Abstract
Solanum sisymbriifolium (SSI), also known as “Litchi Tomato” or “Sticky Nightshade,” is an undomesticated and poorly researched plant related to potato and tomato. Unlike the latter species, SSI induces eggs of the cyst nematode, Globodera pallida, to hatch and migrate into its roots, but then arrests further nematode maturation. In order to provide researchers with a partial blueprint of its genetic make-up so that the mechanism of this response might be identified, we used single molecule real time (SMRT) sequencing to compile a high quality de novo transcriptome of 41,189 unigenes drawn from individually sequenced bud, root, stem, and leaf RNA populations. Functional annotation and BUSCO analysis showed that this transcriptome was surprisingly complete, even though it represented genes expressed at a single time point. By sequencing the 4 organ libraries separately, we found we could get a reliable snapshot of transcript distributions in each organ. A divergent site analysis of the merged transcriptome indicated that this species might have undergone a recent genome duplication and re-diploidization. Further analysis indicated that the plant then retained a disproportionate number of genes associated with photosynthesis and amino acid metabolism in comparison to genes with characteristics of R-proteins or involved in secondary metabolism. The former processes may have given SSI a bigger competitive advantage than the latter did. Further, SSI was found to be representative of some undomesticated plant species that appear to be recalcitrant to Agrobacterium-mediated infection. Transient expression assays in this weed using β-glucuronidase expression have proven highly variable and often failed. Systematic optimization experiments revealed that reducing wounding when bacteria were applied reduced variability. Transfection levels were also influenced by the number of leaves infected/plant, and by total leaves at the time of infection. This inverse relationship between leaf number and GUS expression resembled age-related resistance, but did not correlate with flowering, the accumulation of SA during bac infection, or with overt signs of senescence.