Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies

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 number of transcript sequences 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 a good identification efficiency for three different LC-MS/MS proteomics experiments, though a seed proteome showed considerable variability in the identification of peptides based on seed protein sequence inclusion. If a proteomics experiment emphasizes a particular tissue, an RNA-Seq experiment incorporating that same tissue is more likely to support a database search identification of that proteome.

Automated summary

Proteomics has been more valuable in model organisms with genome sequence annotations than in nonmodel organisms lacking such annotations. This study aimed to establish a protein sequence set for the nonmodel organism chia using RNA-Seq experiments. The results showed that assembling RNA-Seq datasets for chia resulted in high completeness of transcript sequences, though the number of sequences and genes varied. After six-frame translation, orthologs were detected among other species within the same taxonomic order.