De novo sequencing and transcriptome assembly of Arisaema heterophyllum Blume and identification of genes involved in isoflavonoid biosynthesis

Abstract

Arisaema heterophyllum Blume (AhBl) is one of the valued medicinal plants. However, its genetic information is limited, which impedes further studies of this valuable resource. To investigate the genes involved in the isoflavonoid biosynthesis, we deeply performed transcriptome sequencing for AhBl. An average of 10.98 Gb clean reads were obtained based on root, tuber and leaf tissues, and 109,937 unigenes were yielded after de novo assembly. In total, 72,287 of those unigenes were annotated in at least one public database. The numbers of expressed unigenes in each tissue were 35,686, 43,363 and 47,783, respectively. The overall expression levels of transcripts in leaf were higher than those in root and tuber. Differentially expressed genes analysis indicated that a total of 12,448 shared unigenes were detected in all three tissues, 10,215 of which were higher expressed in tuber than that in root and leaf. Besides, 87 candidate unigenes that encode for enzymes involved in biosynthesis of isoflavonoid were identified and analyzed, and some key enzyme genes were experimentally validated by quantitative Real-Time PCR (qRT-PCR). This study provides a unique dataset for the systematic analysis of AhBl functional genes and expression characteristics, and facilitates the future study of the pharmacological mechanism of AhBl.

De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis

“…In addition, 119,177 (68.52%) genes were mapped in at least one public database, while 54,761 (31.48%) genes remained unannotated because of the lack of available genomic information. The KEGG database is a useful tool for determining candidate genes in biological processes (Liu et al, 2017;Shi et al, 2019;Wang et al, 2018). We identified numerous unigenes participating in coumarin biosynthesis through KEGG annotations.…”

“…The KEGG database is a useful tool for determining candidate genes in biological processes ( Liu et al, 2017 ; Shi et al, 2019 ; Wang et al, 2018 ). We identified numerous unigenes participating in coumarin biosynthesis through KEGG annotations.…”

“…RNA-sequencing (RNA-Seq) has been widely applied as a powerful method for discovering and predicting functional genes, and revealing gene expression patterns, especially in non-model species for which reference genome sequences are insufficient ( Chu & Corey, 2012 ). To date, dozens of medicinal plants have been subjected to RNA-Seq analysis, including recent transcriptome analyses of Melilotus albus ( Luo et al, 2017 ), Artemisia argyi ( Liu et al, 2017 ), Arisaema heterophyllum ( Wang et al, 2018 ), Clinopodium chinense ( Shi et al, 2019 ) and Polygonatum cyrtonema ( Wang et al, 2019 ). However, such analytical approaches have not been used to obtain comprehensive transcriptomic resources for C. monnieri .…”

De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway

“…RNA-seq has been used by scientific community in the identification of functional genes involved in the biosynthesis of active compounds and metabolic engineering of important pathways in plants 7–9 . Recent studies with Curcuma longa 10 , Withania somnifera 11 , Camelina sativa 12 , Andrographis paniculata 13 , Solanum trilobatum 14 , Foeniculum vulgare 15 and Arisaema heterophyllum 16 have demonstrated the effectiveness of de novo assembly of transcriptomes. Despite the importance of this plant, there is a dearth of data relating to its functional genomics profile except for a recent report describing polyoxypregnane glycoside biosynthesis pathway 17 .…”

De novo Assembly and Transcriptome Analysis of Polygonatum odoratum (Mill.) Druce : Detection of Potential Genes Involved in Polysaccharide Synthesis

“…RNA-sequencing can provide comprehensive information for gene expression to improve our understanding of gene regulation and metabolic pathways [21]. Some medicinal plant genomes have been sequenced, including Artemisia argyi [22], Dendrobium officinale [23], Pueraria lobata [24], Gentiana rigescens [25] and Arisaema heterophyllum Blume [26], and novel genes encoding key enzymes involved in specific metabolic pathways have been identified. However, genomic information 4 for P. odoratum has not yet been reported, which hinders further research on this species.…”