Boas Pucker

NanoPlasmiQC provides a cost-effective workflow for full plasmid sequencing using ONT long-reads and automated data analysis.

The paper compares genome sequences of pigmented and unpigmented Muscari commutatum individuals to identify the genetic basis of flower color variation, finding a loss of the F3H gene in the unpigmented plant.

The paper identifies a R2R3-MYB transcription factor as a genetic determinant of anthocyanin pigmentation variation in cassava cultivars through comparative genomics and phylogenetic analysis.

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

The paper introduces XpBrew, a Python workflow for RNA-seq processing, and PanXpresso, a gene expression dataset collection across multiple taxa.

This study shows nitrogen deprivation in Utricularia gibba triggers anthocyanin biosynthesis only under light, not darkness.

This paper reports the first genome sequence of Valeriana officinalis, identifies candidate genes for valerenic acid biosynthesis and flavonoid metabolism, and provides a foundation for studying specialized metabolism in valerian.

The paper investigates the evolutionary and functional diversity of eukaryotic Mo-insertases using phylogenetic analysis, sequence comparison, and structural modeling, revealing domain organization plasticity and strict active site conservation.

DupyliCate is a Python tool for analyzing gene duplications across species, demonstrating its use on plant and microbial datasets.

The paper presents the genome sequence of Urtica dioica and identifies genes involved in flavonoid biosynthesis, particularly anthocyanin synthesis, linked to stress responses.

The paper presents a phased genome of Rubus armeniacus and identifies genes and metabolic changes responsible for dark pigmentation in blackberries.

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

The paper reanalyzes RNA-seq data from Zhang et al., 2024 to show no evidence of anthocyanin biosynthesis in Chenopodium quinoa, supporting betalain and carotenoid pigmentation instead.

The paper identifies a T-DNA-linked inversion-duplication in Arabidopsis that enhances gene expression and exacerbates a light-dependent phenotype in mdh1xme2 mutants.

This study shows that mitochondrial malate metabolism regulates photosynthesis and carbon-nitrogen balance in Arabidopsis under low-light conditions.

The paper presents the genome sequence of Tacca chantrieri to identify genetic basis of its dark floral pigmentation, focusing on anthocyanin biosynthesis genes.

The paper presents the genome sequence of Begonia manicata and identifies genes responsible for red pigmentation in its leaves and stems.

The paper shows that higher anthocyanin levels in flowers correlate with increased resistance to Botrytis cinerea, and that this defense is conserved in Asteraceae but lost in cultivated species.

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

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

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

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.

This study identifies PHO2 as a negative regulator of arbuscular mycorrhizal symbiosis in high phosphate conditions in rice and Nicotiana benthamiana.

Comparing nine Solanaceae genomes reveals a conserved withanolide gene cluster; three of its P450s, expressed in yeast and N. benthamiana, oxidise 24-methyldesmosterol toward the withanoside V aglycone.

The paper presents a method to estimate genome size using mapping-based approaches and demonstrates its application across various organisms.

This study identifies immune response genes in cassava during early CBSV infection by comparing gene expression in resistant and susceptible lines.

The paper reports a high-quality haplotype-resolved genome assembly of a cassava line resistant to cassava brown streak disease, revealing structural variations linked to resistance.

NAVIP predicts the functional impact of sequence variants by considering neighboring variants, improving accuracy over single-variant tools like SnpEff.

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