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Background <p>Plant-parasitic nematodes (PPNs) pose a major threat to global agricultural production, yet fundamental research on their biology remains limited. The origin and evolutionary trajectory of PPNs remain elusive, largely due to the scarcity of chromosome-level genomic data. Among them, migratory PPNs are considered a key transitional form between free-living and obligate parasitic lifestyles, as they exhibit both plant parasitism and fungal feeding behaviors.</p> Results <p>In this study, we assembled a chromosome-level genome of the sweet potato rot nematode <i>Ditylenchus destructor</i> and confirmed the presence of four chromosomes through Hi-C scaffolding and karyotype analysis. Comparative genomic analysis with two others migratory PPNs, <i>Bursaphelenchus xylophilus</i> and <i>Aphelenchoides besseyi</i>, revealed that the Nigon elements in <i>B. xylophilus</i> are largely conserved with those of the model organism <i>Caenorhabditis elegans</i>, while <i>D. destructor</i> and <i>A. besseyi</i> exhibit extensive Nigon element rearrangements. These rearrangements were strongly correlated with patterns of protein sequence collinearity. Moreover, transcriptomic profiling across five developmental stages of <i>D. destructor</i> identified numerous stage-specific candidate secreted proteins, including putative effectors, and transcription factors. Functional analysis via RNA interference demonstrated that many of these genes play important roles in either embryonic development or parasitism.</p> Conclusions <p>Together, our results provide valuable genomic and transcriptomic resources for studying PPNs, uncovering critical insights into their genome evolution and parasitism-related gene functions, and laying a crucial foundation for advancing the understanding of PPN biology and their impact on agricultural systems.</p>

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Developmental dynamic transcriptomics reveals multiple effectors and transcription factors critical for Ditylenchus destructor parasitism

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月18日

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  • Yangyang Chen,
  • Shurong Zhang,
  • Xueyu Wang,
  • Boyan Hu,
  • Dexin Bo,
  • Yucheng Liao,
  • Yali Zhang,
  • Noha Mohamed Ashry,
  • Yayi Zhou,
  • Donghai Peng,
  • Ming Sun,
  • Dadong Dai

摘要

Background

Plant-parasitic nematodes (PPNs) pose a major threat to global agricultural production, yet fundamental research on their biology remains limited. The origin and evolutionary trajectory of PPNs remain elusive, largely due to the scarcity of chromosome-level genomic data. Among them, migratory PPNs are considered a key transitional form between free-living and obligate parasitic lifestyles, as they exhibit both plant parasitism and fungal feeding behaviors.

Results

In this study, we assembled a chromosome-level genome of the sweet potato rot nematode Ditylenchus destructor and confirmed the presence of four chromosomes through Hi-C scaffolding and karyotype analysis. Comparative genomic analysis with two others migratory PPNs, Bursaphelenchus xylophilus and Aphelenchoides besseyi, revealed that the Nigon elements in B. xylophilus are largely conserved with those of the model organism Caenorhabditis elegans, while D. destructor and A. besseyi exhibit extensive Nigon element rearrangements. These rearrangements were strongly correlated with patterns of protein sequence collinearity. Moreover, transcriptomic profiling across five developmental stages of D. destructor identified numerous stage-specific candidate secreted proteins, including putative effectors, and transcription factors. Functional analysis via RNA interference demonstrated that many of these genes play important roles in either embryonic development or parasitism.

Conclusions

Together, our results provide valuable genomic and transcriptomic resources for studying PPNs, uncovering critical insights into their genome evolution and parasitism-related gene functions, and laying a crucial foundation for advancing the understanding of PPN biology and their impact on agricultural systems.