Assessment of an organ-specific de novo transcriptome of the nematode trap-crop, Solanum sisymbriifolium

Abstract

18Solanum sisymbriifolium, also known as "Litchi Tomato" or "Sticky Nightshade," is an 19 undomesticated and poorly researched plant related to potato and tomato. Unlike the latter 20 species, S. sisymbriifolium induces eggs of the cyst nematode, Globodera pallida, to hatch and 21 migrate into the roots, but then arrests further maturation. In order to provide researchers with a 22 partial blueprint of its genetic make-up so that this response might be identified, we used single

Initial responses of the trap‐crop, Solanum sisymbriifolium, to Globodera pallida invasions

“…Despite these success stories, very few studies have been able to delve into the molecular basis of this resistance since so little is known about the genetics of the plant. In order to address this deficiency, we recently assembled a 4-organ transcriptome of a healthy SSI plant (Wixom et al, 2018b). In order to identify members of this set that change expression during nematode infection, we have now followed this with sequence analysis of transcripts present in G. pallida-infected and mock-infected roots.…”

“…SMRT sequencing of cDNA prepared from nematodeinfected SSI roots was performed by the National Center for Genome Resources (Santa Fe, NM) and subsequently processed as described in Wixom et al (2018b). The final sequences were then combined with the previously described SMRT sequenced transcriptome of SSI using CD-HIT-EST and reduced to a 90% identity as established in Wixom et al (2018b) for the final unigene assignment.…”

“…We recently carried out SMRT sequencing of cDNAs derived from four different organs of a hydroponically grown S. sisymbriifolium plant (Wixom et al, 2018b). This species has been shown to be naturally resistant to nematodes like Globodera pallida, but little is known about the nature of this trait (Scholte, 2000).…”

“…This set of 68,337 sequences consisted of transcripts produced by plants growing in Phytagel:FF cultures together with transcripts produced during nematode infection. These sequences were then combined with the previously established transcriptome (Wixom et al, 2018b) and subsequently reduced to a new, 5-organ data set consisting of 50,625 sequences at a CD-Hit-EST identify of 90% that included 9,716 sequences that had not been detected previously.…”