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<p>Publicly accessible genomic databases facilitate high-throughput identification of simple sequence repeat (SSR) markers, vital for monitoring genetic variation in fungal pathogens. This study mined the 40.92&#xa0;Mb genome of <i>Diplodia bulgarica</i> isolate Sun2024a an emerging Botryosphaeriaceae species causing destructive cankers in apple (<i>Malus domestica</i>) using SSRMMD, identifying ~ 8,200 SSR loci across mono- to hexanucleotide motifs. Genome-wide primer design was accomplished using Primer3 software. In silico electronic PCR (ePCR) validation confirmed the amplification of 613 markers, 83.64% of which were polymorphic. Mononucleotide repeats were the most abundant motif type, followed by trinucleotide and dinucleotide repeats, indicating significant diversity in the sequence composition. SSR markers were mapped to 21 contigs, yielding 1,432 predicted amplicons with an average of 2.34 amplicons per marker, often indicating duplicated or paralogous sequences. These markers offer a foundational resource for diversity assessment, population structure, and epidemiological surveillance of <i>D. bulgarica</i>, supporting sustainable management in pome fruit orchards. Wet-lab validation will refine polymorphism estimates.</p>

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Genome-wide mining and in silico characterization of microsatellite markers in Diplodia bulgarica an apple canker causing pathogen

  • 期刊论文

  • 发表日期：

    2026年3月1日

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  • Tabia Fayaz,
  • Mohammad Najeeb Mughal,
  • Sajad Un Nabi,
  • Bilal A. Padder,
  • Tariq Rasool Rather,
  • Rouf Malik,
  • Shahid A. Paddar,
  • A. A. Khan,
  • Rouf Parray

摘要

Publicly accessible genomic databases facilitate high-throughput identification of simple sequence repeat (SSR) markers, vital for monitoring genetic variation in fungal pathogens. This study mined the 40.92 Mb genome of Diplodia bulgarica isolate Sun2024a an emerging Botryosphaeriaceae species causing destructive cankers in apple (Malus domestica) using SSRMMD, identifying ~ 8,200 SSR loci across mono- to hexanucleotide motifs. Genome-wide primer design was accomplished using Primer3 software. In silico electronic PCR (ePCR) validation confirmed the amplification of 613 markers, 83.64% of which were polymorphic. Mononucleotide repeats were the most abundant motif type, followed by trinucleotide and dinucleotide repeats, indicating significant diversity in the sequence composition. SSR markers were mapped to 21 contigs, yielding 1,432 predicted amplicons with an average of 2.34 amplicons per marker, often indicating duplicated or paralogous sequences. These markers offer a foundational resource for diversity assessment, population structure, and epidemiological surveillance of D. bulgarica, supporting sustainable management in pome fruit orchards. Wet-lab validation will refine polymorphism estimates.