Decoding the garlic transcriptome: unraveling the viral elements towards safeguarding the Philippine garlic industry

Garlic (Allium sativum L.) plays a vital role in the Philippines, offering essential culinary and medicinal benefits, as well as income opportunities for Filipino farmers. However, viruses pose a major economic threat, necessitating in-depth studies on garlic viruses for effective virus management, mass production of virus-free planting materials, and breeding for virus resistance. In this study, the transcriptome of the Batanes White (BW) garlic variety collected from the Ilocos Region was sequenced using Illumina NovaSeq 6000 to unravel the viruses infecting garlic in the Philippines. The RNA sequencing process generated approx 40 million reads, which were subjected to subtractive transcriptome assembly to identify non-garlic RNA sequences, such as viruses, within the BW transcriptome. Transcriptome analysis of BW variety revealed the complete and partial genomes of members within the garlic virus complex, including Garlic virus A, Garlic virus B, Garlic virus C, Garlic virus D, Onion yellow dwarf virus, Leek yellow stripe virus, and the newly characterized garlic yellow curl virus (GYCV), among others. Notably, the BW transcriptome showed the presence of multiple isolates belonging to a single viral species, indicating their intra-species diversity in infected garlic plants. The study also generated the complete genome of GYCV, a novel Betaflexiviridae virus first reported in China this year, with a length of 8,184 bp. To date, this newly discovered and emerging virus does not belong to any known genera of viruses. This is the first detection and complete genome sequence of GYCV in the Philippines and the second globally. Although additional transcriptomes from different garlic varieties and provinces are yet to be analyzed, the current study offers valuable insights into the diverse garlic viruses in the Philippines and their impact on garlic cultivation. These findings contribute to virus management and resistance breeding programs to safeguard the country's garlic industry.