A high-quality chromosome-level genome assembly of Pacific whiteleg shrimp (Penaeus vannamei)
Abstract The Pacific whiteleg shrimp (Penaeus vannamei, synonym Lipopenaeus vannamei) is an important aquaculture species, and its breeding improvement relies heavily on high-quality genomic resources. Here, we sequenced the genome of the Pacific whiteleg shrimp using PacBio and Hi-C technologies, r...
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| Format: | Article |
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Nature Portfolio
2025-02-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04673-x |
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| author | Jian Liao Zhuoxin Lai Chuanmeng He Gaocong Li Zhongdian Dong Yusong Guo Zhongduo Wang |
| author_facet | Jian Liao Zhuoxin Lai Chuanmeng He Gaocong Li Zhongdian Dong Yusong Guo Zhongduo Wang |
| author_sort | Jian Liao |
| collection | DOAJ |
| description | Abstract The Pacific whiteleg shrimp (Penaeus vannamei, synonym Lipopenaeus vannamei) is an important aquaculture species, and its breeding improvement relies heavily on high-quality genomic resources. Here, we sequenced the genome of the Pacific whiteleg shrimp using PacBio and Hi-C technologies, resulting in a 1.7 Gb genome assembly with a Contig N50 of 57.65Kb and a Scaffold N50 of 605Kb.BUSCO analysis indicated that our genome assembly achieved a gene coverage of 84.6%, a figure considered high among crustacean reference genomes. In total, 907,237,377 bp of repetitive sequences (accounting for 50.48% of the assembled genome) and 22,923 protein-coding genes were identified. Utilizing Hi-C technology, we anchored 14,604 contigs onto 44 chromosomes, yielding a chromosome-level genome assembly with a contig N50 of 42,894,961 bp. In summary, our high-quality genome assembly provides valuable reference genomic resources for the improvement and breeding of elite cultivars of the Pacific whiteleg shrimp. |
| format | Article |
| id | doaj-art-0dc46d9acb1f46bf900c028bb6feec85 |
| institution | DOAJ |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
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| series | Scientific Data |
| spelling | doaj-art-0dc46d9acb1f46bf900c028bb6feec852025-08-20T03:03:57ZengNature PortfolioScientific Data2052-44632025-02-011211810.1038/s41597-025-04673-xA high-quality chromosome-level genome assembly of Pacific whiteleg shrimp (Penaeus vannamei)Jian Liao0Zhuoxin Lai1Chuanmeng He2Gaocong Li3Zhongdian Dong4Yusong Guo5Zhongduo Wang6Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean UniversityKey Laboratory of Aquaculture in South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean UniversityKey Laboratory of Aquaculture in South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean UniversityCollege of Electronics and Information Engineering, Guangdong Ocean UniversityKey Laboratory of Aquaculture in South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean UniversityKey Laboratory of Aquaculture in South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean UniversityKey Laboratory of Aquaculture in South China Sea for Aquatic Economic Animals of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean UniversityAbstract The Pacific whiteleg shrimp (Penaeus vannamei, synonym Lipopenaeus vannamei) is an important aquaculture species, and its breeding improvement relies heavily on high-quality genomic resources. Here, we sequenced the genome of the Pacific whiteleg shrimp using PacBio and Hi-C technologies, resulting in a 1.7 Gb genome assembly with a Contig N50 of 57.65Kb and a Scaffold N50 of 605Kb.BUSCO analysis indicated that our genome assembly achieved a gene coverage of 84.6%, a figure considered high among crustacean reference genomes. In total, 907,237,377 bp of repetitive sequences (accounting for 50.48% of the assembled genome) and 22,923 protein-coding genes were identified. Utilizing Hi-C technology, we anchored 14,604 contigs onto 44 chromosomes, yielding a chromosome-level genome assembly with a contig N50 of 42,894,961 bp. In summary, our high-quality genome assembly provides valuable reference genomic resources for the improvement and breeding of elite cultivars of the Pacific whiteleg shrimp.https://doi.org/10.1038/s41597-025-04673-x |
| spellingShingle | Jian Liao Zhuoxin Lai Chuanmeng He Gaocong Li Zhongdian Dong Yusong Guo Zhongduo Wang A high-quality chromosome-level genome assembly of Pacific whiteleg shrimp (Penaeus vannamei) Scientific Data |
| title | A high-quality chromosome-level genome assembly of Pacific whiteleg shrimp (Penaeus vannamei) |
| title_full | A high-quality chromosome-level genome assembly of Pacific whiteleg shrimp (Penaeus vannamei) |
| title_fullStr | A high-quality chromosome-level genome assembly of Pacific whiteleg shrimp (Penaeus vannamei) |
| title_full_unstemmed | A high-quality chromosome-level genome assembly of Pacific whiteleg shrimp (Penaeus vannamei) |
| title_short | A high-quality chromosome-level genome assembly of Pacific whiteleg shrimp (Penaeus vannamei) |
| title_sort | high quality chromosome level genome assembly of pacific whiteleg shrimp penaeus vannamei |
| url | https://doi.org/10.1038/s41597-025-04673-x |
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