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

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.

Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased α‐linolenic (ω‐3) content in S. hispanica seeds

“…Short and long reads were mapped to the assembled genome using bwa‐mem v0.7.17 (H. Li & Durbin, 2009). Genome completeness was evaluated using Benchmarking Universal Single‐Copy Orthologs (BUSCO) v5.2.2 (Simão et al., 2015) with different databases: “eukaryota_odb10,” “eudicots_odb10,” “viridiplantae_odb10,” and “embryophyta_odb10.” Published transcriptomes from different tissues of S. hispanica (Gupta et al., 2021; Klein et al., 2021; Peláez et al., 2019; Sreedhar et al., 2015; Wimberley et al., 2020) were mapped to the assembled genome using blastn v2.10.1 (Camacho et al., 2009) to further validate the completeness of the assembly.…”

“…The average BUSCO score was relatively high (>95%) across all lineage sets. Around 94% of the previously published S. hispanica transcripts (Gupta et al, 2021;Klein et al, 2021;Peláez et al, 2019;Sreedhar et al, 2015;Wimberley et al, 2020) mapped to the assembled genome (Figure S7). The high BUSCO score and the high mapping rate of transcripts indicated that the genome assembly contained nearly all the S. hispanica genes.…”

Comparative Genomics Points to Tandem Duplications ofSADGene Clusters as Drivers of Increased ω-3 Content inS. hispanicaSeeds

“…Genome completeness was evaluated using Benchmarking Universal Single-Copy Orthologs (BUSCO) v5.2.2 (Simão et al, 2015) with different databases: "eukaryota_odb10", "eudicots_odb10", "viridiplantae_odb10", and "embryophyta_odb10". Published transcriptomes from different tissues of S. hispanica (Sreedhar et al, 2015;Peláez et al, 2019;Wimberley et al, 2020;Gupta et al, 2021;Klein et al, 2021) were mapped to the assembled genome using blastn v2.10.1 (Camacho et al, 2009) to further validate the completeness of the assembly.…”

“…The average BUSCO score was relatively high (> 95%) across all lineage sets. Around 94% of the previously published S. hispanica transcripts (Sreedhar et al, 2015;Peláez et al, 2019;Wimberley et al, 2020;Gupta et al, 2021;Klein et al, 2021) mapped to the assembled genome (Supplemental Figure S6). The high BUSCO score and the high mapping rate of transcripts indicated that the genome assembly contained nearly all the S. hispanica genes.…”