Complete genomic analysis of tomato chlorosis virus isolates from Sichuan and Chongqing, China

Abstract

Tomato chlorosis virus (ToCV) has recently emerged as a significant threat to crop production in China. In this study, we collected tomato leaf samples displaying symptoms of interveinal chlorosis, curling, and yellowing from Sichuan Province and Chongqing City. Reverse transcription polymerase chain reaction (RT-PCR) analysis confirmed that 3 out of 10 samples from Sichuan and 9 out of 24 samples from Chongqing were infected with ToCV. Complete genomic sequences of ToCV were assembled from the cDNA of two infected leaves (SC744 and CQ630), which were deposited in GenBank under accession numbers CQ630: PQ153240 and PQ153241 and SC744: PQ261056 and PQ261057. Phylogenetic analysis indicated that ToCV isolates from the Sichuan Province and Chongqing City were closely related to the ToCV-BJ isolate. The sequence identity matrix shows that p22 has the highest variability at 94.3%–98.4%. p6 is the most conserved, with identities between 98% and 100%. In RNA2, p4 varies from 93.9% to 100%, while Hsp70 remains highly conserved at 97.9%–99%. This study provides the first report on the complete genomic sequences of ToCV from Sichuan Province and Chongqing City, enhancing our understanding of ToCV distribution and genetic diversity in China.