De novo Sequencing and Analysis of Salvia hispanica Tissue-Specific Transcriptome and Identification of Genes Involved in Terpenoid Biosynthesis

Chia (Salvia hispanica L.), a functional 'superfood': new insights into its botanical, genetic and nutraceutical characteristics

BACKGROUND

Chia (Salvia hispanica L.) seeds have become increasingly popular among health-conscious consumers owing to their high content of ω-3 fatty acids, which provide various health benefits. Comprehensive chemical analyses of the fatty acids and proteins in chia seeds have been conducted, revealing their functional properties. Recent studies have confirmed the high ω-3 content of chia seed oil and have hinted at additional functional characteristics.

SCOPE

This review article aims to provide an overview of the botanical, morphological and biochemical features of chia plants, seeds and seed mucilage. Additionally, we discuss the recent developments in genetic and molecular research on chia, including the latest transcriptomic and functional studies that examine the genes responsible for chia fatty acid biosynthesis. In recent years, research on chia seeds has shifted its focus from studying the physicochemical characteristics and chemical composition of seeds to understanding the metabolic pathways and molecular mechanisms that contribute to their nutritional benefits. This has led to a growing interest in various pharmaceutical, nutraceutical and agricultural applications of chia. In this context, we discuss the latest research on chia and the questions that remain unanswered, and we identify areas that require further exploration.

CONCLUSIONS

Nutraceutical compounds associated with significant health benefits, including ω-3 polyunsaturated fatty acids, proteins and phenolic compounds with antioxidant activity, have been measured in high quantities in chia seeds. However, comprehensive investigations through both in vitro experiments and in vivo animal and controlled human trials are expected to provide greater clarity on the medicinal, antimicrobial and antifungal effects of chia seeds. The recently published genome of chia and gene-editing technologies, such as CRISPR, facilitate functional studies deciphering molecular mechanisms of biosynthesis and metabolic pathways in this crop. This necessitates development of stable transformation protocols and creation of a publicly available lipid database, mutant collection and large-scale transcriptomic datasets for chia.

Satellite observations indicate that chia uses less water than other crops in warm climates

Many parts of the world face severe and prolonged drought conditions, stressing the sustainability of water resources and agriculture. Transitioning to water-efficient crops is one strategy that can help adapt to water scarcity. An emerging drought-tolerant crop of interest is chia (Salvia hispanica). Yet, no study has compared its large-scale water use dynamics to those of widely established crops across the globe. Here, we use satellite data over multiple years to assess the water use efficiency of chia, alfalfa, corn, and soybean globally. Results show that chia consumed 13-38% less water than alfalfa, corn, and soy and assimilated 14-20% more carbon per amount of water used. Substituting 10% of Southwest United States alfalfa cultivation with chia would save 184 million liters of water per growing season, equivalent to the annual water consumption of 1,300 households. Future research shall explore the economic, societal, and environmental ramifications of substituting alfalfa with chia in dry areas worldwide. These insights can guide decision-makers in promoting sustainable agriculture and water resource management.

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

Salvia hispanica L. (chia) is a source of abundant ω-3 polyunsaturated fatty acids (ω-3-PUFAs) that are highly beneficial to human health. The genomic basis for this accrued ω-3-PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica. The highly contiguous 321.5-Mbp genome assembly covering all six chromosomes enabled the identification of 32,922 protein-coding genes. Two whole-genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high α-linolenic acid (ALA, ω-3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein desaturase (ShSAD) gene family, is the main driver of the abundance of ω-3-PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help establish a molecular breeding target that can be leveraged through genome editing techniques to increase ω-3 content in oil crops.

Comparative Analysis of Metabolic Variations, Antioxidant Profiles and Antimicrobial Activity of Salvia hispanica (Chia) Seed, Sprout, Leaf, Flower, Root and Herb Extracts

The purpose of this study was to evaluate the phytochemical profiles of the seeds, sprouts, leaves, flowers, roots and herb of Salvia hispanica and to demonstrate their significant contribution to antioxidant and antimicrobial activities. Applied methods were: HPLC-DAD coupled with post-column derivatization with ABTS reagent, untargeted metabolomics performed by LC-Q-Orbitrap HRMS, and two-fold micro-dilution broth method, which involved suspending a solution of tested compounds dissolved in DMSO in Mueller–Hinton broth for bacteria or Mueller–Hinton broth with 2% glucose for fungi. Metabolomic profiling using LC-Q-Orbitrap HRMS used in this study yielded the identification and preliminary characterization of one hundred fifteen compounds. The dominant class of compounds was terpenoids (31 compounds), followed by flavonoids (21 compounds), phenolic acids and derivatives (19 compounds), organic acids (16 compounds) and others (fatty acids, sugars and unidentified compounds). The organic and phenolic acids were the most abundant classes in terms of total peak area, with distribution depending on the plant raw materials obtained from S. hispanica. The main compound among this class for all types of extracts was rosmarinic acid which was proven to be the most abundant for antioxidant potential. All tested extracts exhibited considerable antibacterial and antifungal activity. The strongest bioactivity was found in leaf extracts, which presented bactericidal activity against Gram-positive bacteria (S. aureus, S. epidermidis, M. luteus and E. faecalis). The work represents the first compendium of knowledge comparing different S. hispanica plant raw materials in terms of the profile of biologically active metabolites and their contribution to antioxidant, antimicrobial and antifungal activity.

A chromosome-level genome assembly of chia provides insights into high omega-3 content and coat color variation of its seeds

Chia (Salvia hispanica) is a functional food crop for humans. Although its seeds contain high omega-3 fatty acids, the seed yield of chia is still low. Genomic resources available for this plant are limited. We report the first high-quality chromosome-level genome sequence of chia. The assembled genome size was 347.6 Mb and covered 98.1% of the estimated genome size. A total of 31 069 protein-coding genes were predicted. The absence of recent whole-genome duplication and the relatively low intensity of transposable element expansion in chia compared to its sister species contribute to its small genome size. Transcriptome sequencing and gene duplication analysis reveal that the expansion of the fab2 gene family is likely to be related to the high content of omega-3 in seeds. The white seed coat color is determined by a single locus on chromosome 4. This study provides novel insights into the evolution of Salvia species and high omega-3 content, as well as valuable genomic resources for genetic improvement of important commercial traits of chia and its related species.

Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development

Chia (Salvia hispanica L.), now a popular superfood and a pseudocereal, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids (PUFAs). At present, the genomic and genetic information available in the public domain for this crop are scanty, which hinders an understanding of its growth and development and genetic improvement. We report an RNA-sequencing (RNA-Seq)-based comprehensive transcriptome atlas of Chia sampled from 13 tissue types covering vegetative and reproductive growth stages. We used ~355 million high-quality reads of total ~394 million raw reads from transcriptome sequencing to generate de novo reference transcriptome assembly and the tissue-specific transcript assemblies. After the quality assessment of the merged assemblies and implementing redundancy reduction methods, 82,663 reference transcripts were identified. About 65,587 of 82,663 transcripts were translated into 99,307 peptides, and we were successful in assigning InterPro annotations to 45,209 peptides and gene ontology (GO) terms to 32,638 peptides. The assembled transcriptome is estimated to have the complete sequence information for ~86% of the genes found in the Chia genome. Furthermore, the analysis of 53,200 differentially expressed transcripts (DETs) revealed their distinct expression patterns in Chia's vegetative and reproductive tissues; tissue-specific networks and developmental stage-specific networks of transcription factors (TFs); and the regulation of the expression of enzyme-coding genes associated with important metabolic pathways. In addition, we identified 2,411 simple sequence repeats (SSRs) as potential genetic markers from the transcripts. Overall, this study provides a comprehensive transcriptome atlas, and SSRs, contributing to building essential genomic resources to support basic research, genome annotation, functional genomics, and molecular breeding of Chia.

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.

Characterization of a novel levopimaradiene synthase gene responsible for the biosynthesis of terpene trilactones in Ginkgo biloba

Terpene trilactones (TTLs) are the main medicinal compounds of Ginkgo biloba. Levopimaradiene synthase (LPS) is the crucial enzyme that catalyzes TTLs biosynthesis in G. biloba. In this study, a novel LPS gene (designated as GbLPS2) was cloned from G. biloba leaves. The open reading frame of GbLPS2 gene was 2520 bp in length, encoding a predicted polypeptide of 840 amino acids. Phylogenetic analysis revealed that the GbLPS2 was highly homologous with reported LPS proteins in other plants. On the basis of the genomic DNA (gDNA) template, a 4308 bp gDNA sequence of GbLPS2 and a 913 bp promoter sequence were amplified. Cis-acting elements in promoter analysis indicated that GbLPS2 could be regulated by methyl jasmonate (MeJA) and abscisic acid (ABA). Tissue-specific expression analysis revealed that GbLPS2 was mainly expressed in roots and ovulate strobilus. MeJA treatment could significantly induce the expression level of GbLPS2 and increase the content of TTLs. This study illustrates the structure and the tissue-specific expression pattern of GbLPS2 and demonstrates that exogenous hormones regulated the expression of GbLPS2 and TTL content in G. biloba. Our results provide a target gene for the enhancement of TTL content in G. biloba via genetic engineering.