Molecular Detection and Genome Characterization of Tomato Chlorosis Virus (ToCV) Using High-Throughput Sequencing

Abstract

Tomato chlorosis virus (ToCV) is an emerging whitefly-transmitted crinivirus that causes significant yield and quality losses in tomato production worldwide. The present study was undertaken to achieve rapid molecular detection and comprehensive genome characterization of ToCV using high-throughput sequencing (HTS). Symptomatic leaf samples showing interveinal chlorosis, yellowing, and reduced plant vigor were collected from Tomato fields and subjected to total RNA extraction. Libraries were prepared and sequenced using next-generation sequencing platforms, and the obtained raw reads were processed through quality filtering, de novo assembly, and reference-based mapping approaches. Bioinformatic analysis enabled the reconstruction of near-complete ToCV genome segments, including RNA1 and RNA2 components. Comparative sequence analysis revealed a high level of nucleotide identity with previously reported ToCV isolates, while also identifying distinct genetic variations and mutation hotspots in specific coding regions. Phylogenetic analysis placed the studied isolate within a well-supported clade of global ToCV isolates, suggesting possible regional adaptation and evolutionary divergence. The study further confirmed the presence of mixed viral populations in certain samples, indicating co-infection and genetic complexity in field conditions. The use of HTS provided high sensitivity for virus detection, including low-titer infections that may be missed by conventional RT-PCR assays. The findings highlight the effectiveness of genome-wide approaches for accurate virus diagnostics and epidemiological studies. This research contributes valuable genomic information on ToCV diversity and supports the development of improved diagnostic tools, resistance breeding programs, and integrated virus management strategies in tomato cultivation systems.