Abstract
Rooibos (Aspalathus linearis), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health promoting properties of the plant. The species comprises several growth forms that differ in their morphology and biochemical composition, only one of which is cultivated and used commercially. Here, we established methodologies for non-invasive transcriptome research of wild-growing South African plant species, including (1) harvesting and transport of plant material suitable for RNA sequencing; (2) inexpensive, high-throughput biochemical sample screening; (3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol rich plant material; and (4) biocomputational analysis of Illumina sequencing data, together with the evaluation of programs for transcriptome assembly (Trinity, IDBA-Trans, SOAPdenovo-Trans, CLC), protein prediction, as well as functional and taxonomic transcript annotation. In the process, we established a biochemically characterized sample pool from 44 distinct rooibos ecotypes (1–5 harvests) and generated four in-depth annotated transcriptomes (each comprising on average ≈86,000 transcripts) from rooibos plants that represent distinct growth forms and differ in their biochemical profiles. These resources will serve future rooibos research and plant breeding endeavours.
Highlights
Rooibos (Aspalathus linearis) is an indigenous South African shrub widely used to brew the popular rooibos herbal tea
44 plants were sampled in spring (October 2016), when plants are actively growing
This study represents a first undertaking to investigate the genomic background of an endemic study represents a first undertaking to investigate the genomic of an endemic
Summary
Rooibos (Aspalathus linearis) is an indigenous South African shrub widely used to brew the popular rooibos herbal tea. The genus Aspalathus (Fabaceae) includes more than 270 species, most of which are endemic to the Cape Floristic Region of South Africa. Eight distinct A. linearis growth types have been described [1], which vary in their geographic distribution as well as in their morphological, chemical and genetic characteristics [2,3,4]. The Southern and Northern sprouters are prostrate shrublets (max 50 cm high). The Grey sprouters, Nieuwoudtville sprouters, and Wupperthal type plants are medium sized densely branched shrubs. The Red type, Black type, and Tree type plants are erect, slender bushes that can reach up to 2 m in height. The rooibos growth types can be further categorized
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