Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium
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 t...
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| Format: | Article |
| Language: | English |
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Oxford University Press
2018-07-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.118.200327 |
| _version_ | 1818657283785097216 |
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| author | Alexander Q. Wixom N. Carol Casavant Joseph C. Kuhl Fangming Xiao Louise-Marie Dandurand Allan B. Caplan |
| author_facet | Alexander Q. Wixom N. Carol Casavant Joseph C. Kuhl Fangming Xiao Louise-Marie Dandurand Allan B. Caplan |
| author_sort | Alexander Q. Wixom |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-17T03:39:01Z |
| format | Article |
| id | doaj.art-484d4c9d319347cb994da797472efc64 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-17T03:39:01Z |
| publishDate | 2018-07-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-484d4c9d319347cb994da797472efc642022-12-21T22:05:03ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362018-07-01872135214310.1534/g3.118.2003271Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifoliumAlexander Q. WixomN. Carol CasavantJoseph C. KuhlFangming XiaoLouise-Marie DandurandAllan B. CaplanSolanum 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.http://g3journal.org/lookup/doi/10.1534/g3.118.200327S. sisymbriifoliumsolanumtranscriptomeR-genesSMRT |
| spellingShingle | Alexander Q. Wixom N. Carol Casavant Joseph C. Kuhl Fangming Xiao Louise-Marie Dandurand Allan B. Caplan Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium G3: Genes, Genomes, Genetics S. sisymbriifolium solanum transcriptome R-genes SMRT |
| title | Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium |
| title_full | Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium |
| title_fullStr | Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium |
| title_full_unstemmed | Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium |
| title_short | Assessment of an Organ-Specific de Novo Transcriptome of the Nematode Trap-Crop, Solanum sisymbriifolium |
| title_sort | assessment of an organ specific de novo transcriptome of the nematode trap crop solanum sisymbriifolium |
| topic | S. sisymbriifolium solanum transcriptome R-genes SMRT |
| url | http://g3journal.org/lookup/doi/10.1534/g3.118.200327 |
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