Plant Gene Expression Analysis

Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae

The paper investigates anthocyanin pigmentation loss in Cucurbitaceae, finding systematic absence of biosynthesis genes and proposing a stepwise loss mechanism.

CRK5 preserves antioxidant homeostasis and prevents cell death during dark-induced senescence through inhibiting the salicylic acid signaling pathway

This paper shows CRK5 inhibits the salicylic acid signaling pathway to preserve antioxidant balance and prevent cell death during dark-induced senescence in Arabidopsis.

Engineering auronidin production in Marchantia polymorpha enables a new class of plant-derived textile pigments

This study engineers auronidin production in Marchantia polymorpha to create sustainable textile pigments, demonstrating their feasibility for dyeing cotton yarn.

A cyclo-DOPA 6-O-glucosyltransferase-mediated route for gomphrenin I biosynthesis in Basella alba and Gomphrena globosa

The paper identifies cyclo-DOPA glucosyltransferases from Basella alba and Gomphrena globosa that mediate gomphrenin I biosynthesis and shows their structural and functional differences.

Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation

The paper presents the genome sequence of Digitalis purpurea and identifies genetic variations associated with flower color and morphology.

Replicated repurposing of an ancestral transcriptional complex in land plants

The paper identifies ancestral MBW transcriptional complexes in liverworts, showing their role in flavonoid pathway regulation and oil body maturation, and suggests a pattern of evolutionary duplication and co-option in land plants.

Identification and Functional Characterization of Isoflavone Synthase Gene Family in Pea (Pisum sativum): The Entry Point to Pisatin Biosynthesis

This study identifies and functionally characterizes IFS genes in pea, showing their role in pisatin biosynthesis and disease resistance.

Genomic Structural Variation Underlies Cell-Type-Specific Betacyanin Variegation in Chenopodium quinoa

The paper identifies a genomic insertion in quinoa that restores a functional CYP76AD gene, leading to cell-type-specific betacyanin accumulation in epidermal bladder cells.

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.

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.

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.

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.

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.

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.

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.

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.

Arabidopsis thaliana ACTIN DEPOLYMERIZING FACTORs play a role in leaf senescence regulation

This study shows subclass I ADFs, especially ADF4, regulate leaf senescence in Arabidopsis by affecting gene expression and nuclear localization.

SnRK1 acts upstream of PAP1, contributing to fine-tuning flavonoid biosynthesis in high-light.

This study shows SnRK1 regulates flavonoid biosynthesis by suppressing MYBL2 and promoting PAP1, which fine-tunes anthocyanin and flavonol production in high-light conditions.

In silico characterisation of PAL homologs and metabolomic profiling of shade response indicates potential presence of PTALs and Tyr as a probable precursor of lignin biosynthesis in conifers

The paper characterizes PAL homologs and metabolomic profiles in conifers under shade, suggesting potential PTALs and Tyr as a lignin precursor.

Loss of pleiotropic regulatory functions in Tannin1, the sorghum ortholog of Arabidopsis master regulator TTG1

The paper investigates the pleiotropic regulatory functions of Tannin1 in sorghum, finding no conserved pleiotropic effects in leaf tissue compared to Arabidopsis TTG1.

Ethylene Modulates the Phenylpropanoid Pathway by Enhancing VvMYB14 Expression via the ERF5-Melatonin-ERF104 Pathway in Grape Seeds

This study shows ethylene enhances VvMYB14 expression through the ERF5-melatonin-ERF104 pathway, modulating the phenylpropanoid pathway in grape seeds.

CRISPR-Cas9 mediated deletions of FvMYB46 reduces fruit set and biosynthesis of flavonoids in Fragaria vesca

This study shows that deleting FvMYB46 in Fragaria vesca reduces fruit set and flavonoid biosynthesis by affecting pollen germination, cell wall structure, and ROS signaling.

Coding-sequence evolution does not explain divergence in petal anthocyanin pigmentation between Mimulus luteus var. luteus and M. l. variegatus

The paper investigates whether coding-sequence changes in MYB5a contributed to anthocyanin pigmentation divergence between two Mimulus species, finding non-coding cis-regulatory evolution was the key factor.

Genome-wide analysis of flavonoid biosynthetic genes in Musaceae (Ensete, Musella, and Musa species) reveals amplification of flavonoid 3',5'-hydroxylase

The paper identifies and analyzes flavonoid biosynthetic genes in Musaceae species, revealing gene amplification and copy number variation linked to stress responses and pigmentation.

T and Z, Partial Seed Coat Patterning Genes in Common Bean, Provide Insight into the Structure and Protein Interactions of a Plant MBW Complex

The paper identifies and characterizes the Z, P, and T genes in common bean that form an MBW complex regulating flavonoid gene expression through protein interactions.