Gene Expression Atlas for Common Bean

Phaseolus vulgaris (common bean) comprises approximately 50% of the grain legumes consumed worldwide and is important as a primary source of dietary protein in developing countries.   We performed next generation sequencing (RNAseq) on 24 samples isolated from five tissues (seeds, pods, leaves, roots, and nodules) of Phaseolus vulgaris cv. Negro Jamapa inoculated with either an effective rhizobium, an ineffective rhizobium mutant strain (fix-), or provided nitrogen via fertilization.  Tissue samples were collected at various developmental timepoints.  Using bioinformatics we have been able to combine our RNAseq data and the recently released P. vulgaris gene predictions to examine gene expression patterns and have created a gene expression atlas for common bean.  We have identified genes uniquely expressed in each tissue and genes differentially expressed within and between tissues at important developmental time-points.  We have examined the processes of nodulation, symbiosis, de-novo purine biosynthesis, seed and pod development.   We also confirmed that different sources of nitrogen induce different suites of genes and these differences have a long-term impact on gene expression patterns.    Lastly, using sequences from known duplicated genes in soybean, we have identified the homologous sequence in P. vulgaris and examined expression patterns to identify genes in soybean that have undergone neo, loss, or sub-functionalization compared to the ‘diploid’ ancestral gene expression state.