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Title: Discovery of a new genotype of Squash mosaic virus through deep sequencing of small RNAs and development of a qRT-PCR for broad spectrum detection

Author
item Li, Rugang
item GAO, SHAN - Boyce Thompson Institute
item BERENDSEN, SVEN - Rijk Zwaan Breeding Bv
item FEI, ZHANGJUN - Boyce Thompson Institute
item Ling, Kai-Shu

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 5/12/2014
Publication Date: 11/1/2014
Citation: Li, R., Gao, S., Berendsen, S., Fei, Z., Ling, K. 2014. Discovery of a new genotype of Squash mosaic virus through deep sequencing of small RNAs and development of a qRT-PCR for broad spectrum detection. Meeting Abstract. 104(S3):68.

Interpretive Summary:

Technical Abstract: Squash mosaic virus (SqMV), a seed-borne virus belonging to the genus Commovirus in the family Comoviridae, could cause a serious yield loss on cucurbit crops worldwide. SqMV has a bipartite single-stranded ribonucleic acid (RNA) genome (RNA-1 and RNA-2) encapsidated separately with two capsid proteins. Both RNA molecules contain a genome-linked viral protein (Vpg) and a poly (A) tail. At present, two serotypes (genotypes) of SqMV with only 87% sequence identity between them are recognized and a qRT-PCR has been developed to detect SqMV isolates belonging to both genotypes. However, a novel SqMV isolate collected on squash in 2010 in Spain was not detectable by this qRT-PCR, which prompted us to characterize its genome sequence. The genome sequences of both RNA molecules were obtained using small RNA deep sequencing and assembly technology and validated with Sanger sequencing of RT-PCR products. Both RNA genomes generated approximately 87% sequence identity to isolates in two known genotypes, suggesting the need to create a third genotype for SqMV. To improve primer and probe design for broad spectrum detection in qRT-PCR to all known SqMV genotypes, a conserved sequence in the 3’-terminal region of RNA-2 was identified through a multiple sequence alignment. This new qRT-PCR was shown to allow sensitive and reliable detection of various SqMV isolates in seed and plant tissues.