Biology subjects

Donath, A.

Publications and source records attributed to Donath, A..

8 recordsLinked to original sources

bioRxiv2025

Samplify: A versatile tool for image-based segmentation and annotation of seed abortion phenotypes

Automated seed phenotyping has wide applications in research and agriculture and relies on easy-to-use platforms and pipelines. Seed phenotyping in the model species Arabidopsis thaliana poses a significant challenge due to the large number of tiny seeds produced by individual plants, which are difficult to manually separate and count. Manual counting methods are time-consuming and prone to user bias, particularly for subtle phenotypic changes. To address these limitations, we developed Samplify, a scalable, automated pipeline for seed segmentation and classification. By integrating classical image processing techniques with Metas Segment Anything Model (SAM), Samplify effectively segments Arabidopsis seeds, even in dense clusters where conventional methods fail. To demonstrate its versatility, we quantified the seed abortion occurring in interploidy crossings in Arabidopsis, often referred to as triploid block. Samplify includes a Random Forest classifier trained on a set of computed seed shape features that enables the categorization of seeds into normal, partially aborted, and fully aborted seeds, automating the manual classification process. The tool, designed as a command-line application, significantly reduces manual annotation workload. Our validation across multiple datasets demonstrates high segmentation and classification reliability, making Samplify a valuable resource for the plant research community.

plant biology↗

bioRxiv2024

Genetic architecture of the tomato fruit lipidome; new insights link lipid and volatile compounds

Tomato (Solanum lycopersicum L.) fruit flavor is determined by a combination of multiple volatile compounds, including several derived from lipids and fatty acids. Although fruit flavor has been intensively studied, the linkage between lipid metabolism and flavor remains largely undefined. Here, we performed a genome-wide association study (GWAS) and QTL mapping for the fruit lipid content from 550 tomato accessions and 107 backcross inbred lines (BILs) in two consecutive seasons. Over 130 lipid compounds were identified and mapped, allowing for the identification of over 600 metabolic QTL (mQTL). We further described and validated candidate genes associated with lipid content. Among them is a lipase-like protein (TomLLP) whose function was validated in vivo using overexpression lines in tomato and knockout mutants in Arabidopsis. We also identified functions for three enzymes: a class III lipase (Sl-LIP8), a cyclopropane-fatty-acyl-phospholipid synthase (CFAPS1), and Lipoxygenase C (TomLoxC). By utilizing knockout lines for CFAPS1 and CRISPR-Cas9 loss-of-function lines for Sl-LIP8 and TomLoxC, we demonstrated the functional importance of these enzymes in fruit lipid metabolism. Our study provides a comprehensive analysis of the tomato fruit lipidome and insights into key genes that shaped the natural variation in tomato lipid content and their links to flavor-associated volatile compounds.

molecular biology↗

bioRxiv2023

Phylogenomics recovers multiple origins of portable case-making in caddisflies (Insecta: Trichoptera), the world's most common underwater architects

Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16,000 described species. They play an outsized role in freshwater ecology and environmental engineering in streams, rivers, and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programs. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case-making, have been unanswered due to the lack of a well-resolved phylogenetic tree. To shed light on these questions in Trichoptera, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 206 species, representing 48 of 52 extant families and 174 genera. We calibrated and dated the tree with a set of 33 carefully selected fossils. The first caddisflies originated in the Permian and the major suborders began to diversify in the Triassic. Ancestral state reconstruction and diversification analysis revealed that portable case-making evolved in three separate lineages and shifts in diversification occurred in concert with key evolutionary innovations other than case-making.

evolutionary biology↗

bioRxiv2021

Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in Hymenoptera

Cuticular hydrocarbons (CHCs) cover the cuticle of insects and serve as desiccation barrier and for chemical communication. While the main enzymatic steps of CHC biosynthesis are well understood, few of the underlying genes have been identified. Here we show how exploitation of intrasexual CHC dimorphism in a mason wasp, Odynerus spinipes, in combination with whole-genome sequencing and comparative transcriptomics facilitated identification of such genes. RNAi-mediated knockdown of twelve candidate gene orthologs in honey bees, Apis mellifera, confirmed nine genes impacting CHC profile composition. Most of them have predicted functions consistent with current knowledge of CHC metabolism. However, we found first-time evidence for a fatty acid amide hydrolase also influencing CHC profile composition. In situ hybridization experiments furthermore suggest trophocytes participating in CHC biosynthesis. Our results set the base for experimental CHC profile manipulation in Hymenoptera and imply that the evolutionary origin of CHC biosynthesis predates the arthropods colonization of land.

molecular biology↗

bioRxiv2020

Are fleas highly modified Mecoptera? Phylogenomic resolution of Antliophora (Insecta: Holometabola)

Insect orders have been defined and stable for decades, with few notable exceptions (e.g., Blattodea and Psocoptera). One of the few remaining questions of order-level monophyly is that of Mecoptera in respect to the phylogenetic placement of Siphonaptera (fleas). We used a large set of transcriptomic nucleotide sequence data representing 56 species and more than 3,000 single-copy genes to resolve the evolutionary history of Antliophora, including fleas (Siphonaptera), scorpionflies and relatives (Mecoptera), and true flies (Diptera). We find that fleas and mecopterans together are the sister group of flies. However, our data and/or analyses are unable to distinguish whether fleas are sister to a monophyletic Mecoptera, or whether they arose from within extant mecopteran families, rendering Mecoptera paraphyletic. We did not detect parameter bias in our dataset after applying a broad range of detection methods. Counter to a previous hypothesis that placed fleas within Mecoptera as the sister group to wingless boreids (snow fleas), we found a potential sister group relationship between fleas and the enigmatic family Nannochoristidae. Although we lack conclusive evidence, it seems possible that fleas represent the most-species rich group of modern mecopterans and that their parasitic lifestyle and morphological adaptations have simply made them unrecognizable in respect to their order-level classification.

evolutionary biology↗

bioRxiv2020

Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

BackgroundCladobranch sea slugs represent roughly half of the biodiversity of soft-bodied, marine gastropod molluscs (Nudibranchia) on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as bioindicators and providers of medical drug leads), the evolutionary history of cladobranch sea slugs is not yet fully understood. Here, we amplify the current knowledge on the phylogenetic relationships by extending the cladobranch and outgroup taxon sampling using transcriptome data. ResultsWe generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa. We complemented our taxon sampling with previously published transcriptome data, resulting in a final supermatrix covering 56 species from all but one accepted cladobranch superfamilies. Transcriptome assembly using six different assemblers, selection of those assemblies providing the largest amount of potentially phylogenetically informative sites, and quality-driven compilation of data sets resulted in three different supermatrices: one with a full coverage of genes per species (446 single-copy protein-coding genes) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1,767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximum statistical support for all major splits and phylogenetic relationships on family level. The only discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. ConclusionsOur data matrices and the inferred trees inferred can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The correct placement of E. pulchra, however, proves challenging, even with large data sets. Moreover, quartet mapping shows that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

evolutionary biology↗

bioRxiv2020

How old are dragonflies and damselflies? Odonata (Insecta) transcriptomics resolve familial relationships

Dragonflies and damselflies, representing the insect order Odonata, are among the earliest flying insects with living (extant) representatives. However, unravelling details of their long evolutionary history, such as egg laying (oviposition) strategies, is impeded by unresolved phylogenetic relationships, an issue particularly prevalent in damselfly families and fossil lineages. Here we present the first transcriptome-based phylogenetic reconstruction of Odonata, analyzing 2,980 protein-coding genes in 105 species representing nearly all of the orders families (except Austropetaliidae and Neopetaliidae). All damselfly families and most dragonfly families are recovered as monophyletic groups. Our Molecular clock estimates suggest that crown-Zygoptera (damselflies) and -Anisoptera (dragonflies) both arose during the late Triassic. Several of the observed long inner branches in our topology are indicative of the extinction of once flourishing lineages. We also find that exophytic egg laying behaviour with a reduced ovipositor evolved in certain dragonflies during the late Jurassic / early Cretaceous. Lastly, we find that certain fossils have an unexpected deterring impact in divergence dating analysis.

evolutionary biology↗

bioRxiv2020

ProminTools: Shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences

Biominerals are crucial to the fitness of many organism and studies of the mechanisms of biomineralization are driving research into novel materials. Biomineralization is generally controlled by a matrix of organic molecules including proteins, so proteomic studies of biominerals are important for understanding biomineralization mechanisms. Many such studies identify large numbers of proteins of unknown function, which are often of low sequence complexity and biased in their amino acid composition. A lack of user-friendly tools to find patterns in such sequences and robustly analyse their statistical properties relative to the background proteome means that they are often neglected in follow-up studies. Here we present ProminTools, a user-friendly package for comparison of two sets of protein sequences in terms of their global properties and motif content. Outputs include data tables, graphical summaries in an html file and an R-script as a starting point for data-set specific visualizations. We demonstrate the utility of ProminTools using a previously published shell matrix proteome of the giant limpet Lottia gigantea.

bioinformatics↗