ArticleBMC genomics2005
Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts.
Article in BMC genomics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed, 99 citations in OpenAlex.
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- A reverse genetics approach identifies novel mutants in light responses and anthocyanin metabolism in petunia.Physiology and molecular biology of plants : an international journal of functional plant biology · 2014Article
- Solanum torvum responses to the root-knot nematode Meloidogyne incognita.BMC genomics · 2013Article
- De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana.PloS one · 2013Article
- Transcriptome analysis of symptomatic and recovered leaves of geminivirus-infected pepper (Capsicum annuum).Virology journal · 2012Article
- Fractionation, stability, and isolate-specificity of QTL for resistance to Phytophthora infestans in cultivated tomato (Solanum lycopersicum).G3 (Bethesda, Md.) · 2012Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Solanaceae is a family of closely related species with diverse phenotypes that have been exploited for agronomic purposes. Previous studies involving a small number of genes suggested sequence conservation across the Solanaceae. The availability of large collections of Expressed Sequence Tags (ESTs) for the Solanaceae now provides the opportunity to assess sequence conservation and divergence on a genomic scale.
resultsAll available ESTs and Expressed Transcripts (ETs), 449,224 sequences for six Solanaceae species (potato, tomato, pepper, petunia, tobacco and Nicotiana benthamiana), were clustered and assembled into gene indices. Examination of gene ontologies revealed that the transcripts within the gene indices encode a similar suite of biological processes. Although the ESTs and ETs were derived from a variety of tissues, 55-81% of the sequences had significant similarity at the nucleotide level with sequences among the six species. Putative orthologs could be identified for 28-58% of the sequences. This high degree of sequence conservation was supported by expression profiling using heterologous hybridizations to potato cDNA arrays that showed similar expression patterns in mature leaves for all six solanaceous species. 16-19% of the transcripts within the six Solanaceae gene indices did not have matches among Solanaceae, Arabidopsis, rice or 21 other plant gene indices.
conclusionResults from this genome scale analysis confirmed a high level of sequence conservation at the nucleotide level of the coding sequence among Solanaceae. Additionally, the results indicated that part of the Solanaceae transcriptome is likely to be unique for each species.
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