Chromosome-level genome assembly of the sweet potato rot nematode Ditylenchus destructor
Abstract Ditylenchus destructor, commonly known as the potato rot nematode, is a significant plant-parasitic pathogen affecting over 120 plant species globally. Effective control measures for D. destructor are limited, underscoring the need a high-quality reference genome to understand its pathogeni...
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| Format: | Article |
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Nature Portfolio
2025-01-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-024-04293-x |
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| author | Yiwei Yang Ruirui Feng Bo Hong Yuchuan Fang Chen Liu Kui Wang Deliang Peng Yingmei Li Huan Peng Qing Chang |
| author_facet | Yiwei Yang Ruirui Feng Bo Hong Yuchuan Fang Chen Liu Kui Wang Deliang Peng Yingmei Li Huan Peng Qing Chang |
| author_sort | Yiwei Yang |
| collection | DOAJ |
| description | Abstract Ditylenchus destructor, commonly known as the potato rot nematode, is a significant plant-parasitic pathogen affecting over 120 plant species globally. Effective control measures for D. destructor are limited, underscoring the need a high-quality reference genome to understand its pathogenic mechanisms. Herein, we combined Illumina short reads, PacBio long reads, and Hi-C mapping technology to construct a chromosome-scale reference genome assembly for D. destructor. The genome assembly totals 133.86 Mb, with 129.51 Mb (96.74%) of sequences anchored onto 4 pseudo-chromosomes, achieving a scaffold N50 of 32.25 Mb. The assembled genome contains 28.14% repeat sequences and identifies 19,165 protein-coding genes, of which 18,444 (96.24%) are functionally annotated. The genome assembly demonstrates a high level of completeness, with 73.8% complete the nematoda-specifc Benchmarking Universal Single-Copy Orthologs (BUSCO) genes, significantly higher than that of other reported plant-parasitic nematode genomes. This high-quality reference genome will serve as a valuable genomic resource for future research aimed at understanding the pathogenesis of D. destructor and developing effective control strategies. |
| format | Article |
| id | doaj-art-3c83cf283dda474686a7dd32eb5de22a |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-3c83cf283dda474686a7dd32eb5de22a2025-02-02T12:08:15ZengNature PortfolioScientific Data2052-44632025-01-0112111010.1038/s41597-024-04293-xChromosome-level genome assembly of the sweet potato rot nematode Ditylenchus destructorYiwei Yang0Ruirui Feng1Bo Hong2Yuchuan Fang3Chen Liu4Kui Wang5Deliang Peng6Yingmei Li7Huan Peng8Qing Chang9Shaanxi Key Laboratory of Plant Nematology, Bio-Agriculture Institute of ShaanxiYulin Academy of Agricultural Sciences of Shaanxi ProvinceShaanxi Key Laboratory of Plant Nematology, Bio-Agriculture Institute of ShaanxiYulin Academy of Agricultural Sciences of Shaanxi ProvinceShaanxi Key Laboratory of Plant Nematology, Bio-Agriculture Institute of ShaanxiYulin Academy of Agricultural Sciences of Shaanxi ProvinceState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesShaanxi Key Laboratory of Plant Nematology, Bio-Agriculture Institute of ShaanxiState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesShaanxi Key Laboratory of Plant Nematology, Bio-Agriculture Institute of ShaanxiAbstract Ditylenchus destructor, commonly known as the potato rot nematode, is a significant plant-parasitic pathogen affecting over 120 plant species globally. Effective control measures for D. destructor are limited, underscoring the need a high-quality reference genome to understand its pathogenic mechanisms. Herein, we combined Illumina short reads, PacBio long reads, and Hi-C mapping technology to construct a chromosome-scale reference genome assembly for D. destructor. The genome assembly totals 133.86 Mb, with 129.51 Mb (96.74%) of sequences anchored onto 4 pseudo-chromosomes, achieving a scaffold N50 of 32.25 Mb. The assembled genome contains 28.14% repeat sequences and identifies 19,165 protein-coding genes, of which 18,444 (96.24%) are functionally annotated. The genome assembly demonstrates a high level of completeness, with 73.8% complete the nematoda-specifc Benchmarking Universal Single-Copy Orthologs (BUSCO) genes, significantly higher than that of other reported plant-parasitic nematode genomes. This high-quality reference genome will serve as a valuable genomic resource for future research aimed at understanding the pathogenesis of D. destructor and developing effective control strategies.https://doi.org/10.1038/s41597-024-04293-x |
| spellingShingle | Yiwei Yang Ruirui Feng Bo Hong Yuchuan Fang Chen Liu Kui Wang Deliang Peng Yingmei Li Huan Peng Qing Chang Chromosome-level genome assembly of the sweet potato rot nematode Ditylenchus destructor Scientific Data |
| title | Chromosome-level genome assembly of the sweet potato rot nematode Ditylenchus destructor |
| title_full | Chromosome-level genome assembly of the sweet potato rot nematode Ditylenchus destructor |
| title_fullStr | Chromosome-level genome assembly of the sweet potato rot nematode Ditylenchus destructor |
| title_full_unstemmed | Chromosome-level genome assembly of the sweet potato rot nematode Ditylenchus destructor |
| title_short | Chromosome-level genome assembly of the sweet potato rot nematode Ditylenchus destructor |
| title_sort | chromosome level genome assembly of the sweet potato rot nematode ditylenchus destructor |
| url | https://doi.org/10.1038/s41597-024-04293-x |
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