Abstract
BackgroundThe most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. St.-Hil., an aboriginal ancestral beverage known for its high polyphenols concentration currently consumed in > 90% of homes in Argentina, in Paraguay and Uruguay. The economy of entire provinces heavily relies on the production, collection and manufacture of Ilex paraguariensis, the fifth plant species with highest antioxidant activity. Polyphenols are associated to relevant health benefits including strong antioxidant properties. Despite its regional relevance and potential biotechnological applications, little is known about functional genomics and genetics underlying phenotypic variation of relevant traits. By generating tissue specific transcriptomic profiles, we aimed to comprehensively annotate genes in the Ilex paraguariensis phenylpropanoid pathway and to evaluate differential expression profiles.ResultsIn this study we generated a reliable transcriptome assembly based on a collection of 15 RNA-Seq libraries from different tissues of Ilex paraguariensis. A total of 554 million RNA-Seq reads were assembled into 193,897 transcripts, where 24,612 annotated full-length transcripts had complete ORF. We assessed the transcriptome assembly quality, completeness and accuracy using BUSCO and TransRate; consistency was also evaluated by experimentally validating 11 predicted genes by PCR and sequencing. Functional annotation against KEGG Pathway database identified 1395 unigenes involved in biosynthesis of secondary metabolites, 531 annotated transcripts corresponded to the phenylpropanoid pathway. The top 30 differentially expressed genes among tissue revealed genes involved in photosynthesis and stress response. These significant differences were then validated by qRT-PCR.ConclusionsOur study is the first to provide data from whole genome gene expression profiles in different Ilex paraguariensis tissues, experimentally validating in-silico predicted genes key to the phenylpropanoid (antioxidant) pathway. Our results provide essential genomic data of potential use in breeding programs for polyphenol content. Further studies are necessary to assess if the observed expression variation in the phenylpropanoid pathway annotated genes is related to variations in leaves’ polyphenol content at the population scale. These results set the current reference for Ilex paraguariensis genomic studies and provide a substantial contribution to research and biotechnological applications of phenylpropanoid secondary metabolites.
Highlights
The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A
RNA sequencing and transcriptome de novo assembly To achieve a comprehensive representation and characterisation of the of Ilex paraguariensis transcriptome, we sequenced 15 RNA-seq libraries from four tissues, namely root, seedling, normal leaves and curly leaves (Additional file 1: Figure S1), maximising the number of active genes captured across tissues
Tissue specific gene activity has been verified in several plant species, here we report global expression profiles in Ilex paraguariensis that can clearly identify significant differentially expressed transcripts among tissues
Summary
The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. For centuries the “mate”, a beverage made from an infusion of YM dried leaves, has been widely consumed in South America countries (southern Brazil, Argentina, Paraguay, and Uruguay). A number of research reports confirmed relevant pharmacological properties, such as antioxidant activity [4], protective effects against induced DNA damage and atherosclerosis [5, 6], potent anti-obesity activity and modulatory effect on glucose levels [7]. These properties transform “mate” into a conceivable functional food with active principles with a relevant biochemical profile for the pharmaceutical industry. “mate” is a potential carrier food for functional ingredients or supplements with extensive spread consumption comparable to flour
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