De novo sequencing and comparative analysis of two Phalaenopsis orchid tissue-specific transcriptomes

Gao, Liwei; Jiang, Dong; Yang, Yuming; Li, Y. X.; Sun, Guosheng; H., Z.; Zhang, C. W.

doi:10.1134/s1021443716020072

Cited by 5 publications

(4 citation statements)

References 32 publications

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“…Differential gene expression (DEG) of the different colored buds of Phalaenopsis sp. suggested that most DEGs were of phenylpropanoid biosynthesis which suggests the role of anthocyanins for variable colors (Gao et al, 2016). The number of unigenes annotated to phenylpropanoid varies from 49 unigenes in Phalaenopsis sp.…”

Section: Functional Annotation Of Secondary Metabolism Specific Genesmentioning

confidence: 99%

“…The number of unigenes annotated to phenylpropanoid varies from 49 unigenes in Phalaenopsis sp. (Gao et al, 2016) to 466 in Cymbidium goeringii (Ramya et al, 2019). In a transcriptomic study of Pleione limprichtii, 11,067 genes were mapped to 131 KEGG pathways and 1,294 unigenes were associated with secondary metabolite synthesis (Zhang et al, 2020b).…”

Section: Functional Annotation Of Secondary Metabolism Specific Genesmentioning

confidence: 99%

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A Walk Through the Maze of Secondary Metabolism in Orchids: A Transcriptomic Approach

et al. 2022

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Orchids have a huge reservoir of secondary metabolites making these plants of immense therapeutic importance. Their potential as curatives has been realized since times immemorial and are extensively studied for their medicinal properties. Secondary metabolism is under stringent genetic control in plants and several molecular factors are involved in regulating the production of the metabolites. However, due to the complex molecular networks, a complete understanding of the specific molecular cues is lacking. High-throughput omics technologies have the potential to fill up this lacuna. The present study deals with comparative analysis of high-throughput transcript data involving gene identification, functional annotation, and differential expression in more than 30 orchid transcriptome data sets, with a focus to elucidate the role of various factors in alkaloid and flavonoid biosynthesis. Comprehensive analysis of the mevalonate (MVA) pathway, methyl-d-erythritol 4-phosphate (MEP) pathway, and phenylpropanoid pathway provide specific insights to the potential gene targets for drug discovery. It is envisaged that a positive stimulation of these pathways through regulation of pivotal genes and alteration of specific gene expression, could facilitate the production of secondary metabolites and enable efficient tapping of the therapeutic potential of orchids. This further would lay the foundation for developing strategies for genetic and epigenetic improvement of these plants for development of therapeutic products.

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Section: Functional Annotation Of Secondary Metabolism Specific Genesmentioning

confidence: 99%

Section: Functional Annotation Of Secondary Metabolism Specific Genesmentioning

confidence: 99%

A Walk Through the Maze of Secondary Metabolism in Orchids: A Transcriptomic Approach

et al. 2022

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“…The ower color formation mechanism of Phalaenopsis is an important research topic, but the most of current researches were focused on genetic engineering technology, genetic analysis and breeding selections in Phalaenopsis. At present, only Gao et al investigated the regulation mechanism of ower color by using RNA-seq in transcriptome level and revealed the anthocyanin synthesis pathway was responsible for the differences between red and yellow owers in Phalaenopsis [16]. Recently, RNA-seq had been used to analyze a large number of single nucleotide polymorphisms (SNPs) and associated with plant biological and agronomic traits [17].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of flower color reveals the correlation between SNP and differential expression genes in Phalaenopsis

Ding¹,

Yang²,

Wang³

et al. 2021

Preprint

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Background Phalaenopsis is an important ornamental plant, which occupies an important position in the world flower market and has great economic value due to its rich and diverse flower colors. In order to investigate the flower color formation of Phalaenopsis at transcription level, the flower color formation involved genes were identified from RNA-seq in this study.Results White and purple petals of Phalaenopsis were collected in this study, and results were focused on two aspects: (1) the differential expression genes (DEGs) between white and purple flower color; and (2) association between SNP mutations and DEGs in transcriptome level. Results indicated that a total of 1,175 DEGs were identified, and the up- and down-regulation genes were 718 and 457, respectively. Gene Ontology (GO) and pathway enrichment showed that the biosynthesis of secondary metabolites pathway was key responsible for color formation and twelve crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase and E1.11.17) from them involved in the regulation of flower color in Phalaenopsis. Conclusion This study firstly reported that the SNP mutations strongly associated with DEGs in color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.

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“…The sequenced genome of P. equestris comprises 29,431 predicted protein-coding genes and provides information about the evolution of CAM photosynthesis, flowering MADS-box B-,C/D-class genes and interactions between type I MADS-box genes (Cai et al, 2015). Recently, a genomic study was performed on Phalaenopsis orchid tissue using Illumina sequencing technology to understand the biosynthesis of anthocyanin in two different colors (red and yellow) (Gao et al, 2016). Most of the differentially expressed genes in yellow color were associated to the biosynthesis of anthocyanins.…”

Section: Introductionmentioning

confidence: 99%

Research Article PhalDB:A comprehensive database for molecular mining of the <i>Phalaenopsis</i> genome, transcriptome and miRNome

Lee¹,

Viswanath²,

Huang³

et al. 2018

Genet. Mol. Res.

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©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 17 (4): gmr18051 C.Y. Lee. et al. 2 include information about somaclonal variations and cool temperature treatment, which are important for commercial variety development. PhalDB provides sequence information from 24 samples and covers the above-mentioned tissues or conditions so that comprehensive gene data related to flower development, somaclonal variation and some horticulture traits are available for searching. A user can access DNA level information and miRNA structure, etc. It also provides an opportunity to explore mRNA level information and interactions between genes and miRNA. PhalDB is equipped with a BLAST tool to perform similarity searches among the various gene sequences.

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De novo sequencing and comparative analysis of two Phalaenopsis orchid tissue-specific transcriptomes

Cited by 5 publications

References 32 publications

A Walk Through the Maze of Secondary Metabolism in Orchids: A Transcriptomic Approach

A Walk Through the Maze of Secondary Metabolism in Orchids: A Transcriptomic Approach

Transcriptome analysis of flower color reveals the correlation between SNP and differential expression genes in Phalaenopsis

Research Article PhalDB:A comprehensive database for molecular mining of the <i>Phalaenopsis</i> genome, transcriptome and miRNome

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