Proteomic identification and meta-analysis in Salvia hispanica RNA-Seq de novo assemblies
Klein, Ashwil | Husselmann, Lizex H.H. | Williams, Achmat | Bell, Liam | Cooper, Bret | Ragar, Brent | Tabb, David L.
While proteomics has demonstrated its value for model organisms and for those with mature genome annotations, proteomics has been of less value in non-model organisms that are unaccompanied by draft genome annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a non-model organism, in this case the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcriptomes with high BUSCO completeness, though the number of transcripts and Trinity 'genes' varied considerably among them. After six-frame translation, ProteinOrtho detected substantial numbers of orthologs among other species within the taxonomic order Lamiales. These protein sequence databases demonstrated good identification efficiency for three different LC-MS/MS proteomics experiments, though a seed proteome showed considerable variability in identification of peptides based on seed protein sequence inclusion. These results demonstrate that proteomics laboratories will particularly benefit from generating sequence databases from RNA-Seq studies that incorporate many tissues, particularly if the LC-MS/MS experiments emphasize one of the tissues included in the RNA-Seq experiment.
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