Genome Characterization of a Novel Bisegmented Positive-Sense RNA Virus Infecting the Bean Flower Thrips (Megalurothrips usitatus) Reveals an Active Antiviral RNAi Response

Abstract

By combining next-generation sequencing (NGS), reverse transcription polymerase chain reaction (RT-PCR), and rapid amplification of cDNA ends (RACE) PCR, we sequenced from adult bean flower thrips (Megalurothrips usitatus) the near-complete genome of a previously undescribed virus (related to Anopheline-associated C virus), which we named “Megalurothrips usitatus associated virus 1” (MUaV1). The viral genome comprises two linear, single-stranded, positive-sense RNA segments, designated RNA1 (3658 nt) and RNA2 (2041 nt), which shared 35.75% and 23.74% nucleotide identity with Anopheline-associated C virus (YP_009011225.1) and chronic bee paralysis virus (ASM62179.1), respectively. According to phylogenetic analysis, MUaV1 shares the closest evolutionary relationship with Anopheline-associated C virus, followed by chronic bee paralysis virus. A clear predominance of 22 nt vsiRNAs, characteristic of Dicer-mediated siRNA processing in insects, was observed, demonstrating that MUaV1 is capable of infecting the bean flower thrips and activating its antiviral RNAi response. Our study provides the first characterization of this virus in the bean flower thrips, enhancing our understanding of the bean flower thrips virome.