Biology subjects

de Oliveira, J. A. V. S.

Publications and source records attributed to de Oliveira, J. A. V. S..

7 recordsLinked to original sources

bioRxiv2026

Anthocyanin biosynthesis gene activation in nitrogen deprived Utricularia gibba L. under light or darkness

Utricularia gibba L. is an aquatic carnivorous plant with a diverse set of capabilities. Reddening of traps frequently occurs in old in vitro cultures. While anthocyanins are often responsible for red coloration in plants, not every plant turns red. Stress factors like high light or excess sucrose have previously been shown to induce the formation of anthocyanins. Here, we hypothesized the red trap formation to be dependent on nutrient deprivation and tested nitrogen deprivation. The results suggest, that only in combination with light, nitrogen deficiency leads to the activation of the complete anthocyanin biosynthesis pathway and visible red coloration. However, in darkness, anthocyanin biosynthesis appears generally less active compared to light conditions and expression of most anthocyanin biosynthesis genes is not significantly upregulated under nitrogen deficiency.

plant biology↗

bioRxiv2026

Valeriana officinalis genome sequence reveals candidate genes for valerenic acid biosynthesis and flavonoid metabolism

Valeriana officinalis is the scientific name for valerian, a plant known for producing valerenic acid, a compound with anxiolytic properties. Anxiety disorders represent a significant global health crisis, impacting everyday lives. As the global demand for natural, non-synthetic anxiety treatments rises, V. officinalis has emerged as a promising, yet underutilized, medicinal resource. Understanding its genome is the first step toward unraveling the biosynthetic genes underlying valerenic acid production, facilitating further research into its production. Here, we report the first genome sequence of valerian, with an assembly size of 3.3 Gbp and an N50 of 110.8 Mbp, and its corresponding annotation with 96.6% completeness, providing a foundational resource for studying the genetic basis of specialized metabolism in valerian. The value of this genome sequence for discoveries in specialized metabolism is demonstrated by the identification of the flavonoid biosynthesis gene repertoire and the selection of strong candidate genes for valerenic acid biosynthesis. This genome sequence holds the potential to support future functional studies aimed at elucidating the regulation of medically relevant metabolite pathways in V. officinalis.

genomics↗

bioRxiv2026

Genome sequence of the medicinal plant Urtica dioica reveals the genetic basis of the flavonoid metabolism

BackgroundUrtica dioica, also known as stinging nettle, is a widespread plant that can indicate high nitrogen availability in the soil. It is probably best known for the pain caused by touching it. U. dioica is also recognized as a medicinal plant with reports claiming applicability against numerous diseases. ResultsA highly continuous genome sequence was constructed based on nanopore long read sequencing data. The total assembly size is 1.1 Gbp with an N50 of 40.7 Mbp. RNA-seq data and hints from other species were integrated to produce a high quality annotation of the protein encoding genes. This genomic resource enabled the identification of genes involved in the flavonoid biosynthesis. A particular focus was on anthocyanin biosynthesis genes as these are crucial for high light and nitrogen deprivation stress response, which is revealed by redding of the leaves. ConclusionThis genomic resource provides the basis for future studies unraveling the biosynthesis pathways underlying various medically important compounds produced by stinging nettles.

plant biology↗

bioRxiv2026

NanoPlasmiQC: Full plasmid sequencing with ONT long-reads and automatic data analysis

Long-read sequencing has shown a rapid technological development during the last years. It has been established as the standard method for the sequencing of plant genomes and has also gained importance for full plasmid sequencing. As Sanger sequencing has a limited read length of about 1 kb, long read sequencing offers a great advantage, as the full plasmid can be sequenced in one read. Here, we present a cost-effective workflow to sequence full plasmids and compare the results against an expectation. The per plasmid cost of this workflow is determined by the number of plasmids investigated simultaneously, but can be lower than the price of a single Sanger sequencing reaction. We developed a workflow for automatic data processing, which allows us to complete sequencing and data analysis within a day.

genomics↗

bioRxiv2026

A hidden T-DNA-linked inversion-duplication causes a pronounced light-dependent phenotype in Arabidopsis

T-DNA insertion mutants are widely used to disrupt genes and infer their functions, yet the insertions can also trigger unintended genomic changes that confound phenotypic interpretation. Here, we used T-DNA insertion mutants affecting the major mitochondrial malate dehydrogenase (MDH1) and the heterodimeric NAD-dependent malic enzymes (ME1 and ME2) to examine their functional coordination across photoperiods and irradiance regimes. Under short days, especially at low light intensity, mdh1xme2 mutants were markedly smaller than wild type and, unexpectedly, than the mdh1xme1xme2 triple mutant, and they showed a more pronounced reduction in photosynthetic capacity. ME1 was undetectable in mdh1xme2, implying that the double and triple mutants effectively lack heterodimeric ME and should therefore behave similarly, contrary to what we observed. Whole-genome analysis resolved this discrepancy by revealing that the MDH1 T-DNA insertion in mdh1xme2 is accompanied by a major rearrangement, a 137-kbp duplication downstream of the insertion site, which was absent in the mdh1xme1xme2 triple mutant. This duplication increased gene dosage and elevated transcript abundance across the duplicated interval, while proteomics detected 5 of the 38 encoded proteins, including PEPC1. mdh1xme2 accumulated oxaloacetate-derived amino acids and displayed an altered carbon/nitrogen balance, making PEPC1 a plausible contributor to the exacerbated mdh1xme2 phenotype. Together, our data indicate that a T-DNA-linked structural variant can amplify expression of dozens of genes and intensify phenotypes at specific conditions, thereby affecting the interpretation of genotype-phenotype relationships. Because Agrobacterium-mediated DNA transfer also underpins many genome-editing workflows, our findings argue that structural validation around insertion/editing loci should be considered essential when interpreting T-DNA-derived plant lines.

plant biology↗

bioRxiv2026

Genome sequence of Tacca chantrieri reveals the genetic basis of floral pigmentation

Tacca chantrieri, black bat flower, has showy flowers often appearing almost black. Here, we present the genome sequence and corresponding annotation to identify the genetic basis of the pigmentation. Candidate genes associated with the anthocyanin biosynthesis were identified based on this genome sequence and investigated with respect to their properties. The best dihydroflavonol 4-reductase (DFR) candidate, which harbours all amino acid residues believed to be required for DFR activity, shows a threonine in the substrate preference determining position where most characterized DFRs display asparagine or aspartate. This amino acid residue appears to be frequent in the Dioscoreaceae family as a comprehensive investigation revealed.

plant biology↗

bioRxiv2026

Mitochondrial malate metabolism acts as a control hub for photosynthesis and carbon-nitrogen balance in Arabidopsis

Malate is a central metabolite in plant energy metabolism and biosynthesis and serves as a major carrier of carbon and reducing equivalents between chloroplasts, the cytosol, and mitochondria. However, how individual malate-converting systems contribute to physiology in specific subcellular compartments remains incompletely understood. Here, we investigated the impact of combined loss of mitochondrial malate dehydrogenase (MDH) and NAD-dependent malic enzyme (NAD-ME) activity in Arabidopsis thaliana by integrating reverse genetics, physiological analyses, transcriptomics, quantitative proteomics, and metabolite profiling. Specifically, we generated triple mutants (mdh1xme1xme2) lacking the predominant mitochondrial isoform MDH1 together with both NAD-ME subunits, thereby reducing overall mitochondrial malate conversion capacity. By growing plants under contrasting photoperiod and irradiance regimes to vary photosynthetic demand on malate-linked fluxes, we uncovered a conditional phenotype that was most pronounced under short-day/low-light conditions. Under these conditions, mdh1xme1xme2 exhibited impaired growth and photosynthetic performance, accompanied by cytosolic redox imbalance and altered chloroplast ultrastructure. Transcriptomic profiling revealed that low light unmasks a dawn-phase bottleneck in establishing photosynthetic and redox homeostasis. Consistent with this, the low-light plastid proteome revealed a reallocation away from chloroplast translation and photosynthetic capacity toward proteome maintenance, photoprotection/repair, and iron/ROS management, consistent with a protective acclimation state that nevertheless constrains carbon gain under energy limitation. Low light also triggered C/N imbalance and ammonium accumulation in the mutants. In contrast, increasing irradiance or extending the photoperiod largely alleviated these defects. Together, our results identified mitochondrial malate conversion capacity as a key control point coupling respiratory energy supply and redox homeostasis to photosynthetic metabolism when photosynthetic energy input is limiting.

plant biology↗