Abstract
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.
Highlights
Salvia hispanica L. (Chia), an annual herbaceous plant of the Lamiaceae family, is a native of Central America’s highlands (Cahill, 2005; Ixtaina et al, 2008; Baginsky et al, 2016)
The transcriptome data were generated from the 13 Chia plant structures, including mature dry seeds, early seedling shoots, leaves, an internode between P5 and P6 leaves, top and bottom halves of pre-anthesis raceme inflorescence, and flowers from the day of anthesis [Days after flowering (DAF)], and 5 day post-anthesis (Table 1)
To develop a repertoire of genetic and genomic data and knowledge resources on Chia, recent limited efforts have focused on the expression of lipid biosynthesis and terpene synthase genes in developing Chia seeds, roots, and leaves (Sreedhar et al, 2015; Peláez et al, 2019; Wimberley et al, 2020)
Summary
Salvia hispanica L. (Chia), an annual herbaceous plant of the Lamiaceae (mint) family, is a native of Central America’s highlands (Cahill, 2005; Ixtaina et al, 2008; Baginsky et al, 2016). (Chia), an annual herbaceous plant of the Lamiaceae (mint) family, is a native of Central America’s highlands (Cahill, 2005; Ixtaina et al, 2008; Baginsky et al, 2016). The seeds are rich in protein (15–20%), dietary fiber (20–40%), minerals (4–5%), and antioxidants (Reyes-Caudillo et al, 2008; Ayerza and Coates, 2009; Muñoz et al, 2013). These nutritional attributes have made Chia a desirable superfood and a pseudocereal. Its leaves contain various essential oils, such as β-caryophyllene, globulol, γ-muroleno, β-pinene, α-humulene, germacrene, and widdrol, which are known to have insect repellant or insecticidal properties (Amato et al, 2015; Elshafie et al, 2018)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
