Plant Gene Expression Analysis

Biosynthesis of oxyresveratrol in mulberry (Morus alba L.) is mediated by a group of p-coumaroyl-CoA 2'-hydroxylases acting upstream of stilbene synthases

The paper identifies and validates p-coumaroyl-CoA 2'-hydroxylases as key enzymes in oxyresveratrol biosynthesis in mulberry, using genomic, transcriptomic, and functional approaches.

Predictive metabolomics reveals leaf systemic metabolic signatures associated with floral traits in Camellia

This study uses predictive metabolomics to identify leaf metabolic signatures linked to floral traits in Camellia, finding distinct metabolite sets for flower colour and form with higher prediction accuracy for colour.

AMBER and GOLD: Polycistronic Genes for Betaxanthin Production in Plants

The paper develops and characterizes three new polycistronic constructs for producing yellow and fluorescent betaxanthins in plants.

MYB transcription factor, NtMYB308, regulates anthocyanin and lignin content, and fungal tolerance in tobacco

This study identifies NtMYB308 as a negative regulator of anthocyanin and lignin biosynthesis in tobacco, which influences fungal tolerance.

Genome-wide investigation of WRKY gene family in Lagenaria siceraria

This study identifies and classifies 57 WRKY genes in Lagenaria siceraria, revealing their structural organization, evolutionary expansion, and tissue-specific expression patterns.

Genome editing of the flavanone 3-hydroxylase gene produces a green Perilla line with elevated luteolin accumulation

This study uses CRISPR-Cas9 to edit the F3H gene in Perilla, resulting in green plants with increased luteolin accumulation and reduced anthocyanin production.

When flowers turn red: Pathogen induced flavonoid and anthocyanin biosynthesis in Chrysanthemum seticuspe confers resistanceto Botrytis cinerea

This study identifies pathogen-induced flavonoid and anthocyanin biosynthesis in Chrysanthemum seticuspe petals as a defense mechanism against Botrytis cinerea, showing their direct antifungal activity.

Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LAR

This study investigates the evolutionary dynamics and functional divergence of LAR genes across plant lineages through comparative and phylogenetic analyses.

Metabolic engineering of a tyrosine-specific phenylpropanoid pathway in plants

The paper engineers a tyrosine-specific phenylpropanoid pathway in plants and finds that it can overcome a seedling-lethal phenotype but causes developmental defects due to auxin transport inhibitor accumulation.

Dopamine biosynthesis in plants

The paper identifies dopamine biosynthesis pathway in plants using metabolite-based genome-wide association studies and demonstrates its role in tissue browning and stress tolerance.

A haplotype-resolved T2T genome assembly of Indigofera pseudotinctoria reveals the genetic basis of flavonoid biosynthesis in Chinese Indigo

This paper presents a haplotype-resolved T2T genome of Indigofera pseudotinctoria, revealing structural and regulatory basis of flavonoid biosynthesis.

The plant longevity gene AHL15 delays leaf senescence by repressing ORESARA1 and cytokinin degradation

This study shows AHL15 delays leaf senescence in Arabidopsis by repressing ORESARA1 and cytokinin degradation genes.

Discovery of pseudobaptigenin synthase, completing the (-)-maackiain biosynthetic pathway

The paper identifies TpPbS/CYP76F319, a cytochrome P450 enzyme that catalyzes methylenedioxy bridge formation in the biosynthesis of (-)-maackiain in red clover.

Cold-responsive MtCBF4-MtJMJ13 positive feedback loop negatively regulates anthocyanin biosynthesis in Medicago truncatula

The paper identifies a cold-responsive positive feedback loop between MtCBF4 and MtJMJ13 that negatively regulates anthocyanin biosynthesis in Medicago truncatula.

Natural variation in IBF1 disrupts its interaction with CHS1 and affects metabolism of hulls in rice

This study identifies a gene variant in rice that disrupts protein interaction and alters flavonoid and lignin metabolism, affecting hull color and pathogen resistance.

Genetic regulation of anthocyanin biosynthesis in Cornus species: The roles of R2R3-MYB transcription factors

The paper identifies R2R3-MYB transcription factors regulating anthocyanin biosynthesis in Cornus species and their roles in bract coloration.

CoExpPhylo - A Novel Pipeline for Biosynthesis Gene Discovery

CoExpPhylo combines coexpression analysis and phylogenetics to identify candidate genes in specialized biosynthetic pathways across species.

Evolutionary Rewiring of Anthocyanin Biosynthesis Pathway in Poaceae

The paper examines anthocyanin biosynthesis gene evolution in Poaceae, identifying independent lineage replacements and gene losses in Brachypodium.

Expansion of the DFR Gene Family in Fagopyrum

This study identifies three DFR gene copies in Fagopyrum, analyzes their evolutionary origin, and proposes DNA duplication associated with inversion as the mechanism for their emergence.

Salicylic acid accumulation correlates with low anthocyanin production in Arabidopsis

This study shows that high endogenous salicylic acid (SA) correlates with reduced anthocyanin production in Arabidopsis under anthocyanin-inducible conditions, and that SA signaling, not biosynthesis, is responsible for this inhibition.

Organ-Specific Long-Read Transcriptome Assembly of Stenochlaena palustris and Annotation of Anthocyanin Biosynthesis Genes

This paper presents a long-read transcriptome assembly of Stenochlaena palustris leaves and identifies genes involved in anthocyanin biosynthesis.

Iron deprivation activates aboveground cell wall biosynthesis in Populus and the role of PtrbHLH011

The paper shows iron deficiency activates secondary cell wall biosynthesis in poplar by downregulating the repressor PtrbHLH011, which suppresses SCW and iron homeostasis genes.

Temporal analysis of physiological phenotypes identifies novel metabolic and genetic underpinnings of senescence in maize

This study identifies novel metabolic and genetic factors associated with leaf senescence in maize through temporal analysis of physiological and metabolic changes.

Involvement of OsS40-14 in ROS and plastid organization related regulatory networks of dark-induced senescence in rice

This study identifies OsS40-14 as a transcription factor regulating ROS and plastid organization during dark-induced senescence in rice, showing its role in macromolecule metabolism and nutrient recycling.

Coordinated regulation of trichome morphogenesis and flavonoid pathway by a MYB HDZIP JAZ module in banana (Musa sp.)

This study identifies a MYB HDZIP JAZ module regulating trichome morphogenesis and flavonoid pathway in banana, showing their interaction and role in defense.

Chalcone isomerase-like impedes the lactone shunt and enhances flux partitioning in a bifurcated pathway towards isoflavonoid biosynthesis

This study shows that Chalcone isomerase-like proteins reduce lactone by-product formation and increase target compound titers in engineered yeast for isoflavonoid biosynthesis.

Unstable anthocyanin pigmentation in Streptocarpus sect. Saintpaulia (African violet) is due to transcriptional selectivity of a single MYB gene

The paper identifies a single MYB gene, SiMYB2, whose transcriptional selectivity causes unstable anthocyanin pigmentation in African violets through epigenetic regulation.

Dynamic Retuning of Precursor Supply Before and After the Evolution of the Dual Lignin Pathway in Poales

The paper investigates how the regulation of aromatic amino acid biosynthesis evolved in coordination with the emergence of the tyrosine-lignin pathway in Poales.

Type-B response regulators MaRR_B9 and MaRR_B12 coordinate cytokinin-mediated negative regulation of anthocyanin biosynthesis in banana fruits

This study identifies MaRR_B9 and MaRR_B12 as cytokinin-mediated regulators that repress anthocyanin biosynthesis in banana by directly interacting with and repressing key structural genes.

Essential Yet Dispensable: The Role of CINNAMATE 4-HYDROXYLASE in Rice Cell Wall Lignification

This study investigates the role of C4H in rice lignin biosynthesis, showing it is essential but dispensable due to the compensatory PTAL pathway.