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Background  Rhizomania is one of the most devastating diseases of sugar beet. It is caused by  Beet necrotic yellow vein virus  (BNYVV) transmitted by the obligate root-infecting parasite  Polymyxa betae .  Beta macrocarpa , a wild beet species widely used as a systemic host in the laboratory, can be rub-inoculated with BNYVV to avoid variation associated with the presence of the vector  P .  betae . To better understand disease and resistance between beets and BNYVV, we characterized the transcriptome of  B .  macrocarpa  and analyzed global gene expression of  B .  macrocarpa  in response to BNYVV infection using the Illumina sequencing platform.    Results  The overall  de novo  assembly of cDNA sequence data generated 75,917 unigenes, with an average length of 1054 bp. Based on a BLASTX search (E-value ≤ 10 −5 ) against the non-redundant (NR, NCBI) protein, Swiss-Prot, the Gene Ontology (GO), Clusters of Orthologous Groups of proteins (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, there were 39,372 unigenes annotated. In addition, 4,834 simple sequence repeats (SSRs) were also predicted, which could serve as a foundation for various applications in beet breeding. Furthermore, comparative analysis of the two transcriptomes revealed that 261 genes were differentially expressed in infected compared to control plants, including 128 up- and 133 down-regulated genes. GO analysis showed that the changes in the differently expressed genes were mainly enrichment in response to biotic stimulus and primary metabolic process.    Conclusion  Our results not only provide a rich genomic resource for beets, but also benefit research into the molecular mechanisms of beet- BNYV Vinteraction.

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Transcriptome Analysis of Beta macrocarpa and Identification of Differentially Expressed Transcripts in Response to Beet Necrotic Yellow Vein Virus Infection