Chromosome-level genome assembly of hawthorn spider mite, Amphitetranychus viennensis (Acari: Tetranychidae)
Abstract The hawthorn spider mite, Amphitetranychus viennensis, is a major pest of orchards and ornamentals in the Palaearctic region, with adaptability and acaricide resistance. The lack of high-quality genomic resources limits understanding of its detoxification mechanisms and the development of R...
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Nature Portfolio
2025-08-01
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| Online Access: | https://doi.org/10.1038/s41597-025-05683-5 |
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| author | Meifeng Ren Yuying Zhang Yifei Wang Yuanpeng Duan Yue Gao Zhongfang Liu Pengjiu Zhang Lifei He Renjun Fan Xuguo Zhou Jing Yang |
| author_facet | Meifeng Ren Yuying Zhang Yifei Wang Yuanpeng Duan Yue Gao Zhongfang Liu Pengjiu Zhang Lifei He Renjun Fan Xuguo Zhou Jing Yang |
| author_sort | Meifeng Ren |
| collection | DOAJ |
| description | Abstract The hawthorn spider mite, Amphitetranychus viennensis, is a major pest of orchards and ornamentals in the Palaearctic region, with adaptability and acaricide resistance. The lack of high-quality genomic resources limits understanding of its detoxification mechanisms and the development of RNAi-based pest control strategies. In this study, we utilized Illumina, Pacific Biosciences (PacBio), and Hi-C sequencing technologies to assemble a chromosome-level reference genome of A. viennensis. The assembled genome spans 141.96 Mb, with a contig N50 of 1.35 Mb. BUSCO analysis confirmed a high level of completeness, covering 91.6% of annotated genes. The assembly includes 50.97 Mb of repetitive sequences, representing 35.93% of the genome, and annotates 13,968 protein-coding genes. Using Hi-C sequencing, we anchored 47 contigs to three chromosomes, accounting for 97.27% of the estimated nuclear genome and achieving a contig N50 of 45.83 Mb. This high-quality genome assembly provides a valuable foundation for evolutionary and genomic research on spider mites, while also serving as a genetic resource to inform molecular control strategies and support sustainable pest management. |
| format | Article |
| id | doaj-art-50878e9abb924e6894288858bf3b9480 |
| institution | DOAJ |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-50878e9abb924e6894288858bf3b94802025-08-20T03:04:14ZengNature PortfolioScientific Data2052-44632025-08-011211710.1038/s41597-025-05683-5Chromosome-level genome assembly of hawthorn spider mite, Amphitetranychus viennensis (Acari: Tetranychidae)Meifeng Ren0Yuying Zhang1Yifei Wang2Yuanpeng Duan3Yue Gao4Zhongfang Liu5Pengjiu Zhang6Lifei He7Renjun Fan8Xuguo Zhou9Jing Yang10College of Plant Protection, Shanxi Agricultural University, Shanxi Key Laboratory of Integrated Pest Management in AgricultureCollege of Plant Protection, Shanxi Agricultural University, Shanxi Key Laboratory of Integrated Pest Management in AgricultureCollege of Plant Protection, Shanxi Agricultural University, Shanxi Key Laboratory of Integrated Pest Management in AgricultureCollege of Plant Protection, Shanxi Agricultural University, Shanxi Key Laboratory of Integrated Pest Management in AgricultureCollege of Plant Protection, Shanxi Agricultural University, Shanxi Key Laboratory of Integrated Pest Management in AgricultureCollege of Plant Protection, Shanxi Agricultural University, Shanxi Key Laboratory of Integrated Pest Management in AgricultureCollege of Plant Protection, Shanxi Agricultural University, Shanxi Key Laboratory of Integrated Pest Management in AgricultureCollege of Plant Protection, Shanxi Agricultural University, Shanxi Key Laboratory of Integrated Pest Management in AgricultureCollege of Plant Protection, Shanxi Agricultural University, Shanxi Key Laboratory of Integrated Pest Management in AgricultureDepartment of Entomology, School of Integrative Biology, College of Liberal Arts & Sciences, University of Illinois Urbana-ChampaignCollege of Plant Protection, Shanxi Agricultural University, Shanxi Key Laboratory of Integrated Pest Management in AgricultureAbstract The hawthorn spider mite, Amphitetranychus viennensis, is a major pest of orchards and ornamentals in the Palaearctic region, with adaptability and acaricide resistance. The lack of high-quality genomic resources limits understanding of its detoxification mechanisms and the development of RNAi-based pest control strategies. In this study, we utilized Illumina, Pacific Biosciences (PacBio), and Hi-C sequencing technologies to assemble a chromosome-level reference genome of A. viennensis. The assembled genome spans 141.96 Mb, with a contig N50 of 1.35 Mb. BUSCO analysis confirmed a high level of completeness, covering 91.6% of annotated genes. The assembly includes 50.97 Mb of repetitive sequences, representing 35.93% of the genome, and annotates 13,968 protein-coding genes. Using Hi-C sequencing, we anchored 47 contigs to three chromosomes, accounting for 97.27% of the estimated nuclear genome and achieving a contig N50 of 45.83 Mb. This high-quality genome assembly provides a valuable foundation for evolutionary and genomic research on spider mites, while also serving as a genetic resource to inform molecular control strategies and support sustainable pest management.https://doi.org/10.1038/s41597-025-05683-5 |
| spellingShingle | Meifeng Ren Yuying Zhang Yifei Wang Yuanpeng Duan Yue Gao Zhongfang Liu Pengjiu Zhang Lifei He Renjun Fan Xuguo Zhou Jing Yang Chromosome-level genome assembly of hawthorn spider mite, Amphitetranychus viennensis (Acari: Tetranychidae) Scientific Data |
| title | Chromosome-level genome assembly of hawthorn spider mite, Amphitetranychus viennensis (Acari: Tetranychidae) |
| title_full | Chromosome-level genome assembly of hawthorn spider mite, Amphitetranychus viennensis (Acari: Tetranychidae) |
| title_fullStr | Chromosome-level genome assembly of hawthorn spider mite, Amphitetranychus viennensis (Acari: Tetranychidae) |
| title_full_unstemmed | Chromosome-level genome assembly of hawthorn spider mite, Amphitetranychus viennensis (Acari: Tetranychidae) |
| title_short | Chromosome-level genome assembly of hawthorn spider mite, Amphitetranychus viennensis (Acari: Tetranychidae) |
| title_sort | chromosome level genome assembly of hawthorn spider mite amphitetranychus viennensis acari tetranychidae |
| url | https://doi.org/10.1038/s41597-025-05683-5 |
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