De novo transcriptome sequence of Senna tora provides insights into anthraquinone biosynthesis

Abstract

<jats:title>Abstract</jats:title><jats:p><jats:italic>Senna tora</jats:italic> is an annual herb with rich source of anthraquinones that have tremendous pharmacological properties. However, there is little mention of genetic information for this species, especially regarding the biosynthetic pathways of anthraquinones. To understand the key genes and regulatory mechanism of anthraquinone biosynthesis pathways, we performed spatial and temporal transcriptome sequencing of <jats:italic>S. tora</jats:italic> using short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) technologies, and generated two unigene sets composed of 118,635 and 39,364, respectively. A comprehensive functional annotation and classification with multiple public databases identified array of genes involved in major secondary metabolite biosynthesis pathways and important transcription factor (TF) families (MYB, MYB-related, AP2/ERF, C2C2-YABBY, and bHLH). Differential expression analysis indicated that the expression level of genes involved in anthraquinone biosynthetic pathway regulates differently depending on the degree of tissues and seeds development. Furthermore, we identified that the amount of anthraquinone compounds were greater in late seeds than early ones. In conclusion, these results provide a rich resource for understanding the anthraquinone metabolism in <jats:italic>S. tora</jats:italic>.</jats:p>

Genome-enabled discovery of anthraquinone biosynthesis in Senna tora

“…The genes from the S. tora reference genome were predicted using an in-house gene prediction pipeline, which includes three modules: evidence-based gene modeler, ab initio gene modeler, and consensus gene modeler. To improve the accuracy of gene prediction, we downloaded a total of 118,390 Iso-Seq reads in GenBank SRA database (SRP159435) 15 . RNA-Seq from five tissues (leaf, root, stem, flower, and dry seed) and Iso-Seq data were aligned against the S. tora genome.…”

“…As an ancient medicine, anthraquinones from seeds of other Senna species are commonly used for treating various diseases 13 . Despite the extensive applications of Senna plants in medicine and industry 1 , molecular and genomic studies of this remarkable genus of plants have been limited [14][15][16][17] . Elucidating the genes responsible for the biosynthesis of anthraquinones in S. tora will aid molecular breeding and the development of tools for probing its biochemistry.…”