De novo Transcriptome Assembly of Senna occidentalis Sheds Light on the Anthraquinone Biosynthesis Pathway

Abstract

Senna occidentalis is an annual leguminous herb that is rich in anthraquinones, which have various pharmacological activities. However, little is known about the genetics of S. occidentalis, particularly its anthraquinone biosynthesis pathway. To broaden our understanding of the key genes and regulatory mechanisms involved in the anthraquinone biosynthesis pathway, we used short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) to perform a spatial and temporal transcriptomic analysis of S. occidentalis. This generated 121,592 RNA-Seq unigenes and 38,440 Iso-Seq unigenes. Comprehensive functional annotation and classification of these datasets using public databases identified unigene sequences related to major secondary metabolite biosynthesis pathways and critical transcription factor families (bHLH, WRKY, MYB, and bZIP). A tissue-specific differential expression analysis of S. occidentalis and measurement of the amount of anthraquinones revealed that anthraquinone accumulation was related to the gene expression levels in the different tissues. In addition, the amounts and types of anthraquinones produced differ between S. occidentalis and S. tora. In conclusion, these results provide a broader understanding of the anthraquinone metabolic pathway in S. occidentalis.

Identification and Characterization of Compounds that Improve Plant Photosynthesis and Growth under Light Stress Conditions

“…The first is the polyketide pathway, which is observed in Photorhabdus luminescens , a gammaproteobacterium of the family Morganellaceae. It is a lethal pathogen of insects and higher plants, including Senna tora (Brachmann et al, 2007; Kang et al, 2022). In this pathway, octaketide is dehydrated, and several anthraquinone derivatives, including Endocrocin, Physcion, Rhein, and Chryso-obtusin, are synthesized (Kang et al, 2022).…”

“…It is a lethal pathogen of insects and higher plants, including Senna tora (Brachmann et al, 2007; Kang et al, 2022). In this pathway, octaketide is dehydrated, and several anthraquinone derivatives, including Endocrocin, Physcion, Rhein, and Chryso-obtusin, are synthesized (Kang et al, 2022). The second pathway is a combination of shikimate and mevalonate/methyl-D-erythritol 4-phosphate pathways, which is observed in Cinchona officinalis and Rheum tanguticum (Kang et al, 2020; Zhou et al, 2021).…”

Comparative Transcriptome Analyses of Different Rheum officinale Tissues Reveal Differentially Expressed Genes Associated with Anthraquinone, Catechin, and Gallic Acid Biosynthesis

“…PKSs can be divided into types I, II, and III PKSs according to their structure [ 44 ]. Type III PKSs, the chalcone synthase superfamily, are mainly distributed in the plants, but have also been identified recently in bacteria and fungi [ 19 , 44 , 45 ]. At present, the mechanisms underlying most polyketide biosynthetic pathways are still elusive, but PKS III of plants certainly plays a key role in the initial reaction of these pathways [ 46 , 47 ].…”

“…Although previous studies have confirmed the differences in the accumulation of secondary metabolites in different tissues of R. officinale and used RNA-seq to identify candidate genes involved in the biosynthesis of anthraquinones, etc. [ 16 , 19 , 20 , 21 , 22 ], the differences in the expression of the enzyme genes associated with the synthesis of these components are still indefinite in R. officinale .…”

Assembly Arena: Benchmarking RNA isoform reconstruction algorithms for nanopore sequencing

“…Recent studies have compared software for estimating transcript abundances in long read sequencing data (Dong et al 2023;Pardo-Palacios et al 2023b) but few reports have detailed the effectiveness of tools for RNA isoform discovery and qualification using long reads. Transcriptome assembly is an economical method for characterizing gene expression of model (Yang et al 2021;Kuo et al 2020) or non-model organisms (Kang et al 2021;Zagorščak and Petek 2021;Matra et al 2023) and for identifying novel RNAs in diseases such as cancer (Fang et al 2021;Verma et al 2015).…”