Biology subjects

Narbona, E.

Publications and source records attributed to Narbona, E..

5 recordsLinked to original sources

bioRxiv2026

Benchmarking long-read RNA sequencing for de novo transcriptome assembly in non-model plant species: insights from Moricandia arvensis

De novo transcriptome assembly is the standard approach for constructing a reference transcriptome in non-model plants that lack a high-quality genome, yet short-read assemblies struggle to resolve full-length isoforms. Long-read Iso-Seq (PacBio) captures full-length transcripts directly, but its use as a primary reference and the choice of downstream assembly pipeline remains poorly benchmarked. Here, we construct genome-free Iso-Seq reference transcriptomes for two organs, flower and leaf, of the non-model species Moricandia arvensis (L.) DC. (Brassicaceae), and systematically compare pipeline strategies combining Iso-Seq clustering, CD-HIT redundancy reduction, and Cogent graph-based reconstruction, benchmarked by BUSCO completeness, RSEM short-read mapping, and TransDecoder ORF completeness. We find that the optimal pipeline is organ specific. For flower, CD-HIT pre-filtering followed by Cogent reconstruction produced a high-quality reference (95.3% BUSCO complete). For the leaf, the same Cogent step was detrimental, reducing BUSCO completeness from 90.1% to 78.0% by incorrectly merging distinct genes; therefore, CD-HIT at 95% identity without reconstruction was retained. We trace this divergence to organ-specific input-data characteristics: leaf transcripts show extreme full-length-read expression skew and predominantly single-isoform gene support, depriving Cogent's graph algorithm of the multi-isoform evidence it requires. We find that the concentration of full-length reads among the most highly expressed transcripts predicts pipeline suitability before reconstruction, with per-transcript read depth acting as a necessary but non-discriminating floor. Because the leaf reference lacked gene-level structure, we further recovered gene-isoform grouping using expression-aware read-clustering (Corset), which preserved completeness while restoring the paralog structure expected of a paleopolyploid genome and outperformed sequence-only clustering. Our results provide a robust, genome-free framework for constructing full-length reference transcriptomes in non-model plant species and demonstrate that pipeline choice must be evaluated per organ rather than assuming one size fits all.

bioinformatics↗

bioRxiv2024

Transcontinental patterns in floral pigment frequencies among animal-pollinated species

Flower coloration arises primarily from pigments that serve dual functions: attracting pollinators and mitigating environmental stresses. Among major flower pigment groups, anthocyanins and UV-absorbing phenylpropanoids are particularly notable for fulfilling both roles. Their importance suggests that both pigment types should be widespread in flowers. Here, we analyze the UV-Vis absorption profiles of major floral pigments to assess their potential protective role against UV radiation and demonstrate that this protection is largely confined to UV-absorbing phenylpropanoids. We also analyzed the floral pigment composition of 926 animal-pollinated species from California, southern Spain, and southeastern Brazil. UV-absorbing phenylpropanoids were ubiquitous, while anthocyanins occurred in [~]56% of species, carotenoids in [~]37%, and chlorophylls in [~]17%. Pigment frequencies varied with abiotic and biotic factors, such as light environment in Spain, and pollinator type, such as insect versus hummingbird, in California. Despite these local differences, our findings reveal a consistent regional distribution of floral pigments.

plant biology↗

bioRxiv2023

Can a flower color ancestral polymorphism transcend speciation?

Polymorphisms are common in nature, but they are rarely shared among closely related species. They could originate through convergence, ancestral polymorphism, or introgression. Although shared neutral genomic variation is commonplace, very few examples of shared functional traits exist. The blue-orange petal color polymorphisms in two closely related species, Lysimachia monelli and L. arvensis were investigated with UV-vis reflectance spectra, flavonoid biochemistry, and transcriptome comparisons followed by climate niche analysis. The similarities in reflectance spectra, biochemistry, and transcriptomes suggest a single shift from blue-to-orange shared by both lineages is possible. Transcriptome comparisons reveal two orange-specific genes are directly involved in both blue-orange color polymorphisms: DFR-2 specificity redirects flux from the malvidin to the pelargonidin while BZ1-2 stabilizes the pelargonidin with glucose, producing the orange pelargonidin 3-glucoside. The climate niches for each color morph are the same between the two species for three temperature characteristics but differ for four precipitation variables. We suggest that this persistent flower color polymorphism may represent an ancestrally polymorphic trait that has transcended speciation with some unique ecological effects.

evolutionary biology↗

bioRxiv2021

Phenotypic plasticity triggers rapid morphological convergence

Phenotypic convergence, the independent evolution of similar traits, is ubiquitous in nature, happening at all levels of biological organizations and in most kinds of living beings. Uncovering its mechanisms remains a fundamental goal in biology. Evolutionary theory considers that convergence emerges through independent genetic changes selected over long periods of time. We show in this study that convergence can also arise through phenotypic plasticity. We illustrate this idea by investigating how plasticity drives Moricandia arvensis, a mustard species displaying within-individual polyphenism in flowers, across the morphological space of the entire Brassicaceae family. By compiling the multidimensional floral phenotype, the phylogenetic relationships, and the pollination niche of over 3000 Brassicaceae species, we demonstrated that Moricandia arvensis exhibits a plastic-mediated within-individual floral disparity greater than that found not only between species but also between higher taxonomical levels such as genera and tribes. As a consequence of this divergence, M. arvensis moves outside the morphospace region occupied by its ancestors and close relatives, crosses into a new region where it encounters a different pollination niche and converges phenotypically with distant Brassicaceae lineages. Our study suggests that, by inducing phenotypes that explore simultaneously different regions of the morphological space, plasticity triggers rapid phenotypic convergence.

evolutionary biology↗

bioRxiv2020

UV radiation increases flavonoid protection but decreased reproduction in Silene littorea

Plants respond to changes in ultraviolet (UV) radiation via morphological and physiological changes. Among the variety of plant UV-responses, the synthesis of UV-absorbing flavonoids constitutes an effective non-enzymatic mechanism to mitigate photoinhibitory and photooxidative damage caused by UV stress, either reducing the penetration of incident UV radiation or acting as quenchers of reactive oxygen species (ROS). In this study, we designed a UV-exclusion experiment to investigate the effects of UV radiation in Silene littorea. We spectrophotometrically quantified concentrations of both anthocyanins and non-anthocyanin flavonoids (flavones) in petals, calyces, leaves and stems. Furthermore, we analyzed the UV effect on the photosynthetic activity in hours of maximum solar radiation and we tested the impact of UV radiation on male and female reproductive performance. We found that anthocyanin concentrations showed a significant decrease of about 20% with UV-exclusion in petals and stems, and 30% in calyces. Flavone concentrations showed a significant reduction of approximately 25% in calyces and stems, and 12% in leaves. Photochemical efficiency of plants grown under UV stress decreased sharply at maximum light stress, but their ability for recovery after light-stress was not affected. In addition, exposure to UV radiation does not seem to affect ovule production or seed set, but decreases the total seed production per plant and pollen production by 69% and 31%, respectively. Our results demonstrate that UV radiation produced opposite effects on flavonoid accumulation and reproduction in S. littorea. UV stress increased flavonoid concentrations, suggesting a photoprotective role of flavonoids against UV radiation, but had negative consequences for reproduction. We propose that this trade-off helps this species to occupy exposed habitats with high UV radiation.

evolutionary biology↗