plants Article Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies Ashwil Klein 1 , Lizex H. H. Husselmann 1 , Achmat Williams 1, Liam Bell 2 , Bret Cooper 3 , Brent Ragar 4 and David L. Tabb 1,5,6,* 1 Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa;
[email protected] (A.K.);
[email protected] (L.H.H.H.);
[email protected] (A.W.) 2 Centre for Proteomic and Genomic Research, Cape Town 7925, South Africa;
[email protected] 3 USDA Agricultural Research Service, Beltsville, MD 20705, USA;
[email protected] 4 Departments of Internal Medicine and Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02150, USA;
[email protected] 5 Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa 6 Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch 7602, South Africa * Correspondence:
[email protected]; Tel.: +27-82-431-2839 Abstract: While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence 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 nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the Citation: Klein, A.; Husselmann, number of transcript sequences and Trinity “genes” varied considerably among them.