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

Ashwil Klein,Achmat Williams,David L Tabb,Brent Ragar,Liam Bell,Bret Cooper,Lizex H H Husselmann

doi:10.3390/plants10040765

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 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.

Highlights

Pseudocereals are broad-leaf nongrass species that produce fruits and/or seeds similar to conventional cereal crops with considerable nutritive value [1]
We demonstrate that protein identification based on assembled transcript sequence sets is feasible even in the absence of an annotated genome sequence, allowing the identification of tens of thousands of peptides from multiple plant tissues
Having produced two different assemblies for each of four RNA-Seq experiments in Salvia hispanica, we were surprised at the variation in the numbers of transcript sequences among these products (Table 2)

Summary

Introduction

Pseudocereals are broad-leaf nongrass species that produce fruits and/or seeds similar to conventional cereal crops with considerable nutritive value [1]. The cultivation of chia has recently expanded to nations around the world because the plant seeds are rich in dietary nutrients (fiber, antioxidants, minerals and vitamins, proteins, and unsaturated fatty acids) and phenolic compounds often associated with health benefits [2]. Chia has received considerable attention due to its nutritive value and medicinal benefit in various chronic and lifestyle diseases. A few lines of research have shown that chia seed consumption is beneficial in regulating symptoms associated with inflammation, cardiovascular diseases, and insulin resistance [5,6,7]. The high levels of omega-3 fatty acid content in chia seeds may help reduce the risk of cardiovascular disease and stroke. It is hypothesized that the consumption of chia seeds may be beneficial to human health, published human trials have been small and short, and they have assessed the secondary markers of health rather than primary outcomes [9]

Methods

Results

Conclusion