Integrative analysis of metabolome and transcriptome reveals anthocyanins biosynthesis regulation in grass species Pennisetum purpureum

Zhou, Sifan; Chen, Jing; Lai, Yunsong; Yin, Guohua; Chen, Peilin; Pennerman, Kayla K.; Yan, Haidong; Wu, Bingchao; Zhang, Huan; Yi, Xianfeng; Wang, Chengran; Fu, Maojie; Zhang, Xinquan; Huang, Linkai; Ma, Xiao; Yan, Peng; Yan, Yanhong; Nie, Gang; Liu, Lin

doi:10.1016/j.indcrop.2019.111470

Cited by 40 publications

(31 citation statements)

References 50 publications

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“…In our study, 3852 differentially expressed genes (DEGs, adjusted p<0.05) were identi ed in 12 stem samples of elephant grass at different developmental stages. The same method was also used to identify DEGs in the anthocyanin synthesis pathway of elephant grass and mulberry [26,30]. The GO enrichment analysis of DEGs found that the top 10 enriched GO annotation functions included three functions that were directly related to cell wall development such as cell wall, plant-type cell wall, cell wall macromolecule catabolic process.…”

Section: Discussionmentioning

confidence: 99%

“…Although the elephant grass genome has not been deciphered yet, its genetic research has focused on the evaluation of genetic diversity by constructing molecular markers and ngerprints and determining genetic relationships [23][24][25]. Meanwhile, researchers have revealed the biosynthetic pathway of anthocyanins, and the molecular mechanism of early response to cadmium in elephant grass roots and leaves through RNA-seq analysis [26][27]. Some progress has also been made in improving the agronomic traits of elephant grass by using traditional breeding methods based on phenotypic selection [28][29].…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

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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“…protein family (Pfam: http://pfam.sanger.ac.uk/) using cutoff E-value ≤0.01; and KEGG (http://www.genome.jp/kegg) pathways using cutoff E-value ≤1 e-10 [43]. The Blast2GO program (http://www.blast2go.com) was used to annotate GO (http://www.geneontology.org) terms based on the NR annotations (cutoff E-value ≤1 e-6 ).…”

Section: Gene Functional Annotationmentioning

confidence: 99%

Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

Sun

Zhang

Huang

et al. 2020

Preprint

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Background: Heat and drought are the serious threats to crop growth and development. As the sixth cereal crop in the world, pearl millet can be used not only for food and forage but also as bioenergy. Pearl millet has high tolerance under heat and drought. Given this, it is considered as an ideal crop for plant stress tolerance studying and can be used to excavate heat-resistant genes. Results: In this study, we used Pacbio sequencing data as a reference sequence to analyze the Illumina data of pearl millet for 48 hours under heat and drought stress. By taking an overview of previous studies, we found 26,299 new genes and 63,090 new transcripts, and the number of gene annotations increased by 20.18%. We identified 2,792 transcription factors (TFs) and 1,223 transcriptional regulators (TRs). There were 318 TFs and 149 TRs differentially expressed under heat stress, and 315 TFs and 128 TRs were differentially expressed under drought stress. By RNA sequencing, we identified 6,920 genes and 6,484 genes differentially expressed under heat stress and drought stress, respectively. Comparing DEGs under heat tolerance with DEGs under drought stress, we found that even in the same pathway, pearl millet would choose a different protein response. Conclusions: This information will provide new insights to study pearl millet at molecular and genetic level to understand the mechanisms involved in drought and heat stress tolerance.

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“…Recently, the association analyses of different omics platforms (transcriptomics and metabolomics) have gradually emerged as a new trend in the area of plant metabolism research [35][36][37][38][39][40][41]. For this study, we merged transcriptomics and metabolomics and studied eight common hormones in Acer rubrum (ethylene, abscisic acid, cytokinin, auxin, jasmonic acid, salicylic acid, brassinosteroid, and gibberellin).…”

Section: Introductionmentioning

confidence: 99%

Integrating transcriptomic and metabolomic analysis of hormone pathways in Acer rubrum during developmental leaf senescence

Junlan

Xuan

et al. 2020

Preprint

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Background: To fully elucidate the roles and mechanisms of plant hormones in leaf senescence, we adopted an integrated analysis of both non-senescing and senescing leaves from red maple with transcriptome and metabolome data. Results: Transcription and metabolite profiles were generated through a combination of deep sequencing, third-generation sequencing data analysis, and ultrahigh-performance liquid chromatograph Q extractive mass spectrometry (UHPLC-QE-MS), respectively. We investigated the accumulation of compounds and the expression of biosynthesis and signaling genes for eight hormones. The results revealed that ethylene and abscisic acid concentrations increased during the leaf senescence process, while the contents of cytokinin, auxin, jasmonic acid, and salicylic acid continued to decrease. Correlation tests between the hormone content and transcriptional changes were analyzed, and in six pathways, genes closely linked with leaf senescence were identified. Conclusions: These results will enrich our understanding of the mechanisms of plant hormones that regulate leaf senescence in red maple, while establishing a foundation for the genetic modification of Acer in the future.

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Integrative analysis of metabolome and transcriptome reveals anthocyanins biosynthesis regulation in grass species Pennisetum purpureum

Cited by 40 publications

References 50 publications

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.)

Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing

Integrating transcriptomic and metabolomic analysis of hormone pathways in Acer rubrum during developmental leaf senescence

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