Plant Gene Expression Analysis

Biosynthesis and Physiological Significance of Organ-Specific Flavonol Glycosides in Solanaceae

The paper identifies organ-specific flavonol glycosides in Solanaceae and shows that K2 is essential for male fertility while Q2 is not.

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.

Investigating postharvest seed coat darkening in common beans: a molecular perspective beyond the major P gene

The paper identifies the P-PvMYB3A-PvWD9 complex as key regulators of proanthocyanidin biosynthesis in common beans, explaining seed coat darkening and its genetic basis.

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.

Heat stress negatively affects betalain biosynthesis in Amaranthus tricolor through down-regulation of CYP76AD1 and 5GT

The paper identifies CYP76AD1 and 5GT as heat stress-downregulated genes affecting betalain biosynthesis in Amaranthus tricolor.

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.

Genome sequence of the blue flowering Centaurea cyanus

The paper sequences the genome of Centaurea cyanus using long-read sequencing to identify genes involved in blue flower pigmentation.

The miR156/SPL9 interaction mode regulates the anthocyanin accumulation in potato

This study investigates the role of miR156a and its target gene StSPL9 in regulating anthocyanin accumulation in potato tubers through transcriptomic and metabolomic analyses.

Genome sequence of the ornamental plant Aquilegia vulgaris reveals the flavonoid biosynthesis gene repertoire

The paper reports genome sequences of two Aquilegia vulgaris plants with different flower colors and identifies structural variants and candidate genes involved in anthocyanin biosynthesis.

Genome-enabled stilbenoid gene cluster discovery in Pleuropterus multiflorus

The paper identifies a novel stilbenoid biosynthetic gene cluster in Pleuropterus multiflorus using genome sequencing and analysis, revealing key enzymes and regulatory mechanisms.

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 sequence of the medicinal plant Tropaeolum majus provides insights into flavonoid biosynthesis

The paper presents the genome sequence of Tropaeolum majus and identifies genes involved in flavonoid biosynthesis, including those required for flavonol glycoside production.

Multi-omics analysis reveals the mechanism of BnC07MYB3a is involved in seed coat color in Brassica napus L.

The paper identifies BnC07MYB3a as a repressor of flavonoid biosynthesis in rapeseed, leading to yellow seed coat color through interaction with bHLH and WD40 proteins.

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.

Genome-wide Identification of the Laccase Gene Family in White Jute (Corchorus capsularis): Potential Targets for Lignin Engineering in Bast Fiber

This study identifies 32 laccase genes in white jute, showing their expression patterns and potential roles in lignification, with two genes highlighted as candidates for low-lignin fiber development.

Genome sequence and RNA-seq analysis reveal genetic basis of flower coloration in the giant water lily Victoria cruziana

The paper identifies genetic and transcriptional factors responsible for flower color change in Victoria cruziana using genome and RNA-seq analysis.

Comparative transcriptome database for Camellia sinensis reveals genes important for flavonoid synthesis in tea plants

The paper constructs a comparative transcriptome database for Camellia sinensis to identify genes involved in flavonoid synthesis across tea cultivars.

KIPEs3: Automatic annotation of biosynthesis pathways

KIPEs3 automatically annotates biosynthesis pathways, demonstrating its application to flavonoid and carotenoid pathways in multiple plant species.

CrWRKY42 positively regulates chlorophyll degradation and carotenoid biosynthesis in citrus

The paper identifies CrWRKY42 as a transcription factor that coordinates chlorophyll degradation and carotenoid biosynthesis in citrus by directly regulating genes in both pathways, altering fruit color during ripening.

Multi-omics data and analysis reveal the formation of key pathways of different colors in Torenia fournieri flowers

The paper reports the genome of Torenia fournieri and analyzes flower color formation using genomics, transcriptomics, and metabolomics.

Predictive links between petal color and pigment quantities in natural Penstemon hybrids

The paper establishes predictive relationships between petal color and pigment quantities in Penstemon hybrids using spectral reflectance and anthocyanin measurements.

Three R2R3-MYB transcription factors from banana (Musa spp.) activate structural anthocyanin biosynthesis genes as part of an MBW complex

Mutant Ppbbx24-del gene positively regulates light-induced anthocyanin accumulation in the red pear

The paper identifies a mutant Ppbbx24-del gene that enhances light-induced anthocyanin accumulation in red pears through regulatory interactions with PpHY5.

Omics Analysis Unveils the Pathway Involved in the Purple Coloration in Tomato Seedling and Fruits

The paper identifies genes involved in anthocyanin biosynthesis in tomato seedlings and fruits using omics analysis, revealing pathways independent of SlHY5.

Multifaceted roles of a light-responsive factor LhWRKY44 in promoting anthocyanin accumulation in Asiatic hybrid lilies (Lilium spp.)

This study identifies LhWRKY44 as a light-responsive transcription factor that promotes anthocyanin accumulation in Asiatic hybrid lilies by regulating biosynthesis, transport, and downstream gene expression.

Identification, characterisation and recombinant expression of flavonoid 3',5'-hydroxylases and cytochrome P450 reductases from Vaccinium species

The paper identifies and expresses flavonoid 3',5'-hydroxylases and cytochrome P450 reductases from Vaccinium species to test their potential in microbial production of anthocyanin precursors, but finds the recombinant enzymes are inactive.