Transcriptomic analysis of Pseudostellariae Radix from different fields using RNA-seq

Hua, Yujiao; Wang, Shengnan; Liu, Zixiu; Liu, Xunhong; Zou, Lisi; Luo, Yi‐Bo; Liu, Juanxiu

doi:10.1016/j.gene.2016.04.043

Cited by 14 publications

(6 citation statements)

References 48 publications

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“…heterophylla . The number of unigenes (127,334) identified in our study was much higher as compared with previous transcriptomic studies from Pseudostellariae redix [ 14 ]. Our data provides a useful resource for gene identification and regulation in different tissues of P .…”

Section: Discussioncontrasting

confidence: 63%

“…Chemical technology has helped identify the secondary metabolites including flavonoids, an isoquinoline alkaloid, terpenoids, and phenylpropanoid in these plants [ 3 ]; however, there have been no molecular studies on secondary metabolism pathways involved in their biosynthesis and degradation. Hua et al[ 14 ] (2016) performed de novo sequencing and transcriptome analysis of P . heterophylla tuberous roots, but no transcriptomic and genomic information from the aboveground parts (leaf, stem, and flower) is available in the nucleotide databases of National Centre for Biotechnology Information (NCBI).…”

Section: Introductionmentioning

confidence: 99%

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De Novo Sequencing and Assembly Analysis of the Pseudostellaria heterophylla Transcriptome

Wei

Dengkai

et al. 2016

PLoS ONE

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Pseudostellaria heterophylla (Miq.) Pax is a mild tonic herb widely cultivated in the Southern part of China. The tuberous roots of P. heterophylla accumulate high levels of secondary metabolism products of medicinal value such as saponins, flavonoids, and isoquinoline alkaloids. Despite numerous studies on the pharmacological importance and purification of these compounds in P. heterophylla, their biosynthesis is not well understood. In the present study, we used Illumina HiSeq 4000 sequencing platform to sequence the RNA from flowers, leaves, stem, root cortex and xylem tissues of P. heterophylla. We obtained 616,413,316 clean reads that we assembled into 127, 334 unique sequences with an N50 length of 951 bp. Among these unigenes, 53,184 unigenes (41.76%) were annotated in a public database and 39, 795 unigenes were assigned to 356 KEGG pathways; 23,714 unigenes (8.82%) had high homology with the genes from Beta vulgaris. We discovered 32, 095 DEGs in different tissues and performed GO and KEGG enrichment analysis. The most enriched KEGG pathway of secondary metabolism showed up-regulated expression in tuberous roots as compared with the ground parts of P. heterophylla. Moreover, we identified 72 candidate genes involved in triterpenoids saponins biosynthesis in P. heterophylla. The expression profiles of 11 candidate unigenes were analyzed by quantitative real-time PCR (RT-qPCR). Our study established a global transcriptome database of P. heterophylla for gene identification and regulation. We also identified the candidate unigenes involved in triterpenoids saponins biosynthesis. Our results provide an invaluable resource for the secondary metabolites and physiological processes in different tissues of P. heterophylla.

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Section: Discussioncontrasting

confidence: 63%

Section: Introductionmentioning

confidence: 99%

De Novo Sequencing and Assembly Analysis of the Pseudostellaria heterophylla Transcriptome

Wei

Dengkai

et al. 2016

PLoS ONE

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“…The content of HB was the highest in the Jiangsu P. heterophylla ; however, almost no HB was detected in the Fujian P. heterophylla . Previous studies have also shown that there are obvious differences in the quality of different cultivated P. heterophylla from different fields (Hua et al, 2016b; Hua et al, 2016c). These variances might be related to differences in the ecological environment, genetic information, and cultivation techniques.…”

Section: Discussionmentioning

confidence: 95%

The Biosynthesis of Heterophyllin B in Pseudostellaria heterophylla From prePhHB-Encoded Precursor

Zheng

Zhou

et al. 2019

Front. Plant Sci.

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Plant cyclic peptides (CPs) are a large group of small molecule metabolites found in a wide variety of plants, including traditional Chinese medicinal plants. However, the majority of plant CPs have not been studied for their biosynthetic mechanisms, including heterophyllin B (HB), which is one of the characteristic chemical components of Pseudostellaria heterophylla. Here, we screened the precursor gene (prePhHB) of HB in P. heterophylla and functionally identified its correctness in vivo and in vitro. First, we developed a new method to screen the precursors of HB from 16 candidate linear peptides. According to transcriptome sequencing data, we cloned the genes that encoded the HB precursor peptides and confirmed that the prePhHB-encoded precursor peptide could enzymatically synthesize HB. Next, we generated the transgenic tobacco that expressed prePhHB, and the results showed that HB was detected in transgenic tobacco. Moreover, we revealed that prePhHB gene expression is positively correlated with HB accumulation in P. heterophylla. Mutations in the prePhHB gene may influence the accumulation of HB in P. heterophylla. These results suggest that HB is ribosomally synthesized and posttranslationally modified peptide (RiPP) derived from the precursor gene prePhHB-encoded precursor peptide, and the core peptide sequence of HB is IFGGLPPP in P. heterophylla. This study developed a new idea for the rapid identification of Caryophyllaceae-type CP precursor peptides via RNA-sequencing data mining.

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“…NMR has also been developed for identification of wild P. heterophylla from different cultivated fields [ 47 , 53 ]. In addition, high-throughput RNA sequencing (RNA-seq) was employed as de novo assembly for studying the transcriptome in P. heterophylla , and significantly differentially expressed genes in P. heterophylla from different fields were found [ 54 ].…”

Section: Chemical Analysis Of P Heterophyllamentioning

confidence: 99%

Chemistry, pharmacology and analysis of Pseudostellaria heterophylla: a mini-review

Shakerian

Zhao

et al. 2019

Chin Med

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Pseudostellaria heterophylla is one of the well-known traditional Chinese medicines and has been used in clinics for 100 years in China. The chemistry and pharmacology of P. heterophylla were reviewed to understand its active compounds. Then analysis of these compounds related to quality control of this herb was discussed. For the analysis of chemicals, three aspects have been discussed in this review. The first two aspects focused on the methodologies for analysis of cyclic peptides and carbohydrates in P. heterophylla, respectively. The last one dealt with the other methods used for identification of P. heterophylla. Some rich chemicals such as oligosaccharides in this plant were rarely evaluated. Many analyses were performed on this plant, however, few of them were accepted as quality control method.

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Transcriptomic analysis of Pseudostellariae Radix from different fields using RNA-seq

Cited by 14 publications

References 48 publications

De Novo Sequencing and Assembly Analysis of the Pseudostellaria heterophylla Transcriptome

De Novo Sequencing and Assembly Analysis of the Pseudostellaria heterophylla Transcriptome

The Biosynthesis of Heterophyllin B in Pseudostellaria heterophylla From prePhHB-Encoded Precursor

Chemistry, pharmacology and analysis of Pseudostellaria heterophylla: a mini-review

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