Common bean (Phaseolus vulgaris L.) is the most important grain legume for direct human consumption worldwide and represents a rich source of protein, vitamins, minerals, and fiber (Broughton et al., 2003). The recent sequencing of the common bean genome, together with the availability of genomic and transcriptomic data have provided useful information to common bean breeders that will help in the development of genotypes with desirable characteristics (Schmutz et al., 2014; Vlasova et al., 2016).

Endornaviruses are persistent viruses with a non-encapsidated RNA genome that ranges from 9.8 to 17.6 kb, infect plants, fungi, and oomycetes, are transmitted only via gametes, and do not cause apparent symptoms (Stielow et al., 2011; Fukuhara and Gibbs, 2012). Although endornaviruses have been reported in several economically important plant species, little is known about the effect they have on their hosts. One of the major obstacles to study their effect to the host is the lack of a transmission method. In plants, endornaviruses do not move from cell to cell and spread only during cell division.

Recently, Khankhum et al. (2015) reported that most common bean genotypes of Mesoamerican origin are double-infected with Phaseolus vulgaris endornavirus 1 (PvEV1) and Phaseolus endornavirus 2 (PvEV2); in contrast, genotypes of Andean origin are often endornavirus-free. Black Turtle Soup (BTS), a cultivar of Mesoamerican origin has been reported to be double-infected by these two endornaviruses (Okada et al., 2013). A BTS endornavirus-free selection (BTS−), obtained from an endornavirus-infected BTS (BTS+) seed lot has been reported by Okada et al. (2013). To establish the bases for future research on the role that endornaviruses play in the common bean plant, and the effect these viruses have on the host gene expression, we conducted RNAseq on two BTS lines: one endornavirus-infected and the other endornavirus-free.

Currently, there are no sources of gene annotation for any organism infected with endornaviruses. This information will be helpful in determining the nature of the symbiotic interaction between endornaviruses and their host; more specifically between Mesoamerican common bean and PvEV1 and PvEV2.

These data may help to identify relevant genes in common bean that are differentially expressed under endornavirus infections.

Differential expression analysis of RNAseq data revealed that a total of 132 genes were differentially expressed. In the endornavirus-infected line 84 genes were down-regulated while 48 genes up-regulated (Supplementary Tables 1, 2). Figures 1A,B shows a visual reference of the differentially expressed gene vs. samples heatmap and Pearson correlation heatmap. GO distribution data on up-regulated and down-regulated genes is provided as excel files in Data Sheets 1 and 2 respectively in Supplementary Material. Gene ontology distribution show that oxidation-reduction processes were the main process associated with endornavirus infection. Reduction–oxidation (redox) changes have been reported to be associated with plant response to pathogen infection (Frederickson Matika and Loake, 2014), environmental stresses, development, and acclimation (Dietz, 2014; Dietz et al., 2016; Carmody et al., 2016). Data Sheets 3–5 contain excel files with expression levels, p-values, and FPKM (fragments per kilobase of transcript per million mapped reads) values respectively for all genes of the virus-infected and virus-free plants.

RV: conceived the idea and selected the original endornavirus-free BTS plant. SK: conducted the experiments; NS: performed the bioinformatics analysis of the data; JO: conducted the BTS crosses and contributed to the idea; RV, NS: wrote the manuscript. All authors contributed to the review of the manuscript.

This research was conducted with partial support from research grant No. US-4725-14 F from BARD, the United States—Israel Binational Agricultural Research and Development Fund.