Genome-wide analysis of methyl jasmonate-regulated isoform expression in the medicinal plant Andrographis paniculata

Gao, Han; Li, Fuhuang; Xu, Zhichao; Huang, Chenhao; Xiong, Chenglong; Jiang, Chunhong; Xie, Ning; Leng, Liang; Zhang, Yi; Yousaf, Zubaida; Liu, Xia; Sun, Wei

doi:10.1016/j.indcrop.2019.04.023

Cited by 16 publications

(11 citation statements)

References 43 publications

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“…will cause considerable loss of active ingredients ( Gao et al, 2011 ). In addition, the contents of active ingredients in medicinal materials are closely related to the enzyme activity of plant tissues ( Gao et al, 2019 ; Kotwal et al, 2019 ; Yang et al, 2019 ; Liu et al, 2017 ). For medicinal crops that are rich in alkaloids and polysaccharides, the contents of active ingredients as well as the quality of medicinal materials will rapidly decline, due to the absence of high-temperature treatment that can inactivate enzyme activity in tissues and organs after harvest.…”

Section: Introductionmentioning

confidence: 99%

Growth years and post-harvest processing methods have critical roles on the contents of medicinal active ingredients of Scutellaria baicalensis

Bai

Yang

Cao

et al. 2020

Industrial Crops and Products

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Section: Introductionmentioning

confidence: 99%

Growth years and post-harvest processing methods have critical roles on the contents of medicinal active ingredients of Scutellaria baicalensis

Bai

Yang

Cao

et al. 2020

Industrial Crops and Products

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“…After mapping to the GO term, the annotation was conducted with default parameters. Alternative splicing analysis was performed as in our previous study (Gao et al, 2019 ). The 2,000-bp promoter sequences of 56 genes encoding key enzymes in the andrographolide biosynthetic pathway were obtained from the A. paniculata genome database.…”

Section: Methodsmentioning

confidence: 99%

Genomic Characterization of WRKY Transcription Factors Related to Andrographolide Biosynthesis in Andrographis paniculata

et al. 2021

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Andrographolide, which is enriched in the leaves of Andrographis paniculata, has been known as “natural antibiotic” due to its pharmacological activities such as anti-inflammatory, antimicrobial and antioxidant effects. Several key enzymes in andrographolide biosynthetic pathway have been studied since the genome sequences were released, but its regulatory mechanism remains unknown. WRKY transcription factors proteins have been reported to regulate plant secondary metabolism, development as well as biotic and abiotic stresses. Here, WRKY transcription factors related to andrographolide biosynthesis were systematically identified, including sequences alignment, phylogenetic analysis, chromosomal distribution, gene structure, conserved motifs, synteny, alternative splicing event and Gene ontology (GO) annotation. A total of 58 WRKYs were identified in Chuanxinlian genome and phylogenetically classified into three groups. Moreover, nine WRKY genes underwent alternative splicing events. Furthermore, the combination of binding site prediction, gene-specific expression patterns, and phylogenetic analysis suggested that 7 WRKYs (ApWRKY01, ApWRKY08, ApWRKY12, ApWRKY14, ApWRKY19, ApWRKY20, and ApWRKY50) might regulate andrographolide biosynthesis. This study laid a foundation for understanding the regulatory mechanism of andrographolide biosynthesis and the improvement and breeding of Andrographis paniculata varieties.

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“…The IDP results indicate the sites where isoforms are located on the genome. We followed our previous work to identify alternative splicing events ( Gao H. et al, 2019 ). Briefly, we used the original annotated genes as reference isoform (hereinafter ref isoform).…”

Section: Methodsmentioning

confidence: 99%

“…Second, hybrid sequencing, i.e., integrating of NGS sequencing and TGS sequencing technology, could also be applied to the correct the error of PacBio reads ( Au et al, 2010 , 2013 ). TGS sequencing technology is widely used in plant AS studies, e.g., Salvia miltiorrhiza ( Xu et al, 2015 ), Zea mays ( Thatcher et al, 2014 ), Fragaria ananassa ( Li et al, 2018 ), Scutellaria baicalensis ( Gao T. et al, 2019 ) and Andrographis paniculata ( Gao H. et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L.

Gao

Zhang

et al. 2021

Front. Plant Sci.

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Artemisinin is currently the most effective ingredient in the treatment of malaria, which is thus of great significance to study the genetic regulation of Artemisia annua. Alternative splicing (AS) is a regulatory process that increases the complexity of transcriptome and proteome. The most common mechanism of alternative splicing (AS) in plant is intron retention (IR). However, little is known about whether the IR isoforms produced by light play roles in regulating biosynthetic pathways. In this work we would explore how the level of AS in A. annua responds to light regulation. We obtained a new dataset of AS by analyzing full-length transcripts using both Illumina- and single molecule real-time (SMRT)-based RNA-seq as well as analyzing AS on various tissues. A total of 5,854 IR isoforms were identified, with IR accounting for the highest proportion (48.48%), affirming that IR is the most common mechanism of AS. We found that the number of up-regulated IR isoforms (1534/1378, blue and red light, respectively) was more than twice that of down-regulated (636/682) after treatment of blue or red light. In the artemisinin biosynthetic pathway, 10 genes produced 16 differentially expressed IR isoforms. This work demonstrated that the differential expression of IR isoforms induced by light has the potential to regulate sesquiterpenoid biosynthesis. This study also provides high accuracy full-length transcripts, which can be a valuable genetic resource for further research of A. annua, including areas of development, breeding, and biosynthesis of active compounds.

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Genome-wide analysis of methyl jasmonate-regulated isoform expression in the medicinal plant Andrographis paniculata

Cited by 16 publications

References 43 publications

Growth years and post-harvest processing methods have critical roles on the contents of medicinal active ingredients of Scutellaria baicalensis

Growth years and post-harvest processing methods have critical roles on the contents of medicinal active ingredients of Scutellaria baicalensis

Genomic Characterization of WRKY Transcription Factors Related to Andrographolide Biosynthesis in Andrographis paniculata

Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L.

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