial genome assembly and has important implications for strain optimization in industrial HA production