Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium

Pucker, Boas; Reiher, Franziska; Schilbert, Hanna Marie

doi:10.3390/plants9091103

Cited by 57 publications

(96 citation statements)

References 132 publications

(165 reference statements)

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“…The TT8 locus is also involved in the regulation of flavonoid biosynthesis in Arabidopsis (Nesi et al, 2000). The combined role of bHLH42 and MYB123 in plants has been well-investigated and is more well-known in plant responses to thermal stress (Wos, 2016), salt stress (Jiang et al, 2009), and flavonoid biosynthesis (Pucker et al, 2020). Similarly, another bHLH TF GL3 that primarily interacts with GL1 for trichrome development has also been shown to be required for anthocyanin accumulation and is induced by nitrogen depletion (Feyissa et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

Expression Characterization of Flavonoid Biosynthetic Pathway Genes and Transcription Factors in Peanut Under Water Deficit Conditions

et al. 2021

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Drought is one of the hostile environmental stresses that limit the yield production of crop plants by modulating their growth and development. Peanut (Arachis hypogaea) has a wide range of adaptations to arid and semi-arid climates, but its yield is prone to loss due to drought. Other than beneficial fatty acids and micronutrients, peanut harbors various bioactive compounds including flavonoids that hold a prominent position as antioxidants in plants and protect them from oxidative stress. In this study, understanding of the biosynthesis of flavonoids in peanut under water deficit conditions was developed through expression analysis and correlational analysis and determining the accumulation pattern of phenols, flavonols, and anthocyanins. Six peanut varieties (BARD479, BARI2011, BARI2000, GOLDEN, PG1102, and PG1265) having variable responses against drought stress have been selected. Higher water retention and flavonoid accumulation have been observed in BARI2011 but downregulation has been observed in the expression of genes and transcription factors (TFs) which indicated the maintenance of normal homeostasis. ANOVA revealed that the expression of flavonoid genes and TFs is highly dependent upon the genotype of peanut in a spatiotemporal manner. Correlation analysis between expression of flavonoid biosynthetic genes and TFs indicated the role of AhMYB111 and AhMYB7 as an inhibitor for AhF3H and AhFLS, respectively, and AhMYB7, AhTTG1, and AhCSU2 as a positive regulator for the expression of Ah4CL, AhCHS, and AhF3H, respectively. However, AhbHLH and AhGL3 revealed nil-to-little relation with the expression of flavonoid biosynthetic pathway genes. Correlational analysis between the expression of TFs related to the biosynthesis of flavonoids and the accumulation of phenolics, flavonols, and anthocyanins indicated coregulation of flavonoid synthesis by TFs under water deficit conditions in peanut. This study would provide insight into the role of flavonoid biosynthetic pathway in drought response in peanut and would aid to develop drought-tolerant varieties of peanut.

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Section: Discussionmentioning

confidence: 99%

Expression Characterization of Flavonoid Biosynthetic Pathway Genes and Transcription Factors in Peanut Under Water Deficit Conditions

et al. 2021

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“…The final pathway analyses were mostly based on the tool Mercator4 and Mapman4 [35]. In addition, differential expressed MYB genes were functional annotated based on several datasets Arabidopsis thaliana MYBs [36], Beta vulgaris MYBs [37], Musa acuminata MYBs [38], Croton tiglium MYBs [39], Dioscorea rotundata MYBs and Dioscorea dumetorum MYBs via KIPEs (https://github.com/bpucker/KIPEs). GO term assignment and enrichment were performed using Blast2GO [40] via OmicsBox with cutoff 55, Go weight 5, e-value 1.e-6, HSP-hit coverage cutoff 80 and hit filter 500.…”

Section: Methodsmentioning

confidence: 99%

Section: Data Processing and Functional Analysismentioning

confidence: 99%

Transcriptome sequence reveals candidate genes involving in the post-harvest hardening of trifoliate yamDioscorea dumetorum

Siadjeu

Mayland‐Quellhorst

Laubinger

et al. 2021

Preprint

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Storage ability of D. dumetorum is restricted by a severe phenomenon of post-harvest hardening which starts 72h after harvest and renders tubers inedible. Previous work has only focused on the biochemistry changes affecting the PHH on D. dumetorum. To the best of our knowledge nobody has identified candidate genes responsible for hardness on D. dumetorum. Here, transcriptome analysis of D. dumetorum tubers was performed, 4 months after emergence (4MAE), after harvest (AH), 3 days AH (3DAH) and 14 days AH (14DAH) on four accessions using RNA-Seq. In total between AH and 3DAH, 165, 199,128 and 61 differentially expressed genes (DEGs) were detected in Bayangam 2, Fonkouankem 1, Bangou 1 and Ibo sweet 3 respectively. Functional analysis of DEGs revealed that genes encoding for cellulose synthase A, xylan O-acetyltransferase chlorophyll a/b binding protein 1,2,3,4 and transcription factor MYBP were found predominantly and significantly up-regulated 3DAH, implying that genes were potentially involved in the post-harvest hardening. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into genes expression in yam tubers after harvest and valuable information for molecular breeding against the post-harvest hardening. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into genes expression in yam tubers after harvest and valuable information for molecular breeding against the post-harvest hardening.

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“…The final pathway analyses were mostly based on the tools Mercator4 and Mapman4 [34]. In addition, differentially-expressed MYB genes were functional annotated based on several datasets Arabidopsis thaliana MYBs [35], Beta vulgaris MYBs [36], Musa acuminata MYBs [37], Croton tiglium MYBs [38], Dioscorea rotundata MYBs and Dioscorea dumetorum MYBs via KIPEs (https://github.com/bpucker/KIPEs, accessed on 15 April 2021). GO term assignment and enrichment were performed using Blast2GO [39] via OmicsBox with cutoff 55, Go weight 5, e-value 1.e-6, HSP-hit coverage cutoff 80 and hit filter 500.…”

Section: Data Processing and Functional Analysismentioning

confidence: 99%

Transcriptome Sequence Reveals Candidate Genes Involving in the Post-Harvest Hardening of Trifoliate Yam Dioscorea dumetorum

Siadjeu

Mayland‐Quellhorst

Pande

et al. 2021

Plants

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Storage ability of trifoliate yam (Dioscorea dumetorum) is restricted by a severe post-harvest hardening (PHH) phenomenon, which starts within the first 24 h after harvest and renders tubers inedible. Previous work has only focused on the biochemical changes affecting PHH in D. dumetorum. To the best of our knowledge, the candidate genes responsible for the hardening of D. dumetorum have not been identified. Here, transcriptome analyses of D. dumetorum tubers were performed in yam tubers of four developmental stages: 4 months after emergence (4MAE), immediately after harvest (AH), 3 days after harvest (3DAH) and 14 days after harvest (14DAH) of four accessions (Bangou 1, Bayangam 2, Fonkouankem 1, and Ibo sweet 3) using RNA-Seq. In total, between AH and 3DAH, 165, 199, 128 and 61 differentially expressed genes (DEGs) were detected in Bayangam 2, Fonkouankem 1, Bangou 1 and Ibo sweet 3, respectively. Functional analysis of DEGs revealed that genes encoding for CELLULOSE SYNTHASE A (CESA), XYLAN O-ACETYLTRANSFERASE (XOAT), CHLOROPHYLL A/B BINDING PROTEIN 1, 2, 3, 4 (LHCB1, LHCB2, LHCB3, and LCH4) and an MYB transcription factor were predominantly and significantly up-regulated 3DAH, implying that these genes were potentially involved in the PHH as confirmed by qRT-PCR. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into gene expression in yam tubers after harvest and valuable information for molecular breeding against the PHH.

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Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium

Cited by 57 publications

References 132 publications

Expression Characterization of Flavonoid Biosynthetic Pathway Genes and Transcription Factors in Peanut Under Water Deficit Conditions

Expression Characterization of Flavonoid Biosynthetic Pathway Genes and Transcription Factors in Peanut Under Water Deficit Conditions

Transcriptome sequence reveals candidate genes involving in the post-harvest hardening of trifoliate yamDioscorea dumetorum

Transcriptome Sequence Reveals Candidate Genes Involving in the Post-Harvest Hardening of Trifoliate Yam Dioscorea dumetorum

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