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G3 (Bethesda). 2018 Jul 2;8(7):2135-2143. doi: 10.1534/g3.118.200327.

Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium.

Author information

1
Department of Plant Sciences, University of Idaho, Moscow, Idaho 83844-2333.
2
Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, Idaho 83844-2329.
3
Department of Plant Sciences, University of Idaho, Moscow, Idaho 83844-2333 acaplan@uidaho.edu.

Abstract

Solanum sisymbriifolium, also known as "Litchi Tomato" or "Sticky Nightshade," is an undomesticated and poorly researched plant related to potato and tomato. Unlike the latter species, S. sisymbriifolium 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 S. sisymbriifolium a bigger competitive advantage than the latter did.

KEYWORDS:

R-genes; S. sisymbriifolium; SMRT; solanum; transcriptome

PMID:
29769290
PMCID:
PMC6027862
DOI:
10.1534/g3.118.200327
[Indexed for MEDLINE]
Free PMC Article

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