A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila)
Abstract Aythya marila is one of the few species of Anatidae, and the only Aythya to live in the circumpolar. However, there is a relative lack of research on genetics of this species. In this study, we reported and assembled the first high-quality chromosome-level genome assembly of A. marila. This...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-05-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-023-02142-x |
| _version_ | 1797832219805351936 |
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| author | Shengyang Zhou Tian Xia Xiaodong Gao Tianshu Lyu Lidong Wang Xibao Wang Lupeng Shi Yuehuan Dong Honghai Zhang |
| author_facet | Shengyang Zhou Tian Xia Xiaodong Gao Tianshu Lyu Lidong Wang Xibao Wang Lupeng Shi Yuehuan Dong Honghai Zhang |
| author_sort | Shengyang Zhou |
| collection | DOAJ |
| description | Abstract Aythya marila is one of the few species of Anatidae, and the only Aythya to live in the circumpolar. However, there is a relative lack of research on genetics of this species. In this study, we reported and assembled the first high-quality chromosome-level genome assembly of A. marila. This genome was assembled using Nanopore long reads, and errors corrected using Illumina short reads, with a final genome size of 1.14 Gb, scaffold N50 of 85.44 Mb, and contig N50 of 32.46 Mb. 106 contigs were clustered and ordered onto 35 chromosomes based on Hi-C data, covering approximately 98.28% of the genome. BUSCO assessment showed that 97.0% of the highly conserved genes in aves_odb10 were present intact in the genome assembly. In addition, a total of 154.94 Mb of repetitive sequences were identified. 15,953 protein-coding genes were predicted in the genome, and 98.96% of genes were functionally annotated. This genome will be a valuable resource for future genetic diversity and genomics studies of A. marila. |
| first_indexed | 2024-04-09T14:05:23Z |
| format | Article |
| id | doaj.art-548ee6b065ab4991ba09015efd7705d6 |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-04-09T14:05:23Z |
| publishDate | 2023-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj.art-548ee6b065ab4991ba09015efd7705d62023-05-07T11:05:05ZengNature PortfolioScientific Data2052-44632023-05-011011910.1038/s41597-023-02142-xA high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila)Shengyang Zhou0Tian Xia1Xiaodong Gao2Tianshu Lyu3Lidong Wang4Xibao Wang5Lupeng Shi6Yuehuan Dong7Honghai Zhang8College of Life Sciences, Qufu Normal UniversityCollege of Life Sciences, Qufu Normal UniversityCollege of Life Sciences, Qufu Normal UniversityCollege of Life Sciences, Qufu Normal UniversityCollege of Life Sciences, Qufu Normal UniversityCollege of Life Sciences, Qufu Normal UniversityCollege of Life Sciences, Qufu Normal UniversityCollege of Life Sciences, Qufu Normal UniversityCollege of Life Sciences, Qufu Normal UniversityAbstract Aythya marila is one of the few species of Anatidae, and the only Aythya to live in the circumpolar. However, there is a relative lack of research on genetics of this species. In this study, we reported and assembled the first high-quality chromosome-level genome assembly of A. marila. This genome was assembled using Nanopore long reads, and errors corrected using Illumina short reads, with a final genome size of 1.14 Gb, scaffold N50 of 85.44 Mb, and contig N50 of 32.46 Mb. 106 contigs were clustered and ordered onto 35 chromosomes based on Hi-C data, covering approximately 98.28% of the genome. BUSCO assessment showed that 97.0% of the highly conserved genes in aves_odb10 were present intact in the genome assembly. In addition, a total of 154.94 Mb of repetitive sequences were identified. 15,953 protein-coding genes were predicted in the genome, and 98.96% of genes were functionally annotated. This genome will be a valuable resource for future genetic diversity and genomics studies of A. marila.https://doi.org/10.1038/s41597-023-02142-x |
| spellingShingle | Shengyang Zhou Tian Xia Xiaodong Gao Tianshu Lyu Lidong Wang Xibao Wang Lupeng Shi Yuehuan Dong Honghai Zhang A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila) Scientific Data |
| title | A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila) |
| title_full | A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila) |
| title_fullStr | A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila) |
| title_full_unstemmed | A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila) |
| title_short | A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila) |
| title_sort | high quality chromosomal level genome assembly of greater scaup aythya marila |
| url | https://doi.org/10.1038/s41597-023-02142-x |
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