Efficient extraction of RNA from various Camellia species rich in secondary metabolites for deep transcriptome sequencing and gene expression analysis

Jiang, Cong; Wen, Qiang; Chen, Ying; Li, Xu; Min-ren, Huang

doi:10.5897/ajb11.235

Cited by 9 publications

(4 citation statements)

References 11 publications

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“…Illunima's base quality values were expressed as Qphred, and the GC content was counted. The raw reads were ltered to obtain clean reads, and subsequent analyses were based on the clean reads (Jiang et al 2011). The clean reads were mapped to a reference genome sequence and annotated against the reference genome.…”

Section: Transcriptome Sequencing and Data Analysismentioning

confidence: 99%

The PpMYB75-PpDFR module reveals the difference between ‘SR’ and its Bud Variant ‘RMHC’ in Peach Red Flesh

Xu,

Xue,

et al. 2023

Preprint

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‘Red Meat Honey Crisp (RMHC)’ has been widely cultivated by growers in recent years due to its early maturity, and red meat type characteristics. As a bud variant of ‘Super Red (SR)’ peach, red flesh is the most distinctive characteristic of ‘Red Meat Honey Crisp (RMHC)’. However, the mechanism of red flesh formation in ‘RMHC’ remains unclear. In this study, 79 differentially produced metabolites were identified by metabolomics analysis. The anthocyanin content in ‘RMHC’ was significantly higher than that in ‘SR’ during the same period, such as cyanidin O-syringic acid and cyanidin 3-O-glucoside. Other flavonoids also increased during the formation of red flesh, including flavonols (6-hydroxykaempferol-7-O-glucoside, hyperin), flavanols (protocatechuic acid, (+)-gallocatechin), and flavonoids (chrysoeriol 5-O-hexoside, tricetin). In addition, transcriptomic analysis and RT-qPCR showed that the expression levels of the flavonoid synthesis pathway transcription factor MYB75 and some structural genes, such as PpDFR, PpCHS, PpC4H, and PpLDOX increased significantly in ‘RMHC’. Subcellular localization analysis revealed that MYB75 was localized to the nucleus. Yeast single hybridization assays showed that MYB75 bound to the cis-acting element CCGTTG of the PpDFR promoter region. The MYB75-PpDFR regulatory network was identified to be a key pathway in the reddening of ‘RMHC’ flesh. Moreover, this is the first study to describe the cause for red meat reddening in ‘RMHC’ compared to ‘SR’ peaches using transcriptomics, metabolomics and molecular methods. Our study identified a key transcription factor involved in the regulation of the flavonoid synthetic pathway and contributes to peach breeding-related efforts as well as the identification of genes involved in color formation in other species.

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Section: Transcriptome Sequencing and Data Analysismentioning

confidence: 99%

The PpMYB75-PpDFR module reveals the difference between ‘SR’ and its Bud Variant ‘RMHC’ in Peach Red Flesh

Xu,

Xue,

et al. 2023

Preprint

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“…A total of 3 μg of RNA per sample was used for library preparation with insert sizes of 350 bp and sequenced on Novaseq 6000 (Illumina, USA). RNA-seq analysis was conducted using the Illumina platform according to the standard protocols [45].…”

Section: Rna Extraction and Transcriptome Sequencingmentioning

confidence: 99%

Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum)

Zhang

et al. 2020

BMC Plant Biol

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Background The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. However, the research on lignocellulose biosynthesis pathway and key genes is limited because the genome of elephant grass has not been deciphered. Results In this study, RNA sequencing (RNA-seq) combined with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from different development stages as materials were applied to reveal the genes that regulate the synthesis of cellulose and lignin. A total of 3852 differentially expressed genes (DEGs) were identified in three periods of T1, T2, and T3 through RNA-seq analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of all DEGs showed that the two most abundant metabolic pathways were phenylpropane metabolism, starch and sucrose metabolism, which were closely related to cell wall development, hemicellulose, lignin and cellulose synthesis. Through weighted gene co-expression network analysis (WGCNA) of DEGs, a ‘blue’ module highly associated with cellulose synthesis and a ‘turquoise’ module highly correlated with lignin synthesis were exhibited. A total of 43 candidate genes were screened, of which 17 had function annotations in other species. Besides, by analyzing the content of lignocellulose in the stem tissues of elephant grass at different developmental stages and the expression levels of genes such as CesA, PAL, CAD, C4H, COMT, CCoAMT, F5H and CCR, it was found that the content of lignocellulose was related to the expression level of these structural genes. Conclusions This study provides a basis for further understanding the molecular mechanisms of cellulose and lignin synthesis pathways of elephant grass, and offers a unique and extensive list of candidate genes for future specialized functional studies which may promote the development of high-quality elephant grass varieties with high cellulose and low lignin content.

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“…A total of 3μg of RNA per sample was used for library preparation with insert sizes of 350bp and sequenced on Novaseq 6000 (Illumina, USA). RNA-seq analysis was conducted using the Illumina platform according to the standard protocols [34].…”

Section: Rna Extraction and Transcriptome Sequencingmentioning

confidence: 99%

Tissue-Specific Transcriptome Analysis Reveals Lignocellulose Synthesis Regulation in Elephant Grass (Pennisetum purpureum Schum.)

Zhang

et al. 2020

Preprint

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Background: The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. However, the research on lignocellulose biosynthesis pathway and key genes is limited because the genome of elephant grass has not been deciphered.Results: In this study, RNA sequencing (RNA-seq) combined with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from different development stages as materials were applied to reveal the genes that regulate the synthesis of cellulose and lignin. A total of 3852 differentially expressed genes (DEGs) were identified in three periods of T1, T2, and T3 through RNA-seq analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of all DEGs showed that the two most abundant metabolic pathways were phenylpropane metabolism, starch and sucrose metabolism, which were closely related to cell wall development, hemicellulose, lignin and cellulose synthesis. Through weighted gene co-expression network analysis (WGCNA) of DEGs, a ‘blue’ module highly associated with cellulose synthesis and a ‘turquoise’ module highly correlated with lignin synthesis were exhibited. A total of 43 candidate genes were screened, of which 17 had function annotations in other species. Besides, by analyzing the content of lignocellulose in the stem tissues of elephant grass at different developmental stages and the expression levels of genes such as CesA, PAL, CAD, C4H, COMT, CCoAMT, F5H and CCR, it was found that the content of lignocellulose was related to the expression level of these structural genes.Conclusions: This study provides a basis for further understanding the molecular mechanisms of cellulose and lignin synthesis pathways of elephant grass, and offers a unique and extensive list of candidate genes for future specialized functional studies which may promote the development of high-quality elephant grass varieties with high cellulose and low lignin content.

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Efficient extraction of RNA from various Camellia species rich in secondary metabolites for deep transcriptome sequencing and gene expression analysis

Cited by 9 publications

References 11 publications

The PpMYB75-PpDFR module reveals the difference between ‘SR’ and its Bud Variant ‘RMHC’ in Peach Red Flesh

The PpMYB75-PpDFR module reveals the difference between ‘SR’ and its Bud Variant ‘RMHC’ in Peach Red Flesh

Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum)

Tissue-Specific Transcriptome Analysis Reveals Lignocellulose Synthesis Regulation in Elephant Grass (Pennisetum purpureum Schum.)

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