RNA-Sequencing Analysis of the Viral Community in Yellow Catfish (Pelteobagrus fulvidraco) 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 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.