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Background   Maize streak Reunion virus  (MSRV) is a member of the  Mastrevirus  genus in the family  Geminiviridae . Of the diverse and increasing number of mastrevirus species found so far, only  Wheat dwarf virus  and  Sweetpotato symptomless virus  1 have been discovered in China. Recently, a novel, unbiased approach based on deep sequencing of small interfering RNAs followed by  de novo  assembly of siRNA, has greatly offered opportunities for plant virus identification.    Methods  Samples collected from maize leaves was deep sequencing for virus identification. Subsequently, the assay of PCR, rolling circle amplification and Southern blot were used to confirm the presence of a mastrevirus.    Results   Maize streak Reunion virus  Yunnan isolate (MSRV-[China:Yunnan 06:2014], abbreviated to MSRV-YN) was identified from maize collected from Yunnan Province, China, by small RNA deep sequencing. The complete genome of this virus was ascertained as 2,880 nucleotides long by conventional sequencing. A phylogenetic analysis showed it shared 96.3 % nucleotide sequence identity with the isolate of  Maize streak Reunion virus  from La Reunion Island. To our knowledge, this is the first identification of MSRV in China. Analyses of the viral derived small interfering RNAs (vsiRNAs) profile showed that the most abundant MSRV-YN vsiRNAs were 21, 22 and 24 nt long and biased for A and G at their 5’ terminal residue. There was a slightly higher representation of MSRV-YN siRNAs derived from the virion-sense strand genome than the complementary-sense strand genome. Moreover, MSRV-YN vsiRNAs were not uniformly distributed along the genome, and hotspots were detected in the movement protein and coat protein-coding region.    Conclusions  A mastrevirus MSRV-YN collected in Yunnan Province, China, was identified by small RNA deep sequencing. This vsiRNAs profile derived from MSRV-YN was characterized, which might contribute to get an insight into the host RNA silencing defense induced by MSRV-YN, and provide guidelines on designing antiviral strategies using RNAi against MSRV-YN.    Electronic supplementary material  The online version of this article (doi:10.1186/s12985-015-0384-3) contains supplementary material, which is available to authorized users.

Identification and characterization of a maize-associated mastrevirus in China by deep sequencing small RNA populations