Identification of Virus Sequences in Potato Transcriptome Data
Transcriptome sequencing data often contain valuable information about viruses infecting the host.In order to analyze and validate the presence of virus sequences in potato transcriptome data,nine transcriptome sequencing data samples related to potato tuber development,disease resistance,and stress tolerance were collected.After filtering out reads originating from potato transcripts,the remaining unmapped reads were assembled and locally aligned against a virus database to obtain information on the types and quantities of virus sequences in these samples.The results revealed that reads originating from viruses were commonly present in all samples,accounting for 0.12%to 20.24%of the total reads.These reads were assembled into sequences representing 10 different plant viruses,including nine RNA viruses and one DNA virus.Among them,sequences derived from potato virus S(PVS)were the most abundant,with 28 nearly full-length sequences assembled.Further phylogenetic analysis indicated the coexistence of two strain types,PVSA and PVSO,in these samples.Additionally,reverse transcription-polymerase chain reaction(RT-PCR)was performed to detect six viruses including potato virus H(PVH),potato leafroll virus(PLRV),potato virus M(PVM),potato virus S(PVS),potato virus X(PVX),and potato virus Y(PVY)in the original transcriptome data samples.The RT-PCR validation results were generally consistent with the assembly results from the sequencing data.Overall,this study provides a high-throughput approach for analyzing the diversity and evolution of viruses in potatoes.
万方数据
维普
