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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » National Germplasm Resources Laboratory » Research » Publications at this Location » Publication #314705
Title: Genome characterization and genetic diversity of Sweet potato symptomless virus 1: a mastrevirus with an unusual nonanucleotide

Author
item Li, Ruhui
item CAO, MENGJI - Southwest University
item LAN, PINGXIU - US Department Of Agriculture (USDA)
item ABAD, JORGE - US Department Of Agriculture (USDA)
item LI, FAN - Yunnan Agricultural University
item ZHOU, CHANGYONG - Southwest University

Submitted to: APS Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 2/25/2015
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Next generation sequencing of small interfering RNAs (siRNAs) revealed the presence of Sweet potato symptomless virus 1 (SPSMV-1), a recently described virus in the genus Mastrevirus of the family Geminiviridae, in both a diseased and a symptomless sweet potato plant. Its full-length genome of 2602 nucleotides (nt) was determined from PCR products using back-to-back primers. The genome organization of SPSMV-1 is typical of dicot-infecting mastreviruses, containing 5 open reading frames. The virus has an unusual nonanucleotide (TAAGATTCC) in its large intergenic region reported from only a few viruses in the genera Becurtovirus and Eragrovirus. Blast search showed that it had the highest nucleotide sequence identity (64.1%) with Chickpea chlorotic dwarf virus. Subgenomic sequences of 3 distinct sizes were also obtained from the two plants, and analysis showed they were defective DNAs. Analysis of a larger-than-genome sequence (2886 nt) revealed an insertion of a partial host gene of 287-nt in the small intergenic region (SIR), which is prone to recombination. Full-length SPSMV-1 genomes of 2599-2602 nt were also obtained from seven other sweet potato accessions from several countries. The nine isolates shared nucleotide sequence identities of 97-99%, indicating low genetic divergence among them. The distribution of siRNA size frequencies indicated that SPSMV-1 was likely subject to both transcriptional and post-transcriptional gene silencing.