Chromosome-Level Genome Assembly of <i>Protosalanx chinensis</i> and Response to Air Exposure Stress
<i>Protosalanx chinensis</i> is a suitable particular species for genetic studies on nearly scaleless skin, transparency and high sensitivity to hypoxia stress. Here, we generated a high-quality chromosome-level de novo assembly of <i>P. chinensis</i>. The final de novo assem...
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MDPI AG
2023-09-01
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| Series: | Biology |
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| author | Yanfeng Zhou Xizhao Zhang Xuemei Tang Yifan Zhou Yuting Ding Hong Liu |
| author_facet | Yanfeng Zhou Xizhao Zhang Xuemei Tang Yifan Zhou Yuting Ding Hong Liu |
| author_sort | Yanfeng Zhou |
| collection | DOAJ |
| description | <i>Protosalanx chinensis</i> is a suitable particular species for genetic studies on nearly scaleless skin, transparency and high sensitivity to hypoxia stress. Here, we generated a high-quality chromosome-level de novo assembly of <i>P. chinensis</i>. The final de novo assembly yielded 379.47 Mb with 28 pseudo-chromosomes and a scaffold N50 length of 14.52 Mb. In total, 21,074 protein-coding genes were predicted. <i>P. chinensis</i>, <i>Esox lucius</i> and <i>Hypomesus transpacificus</i> had formed a clade, which diverged about 115.5 million years ago. In the air exposure stress experiment, we found that some genes play an essential role during <i>P. chinensis</i> hypoxia, such as <i>bhlh</i>, <i>Cry1</i>, <i>Clock</i>, <i>Arntl</i> and <i>Rorb</i> in the circadian rhythm pathway. These genomic data offer a crucial foundation for <i>P. chinensis</i> ecology and adaptation studies, as well as a deeper understanding of the response to air exposure stress. |
| first_indexed | 2024-03-10T23:01:35Z |
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| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-10T23:01:35Z |
| publishDate | 2023-09-01 |
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| spelling | doaj.art-95022b65474f464c877cc794ac9e4cb22023-11-19T09:39:19ZengMDPI AGBiology2079-77372023-09-01129126610.3390/biology12091266Chromosome-Level Genome Assembly of <i>Protosalanx chinensis</i> and Response to Air Exposure StressYanfeng Zhou0Xizhao Zhang1Xuemei Tang2Yifan Zhou3Yuting Ding4Hong Liu5College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, ChinaKey Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, ChinaWuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, ChinaWuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, ChinaWuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, ChinaCollege of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China<i>Protosalanx chinensis</i> is a suitable particular species for genetic studies on nearly scaleless skin, transparency and high sensitivity to hypoxia stress. Here, we generated a high-quality chromosome-level de novo assembly of <i>P. chinensis</i>. The final de novo assembly yielded 379.47 Mb with 28 pseudo-chromosomes and a scaffold N50 length of 14.52 Mb. In total, 21,074 protein-coding genes were predicted. <i>P. chinensis</i>, <i>Esox lucius</i> and <i>Hypomesus transpacificus</i> had formed a clade, which diverged about 115.5 million years ago. In the air exposure stress experiment, we found that some genes play an essential role during <i>P. chinensis</i> hypoxia, such as <i>bhlh</i>, <i>Cry1</i>, <i>Clock</i>, <i>Arntl</i> and <i>Rorb</i> in the circadian rhythm pathway. These genomic data offer a crucial foundation for <i>P. chinensis</i> ecology and adaptation studies, as well as a deeper understanding of the response to air exposure stress.https://www.mdpi.com/2079-7737/12/9/1266<i>Protosalanx chinensis</i>chromosome-level genomeair exposure stress |
| spellingShingle | Yanfeng Zhou Xizhao Zhang Xuemei Tang Yifan Zhou Yuting Ding Hong Liu Chromosome-Level Genome Assembly of <i>Protosalanx chinensis</i> and Response to Air Exposure Stress Biology <i>Protosalanx chinensis</i> chromosome-level genome air exposure stress |
| title | Chromosome-Level Genome Assembly of <i>Protosalanx chinensis</i> and Response to Air Exposure Stress |
| title_full | Chromosome-Level Genome Assembly of <i>Protosalanx chinensis</i> and Response to Air Exposure Stress |
| title_fullStr | Chromosome-Level Genome Assembly of <i>Protosalanx chinensis</i> and Response to Air Exposure Stress |
| title_full_unstemmed | Chromosome-Level Genome Assembly of <i>Protosalanx chinensis</i> and Response to Air Exposure Stress |
| title_short | Chromosome-Level Genome Assembly of <i>Protosalanx chinensis</i> and Response to Air Exposure Stress |
| title_sort | chromosome level genome assembly of i protosalanx chinensis i and response to air exposure stress |
| topic | <i>Protosalanx chinensis</i> chromosome-level genome air exposure stress |
| url | https://www.mdpi.com/2079-7737/12/9/1266 |
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