RNA-Sequencing Analysis of the Viral Community in Yellow Catfish (<i>Pelteobagrus fulvidraco</i>) in the Upper Reaches of the Yangtze River
Different viruses are abundant in aquatic ecosystems. There has been limited research on the viral communities in the upper reaches of the Yangtze River. Yellow catfish (<i>Pelteobagrus fulvidraco</i>), an important economic fish that is widely distributed in the upper reaches of the Yan...
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MDPI AG
2024-11-01
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| author | Wenzhi Liu Huiwu Tian Jie Ma Mingyang Xue Yong Zhou Mengmeng Li Jingwen Jiang Yuding Fan Mingdian Liu |
| author_facet | Wenzhi Liu Huiwu Tian Jie Ma Mingyang Xue Yong Zhou Mengmeng Li Jingwen Jiang Yuding Fan Mingdian Liu |
| author_sort | Wenzhi Liu |
| collection | DOAJ |
| description | Different viruses are abundant in aquatic ecosystems. There has been limited research on the viral communities in the upper reaches of the Yangtze River. Yellow catfish (<i>Pelteobagrus fulvidraco</i>), an important economic fish that is widely distributed in the upper reaches of the Yangtze River, was selected as the research object. Using RNA sequencing, we identified 11 viruses belonging to the <i>Adintoviridae</i>, <i>Tombusviridae</i>, <i>Caudovirales</i>, <i>Microviridae</i>, <i>Picornavirales</i>, and other bacteriophage families. The predominant viral families/order in Luzhou (LZ), Fuling (FL), and Wanzhou (WZ) were <i>Caudovirales</i>, <i>Adinoviridae,</i> and <i>Microviridae</i>, respectively. The virome from WZ had a unique community composition, with a high abundance of <i>Picornavirales</i> compared with LZ and FL. In LZ, the predominant double-stranded RNA virus family was <i>Siphoviridae</i>. Phylogenetic analyses showed that viruses presented high genetic diversity. Phylogenetically, Wenling pleuronectiformes picornavirus was close to the family <i>Caliciviridae</i>, which includes yellow catfish calicivirus (YcCV), responsible for the massive mortality of yellow catfish in 2020. This study provides insights into the viral community composition in yellow catfish in the upper reaches of the Yangtze River, revealing a diverse and unique river water virome and providing clues for future research on the origin of viral pathogens. |
| format | Article |
| id | doaj-art-7c61c829ec2a4e4da8f2952427de2a3d |
| institution | Kabale University |
| issn | 2076-2615 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
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| series | Animals |
| spelling | doaj-art-7c61c829ec2a4e4da8f2952427de2a3d2024-12-13T16:21:01ZengMDPI AGAnimals2076-26152024-11-011423338610.3390/ani14233386RNA-Sequencing Analysis of the Viral Community in Yellow Catfish (<i>Pelteobagrus fulvidraco</i>) in the Upper Reaches of the Yangtze RiverWenzhi Liu0Huiwu Tian1Jie Ma2Mingyang Xue3Yong Zhou4Mengmeng Li5Jingwen Jiang6Yuding Fan7Mingdian Liu8Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaYangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, ChinaDifferent viruses are abundant in aquatic ecosystems. There has been limited research on the viral communities in the upper reaches of the Yangtze River. Yellow catfish (<i>Pelteobagrus fulvidraco</i>), an important economic fish that is widely distributed in the upper reaches of the Yangtze River, was selected as the research object. Using RNA sequencing, we identified 11 viruses belonging to the <i>Adintoviridae</i>, <i>Tombusviridae</i>, <i>Caudovirales</i>, <i>Microviridae</i>, <i>Picornavirales</i>, and other bacteriophage families. The predominant viral families/order in Luzhou (LZ), Fuling (FL), and Wanzhou (WZ) were <i>Caudovirales</i>, <i>Adinoviridae,</i> and <i>Microviridae</i>, respectively. The virome from WZ had a unique community composition, with a high abundance of <i>Picornavirales</i> compared with LZ and FL. In LZ, the predominant double-stranded RNA virus family was <i>Siphoviridae</i>. Phylogenetic analyses showed that viruses presented high genetic diversity. Phylogenetically, Wenling pleuronectiformes picornavirus was close to the family <i>Caliciviridae</i>, which includes yellow catfish calicivirus (YcCV), responsible for the massive mortality of yellow catfish in 2020. This study provides insights into the viral community composition in yellow catfish in the upper reaches of the Yangtze River, revealing a diverse and unique river water virome and providing clues for future research on the origin of viral pathogens.https://www.mdpi.com/2076-2615/14/23/3386Yangtze Riveryellow catfish<i>Pelteobagrus fulvidraco</i>viral communityRNA sequencinggenetic diversity |
| spellingShingle | Wenzhi Liu Huiwu Tian Jie Ma Mingyang Xue Yong Zhou Mengmeng Li Jingwen Jiang Yuding Fan Mingdian Liu RNA-Sequencing Analysis of the Viral Community in Yellow Catfish (<i>Pelteobagrus fulvidraco</i>) in the Upper Reaches of the Yangtze River Animals Yangtze River yellow catfish <i>Pelteobagrus fulvidraco</i> viral community RNA sequencing genetic diversity |
| title | RNA-Sequencing Analysis of the Viral Community in Yellow Catfish (<i>Pelteobagrus fulvidraco</i>) in the Upper Reaches of the Yangtze River |
| title_full | RNA-Sequencing Analysis of the Viral Community in Yellow Catfish (<i>Pelteobagrus fulvidraco</i>) in the Upper Reaches of the Yangtze River |
| title_fullStr | RNA-Sequencing Analysis of the Viral Community in Yellow Catfish (<i>Pelteobagrus fulvidraco</i>) in the Upper Reaches of the Yangtze River |
| title_full_unstemmed | RNA-Sequencing Analysis of the Viral Community in Yellow Catfish (<i>Pelteobagrus fulvidraco</i>) in the Upper Reaches of the Yangtze River |
| title_short | RNA-Sequencing Analysis of the Viral Community in Yellow Catfish (<i>Pelteobagrus fulvidraco</i>) in the Upper Reaches of the Yangtze River |
| title_sort | rna sequencing analysis of the viral community in yellow catfish i pelteobagrus fulvidraco i in the upper reaches of the yangtze river |
| topic | Yangtze River yellow catfish <i>Pelteobagrus fulvidraco</i> viral community RNA sequencing genetic diversity |
| url | https://www.mdpi.com/2076-2615/14/23/3386 |
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