Complete Genome of Rice Grassy Stunt Tenuivirus in Thailand and Genetic Relationship Analysis
DOI:
https://doi.org/10.14456/thaidoa-agres.2022.10Keywords:
rice grassy stunt virus, virus genome, rice grassy stunt disease, RGSV2 strain, RNA-Seq technologyAbstract
Rice grassy stunt virus (RGSV) belongs to the genus Tenuivirus. The virus caused stunted and prolific tillering of rice plants, which significantly reduce the yield of the rice crop in many countries. Rice grassy stunt disease was first described in Thailand in 1966 however,a complete genome sequence of RGSV has not been available.This study examined an isolate of RGSV from an infected rice plant collected from Prachin Buri province (isolate PRI). Total RNA was extracted from diseased rice leaves and then used for cDNA library construction. Its genome sequence was read using RNA-Seq technology, and de novo assembly was applied to reconstruct the genome. The qualified 9,680,170 short reads were de novo assembled to reconstruct the complete genome sequence. Results showed that the genome of RGSV isolate PRI consisted of 25,118 nucleotides (nt) of six RNA segments. The lengthof RNAs were 9,760 nt (RNA1), 4,059 nt (RNA2), 3,125 nt (RNA3), 2,892 nt (RNA4), 2,692 nt (RNA5), and 2,590 nt (RNA6). The genome of isolate PRI was compared with that of RGSV isolate IRRI from the Philippines by multiple alignments. Result showed that the RGSV isolate PRI shared 96.6% identity with RGSV isolate IRRI. The Maximum likelihood phylogenetic analysis from the concatenated genome indicated that isolate PRI closely related to isolate FZ0403 from China. The phylogenetic tree reconstructed by using RNA1, RNA4, and RNA5 sequences revealed that isolate PRI closely related to isolate FZ0403.
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