Chromosome-Level Genome and Variation Map of Eri Silkworm <i>Samia cynthia ricini</i>
The eri silkworm <i>Samia cynthia ricini</i> (<i>S. ricini</i>) is an economically and scientifically significant lepidopteran species, though its genomic resources have remained limited. Here, we present a chromosome-level genome assembly for <i>S. ricini</i> gen...
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2025-06-01
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| author | Kunpeng Lu Jianghong Shen Wengong Huang Chengyu Zhan Zhengqing Li Shubo Liang Kerui Lai Qun Luo Minjin Han Xiaoling Tong Fangyin Dai |
| author_facet | Kunpeng Lu Jianghong Shen Wengong Huang Chengyu Zhan Zhengqing Li Shubo Liang Kerui Lai Qun Luo Minjin Han Xiaoling Tong Fangyin Dai |
| author_sort | Kunpeng Lu |
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| description | The eri silkworm <i>Samia cynthia ricini</i> (<i>S. ricini</i>) is an economically and scientifically significant lepidopteran species, though its genomic resources have remained limited. Here, we present a chromosome-level genome assembly for <i>S. ricini</i> generated through integrated long-read, short-read, and Hi-C sequencing data. The final 456.16 Mb assembly spans 14 chromosomes, exhibiting 98.5% BUSCO completeness and a 48.51% repetitive content. Functional annotation of the 15,729 protein-coding genes against five major databases (NR, SwissProt, Pfam, GO, and KEGG) revealed a maximum annotation rate of 92.71%, demonstrating high gene set quality. Comparative genomics with <i>B. mori</i> uncovered conserved syntenic blocks interspersed with chromosomal fusion/fission events and inversions. We further identified 4.27 million SNPs, 1.02 million InDels, and 53,367 SVs, establishing the first comprehensive variation map for this species. These genomic variations provide a foundation for marker-assisted breeding programs and trait association studies. All the genomic resources and interactive visualization tools were integrated into the SilkMeta database. This study establishes <i>S. ricini</i> as a pivotal resource for comparative lepidopteran genomics and accelerates molecular breeding programs for this agriculturally valuable insect. |
| format | Article |
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| institution | Kabale University |
| issn | 2079-7737 |
| language | English |
| publishDate | 2025-06-01 |
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| spelling | doaj-art-98d3fa24f33547e9b2f0eb08ecd8099e2025-08-20T03:32:32ZengMDPI AGBiology2079-77372025-06-0114669810.3390/biology14060698Chromosome-Level Genome and Variation Map of Eri Silkworm <i>Samia cynthia ricini</i>Kunpeng Lu0Jianghong Shen1Wengong Huang2Chengyu Zhan3Zhengqing Li4Shubo Liang5Kerui Lai6Qun Luo7Minjin Han8Xiaoling Tong9Fangyin Dai10State Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, ChinaState Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, ChinaGuangxi Key Laboratory of Silkworm Genetic Improvement and Efficient Breeding, Guangxi Research Academy of Sericultural Science, Nanning 530007, ChinaState Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, ChinaState Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, ChinaState Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, ChinaState Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, ChinaGuangxi Key Laboratory of Silkworm Genetic Improvement and Efficient Breeding, Guangxi Research Academy of Sericultural Science, Nanning 530007, ChinaState Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, ChinaState Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, ChinaState Key Laboratory of Resource Insects, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400715, ChinaThe eri silkworm <i>Samia cynthia ricini</i> (<i>S. ricini</i>) is an economically and scientifically significant lepidopteran species, though its genomic resources have remained limited. Here, we present a chromosome-level genome assembly for <i>S. ricini</i> generated through integrated long-read, short-read, and Hi-C sequencing data. The final 456.16 Mb assembly spans 14 chromosomes, exhibiting 98.5% BUSCO completeness and a 48.51% repetitive content. Functional annotation of the 15,729 protein-coding genes against five major databases (NR, SwissProt, Pfam, GO, and KEGG) revealed a maximum annotation rate of 92.71%, demonstrating high gene set quality. Comparative genomics with <i>B. mori</i> uncovered conserved syntenic blocks interspersed with chromosomal fusion/fission events and inversions. We further identified 4.27 million SNPs, 1.02 million InDels, and 53,367 SVs, establishing the first comprehensive variation map for this species. These genomic variations provide a foundation for marker-assisted breeding programs and trait association studies. All the genomic resources and interactive visualization tools were integrated into the SilkMeta database. This study establishes <i>S. ricini</i> as a pivotal resource for comparative lepidopteran genomics and accelerates molecular breeding programs for this agriculturally valuable insect.https://www.mdpi.com/2079-7737/14/6/698eri silkwormgenome assemblyannotationvariation mapdatabase |
| spellingShingle | Kunpeng Lu Jianghong Shen Wengong Huang Chengyu Zhan Zhengqing Li Shubo Liang Kerui Lai Qun Luo Minjin Han Xiaoling Tong Fangyin Dai Chromosome-Level Genome and Variation Map of Eri Silkworm <i>Samia cynthia ricini</i> Biology eri silkworm genome assembly annotation variation map database |
| title | Chromosome-Level Genome and Variation Map of Eri Silkworm <i>Samia cynthia ricini</i> |
| title_full | Chromosome-Level Genome and Variation Map of Eri Silkworm <i>Samia cynthia ricini</i> |
| title_fullStr | Chromosome-Level Genome and Variation Map of Eri Silkworm <i>Samia cynthia ricini</i> |
| title_full_unstemmed | Chromosome-Level Genome and Variation Map of Eri Silkworm <i>Samia cynthia ricini</i> |
| title_short | Chromosome-Level Genome and Variation Map of Eri Silkworm <i>Samia cynthia ricini</i> |
| title_sort | chromosome level genome and variation map of eri silkworm i samia cynthia ricini i |
| topic | eri silkworm genome assembly annotation variation map database |
| url | https://www.mdpi.com/2079-7737/14/6/698 |
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