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<p>This study investigates the genome-wide analysis of the Lumpy Skin Disease Virus (LSDV) isolate from recent outbreaks in Bangladesh. Next-generation sequencing (NGS) revealed high sequence conservation with minor mutations and structural variations. Phylogenetic and genomic diversity assessments revealed 99.9% concordance, and identified several point mutations and small indels that contribute to strain-specific variability. The study identifies 156 unique protein-coding sequences, with 71.8% classified as soluble and 28.2% as membrane-associated proteins, shedding light on functional diversity. Repeat analysis highlights a predominance of short tandem repeats (10–30&#xa0;bp) and low copy numbers (2–3), low entropy (0.39), and high thymine content (92%), suggesting selection for compact, stable elements that support genome integrity. These repeats are closely associated with genes, showing a 2:1 preference for alignment with gene orientation, indicating possible regulatory roles. Additionally, isochore patterns and conserved motifs within the repeats suggest functionality in transcription regulation or genome organization. GC content analysis revealed a bimodal distribution (peaks at 0.05% and 0.3%), indicating non-random placement of repeats. A strong correlation (r = 0.999) between repeat size and conservation score suggests that longer repeats may be essential for genome stability, while shorter repeats offer functional flexibility. These findings suggest the development of targeted LSDV control strategies.</p>

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Genome-wide characterization of lumpy skin disease virus isolate from Bangladesh

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月16日

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  • Md Bashir Uddin,
  • Ruhena Begum,
  • Jibon Kumar Paul,
  • Md. Mahfujur Rahman,
  • Ho-Seong Cho,
  • Md. Mukter Hossain

摘要

This study investigates the genome-wide analysis of the Lumpy Skin Disease Virus (LSDV) isolate from recent outbreaks in Bangladesh. Next-generation sequencing (NGS) revealed high sequence conservation with minor mutations and structural variations. Phylogenetic and genomic diversity assessments revealed 99.9% concordance, and identified several point mutations and small indels that contribute to strain-specific variability. The study identifies 156 unique protein-coding sequences, with 71.8% classified as soluble and 28.2% as membrane-associated proteins, shedding light on functional diversity. Repeat analysis highlights a predominance of short tandem repeats (10–30 bp) and low copy numbers (2–3), low entropy (0.39), and high thymine content (92%), suggesting selection for compact, stable elements that support genome integrity. These repeats are closely associated with genes, showing a 2:1 preference for alignment with gene orientation, indicating possible regulatory roles. Additionally, isochore patterns and conserved motifs within the repeats suggest functionality in transcription regulation or genome organization. GC content analysis revealed a bimodal distribution (peaks at 0.05% and 0.3%), indicating non-random placement of repeats. A strong correlation (r = 0.999) between repeat size and conservation score suggests that longer repeats may be essential for genome stability, while shorter repeats offer functional flexibility. These findings suggest the development of targeted LSDV control strategies.