Automatic identification of players in the flavonoid biosynthesis with application on the biomedicinal plant<i>Croton tiglium</i>

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

doi:10.1101/2020.06.27.175067

Cited by 8 publications

(1 citation statement)

References 130 publications

(127 reference statements)

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“…The annotation of all assembled unigenes was carried out through BLAST search () against various databases such as NR (ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz), COG, KOG, eggNOG, SwissProt, GO, and KEGG, with an e-value threshold (≤10 –5 ) . HMMER software v3.2.1 was used to map the predicted amino acid sequences of the unigenes to the Pfam database, with an e-value threshold (≤10 –10 ). , The annotated data for the unigenes were then retrieved. , …”

Section: Methodsmentioning

confidence: 99%

ZbMYB111 Expression Positively Regulates ZbUFGT-Mediated Anthocyanin Biosynthesis in Zanthoxylum bungeanum with the Involvement of ZbbHLH2

Zhang,

Han,

Zhao

et al. 2024

J. Agric. Food Chem.

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Anthocyanin (ACN)-derived pigmentation in the red Zanthoxylum bungeanum peel is an essential commercial trait. Therefore, exploring the metabolic regulatory networks involved in peel ACN levels in this species is crucial for improving its quality. However, its underlying transcriptional regulatory mechanisms are still unknown. This transcriptomic and bioinformatics study not only discovered a new TF (ZbMYB111) as a potential regulator for ACN biosynthesis in Z. bungeanum peel, but also deciphered the underlying molecular mechanisms of ACN biosynthesis. Overexpression of ZbMYB111 and f lavonoid 3-O-glucosyltransferase (ZbUFGT) induced ACN accumulation in both Z. bungeanum peels and callus along with Arabidopsis thaliana and tobacco flowers, whereas their silencing impaired ACN biosynthesis. Therefore, the dual-luciferase reporter, yeast-one-hybrid, and electrophoretic mobility shift assays showed that ZbMYB111 directly interacted with the ZbUFGT promoter to activate its expression. This diverted the secondary metabolism toward the ACN pathway, thereby promoting ACN accumulation.

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Section: Methodsmentioning

confidence: 99%

ZbMYB111 Expression Positively Regulates ZbUFGT-Mediated Anthocyanin Biosynthesis in Zanthoxylum bungeanum with the Involvement of ZbbHLH2

Zhang,

Han,

Zhao

et al. 2024

J. Agric. Food Chem.

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Mapping-by-Sequencing Reveals Genomic Regions Associated with Seed Quality Parameters in Brassica napus

Schilbert

Pucker

Ries

et al. 2022

Genes

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Rapeseed (Brassica napus L.) is an important oil crop and has the potential to serve as a highly productive source of protein. This protein exhibits an excellent amino acid composition and has high nutritional value for humans. Seed protein content (SPC) and seed oil content (SOC) are two complex quantitative and polygenic traits which are negatively correlated and assumed to be controlled by additive and epistatic effects. A reduction in seed glucosinolate (GSL) content is desired as GSLs cause a stringent and bitter taste. The goal here was the identification of genomic intervals relevant for seed GSL content and SPC/SOC. Mapping by sequencing (MBS) revealed 30 and 15 new and known genomic intervals associated with seed GSL content and SPC/SOC, respectively. Within these intervals, we identified known but also so far unknown putatively causal genes and sequence variants. A 4 bp insertion in the MYB28 homolog on C09 shows a significant association with a reduction in seed GSL content. This study provides insights into the genetic architecture and potential mechanisms underlying seed quality traits, which will enhance future breeding approaches in B. napus.

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Metabolite Profiling and Transcriptome Analysis Provide Insight into Seed Coat Color in Brassica juncea

Shen

Tang

Zhang

et al. 2021

IJMS

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The allotetraploid species Brassica juncea (mustard) is grown worldwide as oilseed and vegetable crops; the yellow seed-color trait is particularly important for oilseed crops. Here, to examine the factors affecting seed coat color, we performed a metabolic and transcriptomic analysis of yellow- and dark-seeded B. juncea seeds. In this study, we identified 236 compounds, including 31 phenolic acids, 47 flavonoids, 17 glucosinolates, 38 lipids, 69 other hydroxycinnamic acid compounds, and 34 novel unknown compounds. Of these, 36 compounds (especially epicatechin and its derivatives) accumulated significantly different levels during the development of yellow- and dark-seeded B. juncea. In addition, the transcript levels of BjuDFR, BjuANS,BjuBAN, BjuTT8, and BjuTT19 were closely associated with changes to epicatechin and its derivatives during seed development, implicating this pathway in the seed coat color determinant in B. juncea. Furthermore, we found numerous variations of sequences in the TT8A genes that may be associated with the stability of seed coat color in B. rapa, B. napus, and B. juncea, which might have undergone functional differentiation during polyploidization in the Brassica species. The results provide valuable information for understanding the accumulation of metabolites in the seed coat color of B. juncea and lay a foundation for exploring the underlying mechanism.

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Automatic identification of players in the flavonoid biosynthesis with application on the biomedicinal plantCroton tiglium

Cited by 8 publications

References 130 publications

ZbMYB111 Expression Positively Regulates ZbUFGT-Mediated Anthocyanin Biosynthesis in Zanthoxylum bungeanum with the Involvement of ZbbHLH2

ZbMYB111 Expression Positively Regulates ZbUFGT-Mediated Anthocyanin Biosynthesis in Zanthoxylum bungeanum with the Involvement of ZbbHLH2

Mapping-by-Sequencing Reveals Genomic Regions Associated with Seed Quality Parameters in Brassica napus

Metabolite Profiling and Transcriptome Analysis Provide Insight into Seed Coat Color in Brassica juncea

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