Biology subjects

Himmelbauer, H.

Publications and source records attributed to Himmelbauer, H..

4 recordsLinked to original sources

bioRxiv2026

Genome and methylome of the root crop table beet (Beta vulgaris)

Table beet (Beta vulgaris subsp. vulgaris var. vulgaris), also known as red beet, garden beet, or beetroot, is an important crop with both nutritional and agricultural value, yet high-quality genomic resources for this taxon are limited. We present the chromosome-scale genome assembly RefTab-1 based on PacBio and Hi-C data of the inbred table beet genotype W357B. The assembly has a size of 668.6 Mbp and an N50 of 72 Mbp, with 96% of the assembly anchored to nine pseudo-chromosomes. We annotated 64% repetitive DNA, 24,863 protein-coding genes, and 10,405 non-coding RNA loci including a 5S rRNA cluster on chromosome 4. Genome-wide methylation profiling using EM-seq revealed high levels of cytosine methylation in repeats and context-specific methylation in gene bodies and promoters. We propose three terpene synthase candidate genes based on functional annotation and based on their location near a genetic marker on chromosome 8 previously associated with geosmin concentration, responsible for the earthy aroma of table beet. Comparative analysis with sugar beet indicated overall structural conservation and a 9 Mbp inversion on chromosome 9. These high-quality resources for table beet will enhance genetic, epigenetic, and comparative studies in Beta vulgaris, advancing beet biology and breeding programs.

genomics↗

bioRxiv2022

Molecular signatures of alternative fitness strategies in a facultatively social hover wasp

Social insect queens and workers represent ideal models with which to understand the expression and regulation of alternative reproductive phenotypes. Most research in this area has focused on the molecular regulation of reproductive castes in obligately social taxa with complex social systems, while relatively few studies have addressed the molecular basis of caste in species in which the division of reproductive labour is more plastic. As a result, it is not clear whether, and to what extent, the mechanisms of caste in species with reproductive plasticity are the same as those that exist at the highest levels of social complexity. To address this knowledge gap, we analyse brain transcriptomic data for non-reproductives and reproductives of the facultatively social hover wasp Liostenogaster flavolineata, a representative of one of the simplest forms of social living. By experimentally manipulating the reproductive queues exhibited by social groups of this species, we show that reproductive division of labour in this species is associated with surprisingly distinct transcriptomic signatures, similar to those observed in more complex social taxa; that variation in gene expression among non-reproductives reflects their investment into foraging effort more than their social rank; and that distinct co-expressed gene sets are associated with differential investment into alternative reproductive strategies. These results elucidate robust transcriptomic signals that represent the proximate basis of division of labour at the simplest level of insect sociality, and show these signals to be remarkably similar to those in more derived species.

evolutionary biology↗

bioRxiv2018

The genome of Ectocarpus subulatus highlights unique mechanisms for stress tolerance in brown algae

Brown algae are multicellular photosynthetic stramenopiles that colonize marine rocky shores worldwide. Ectocarpus sp. Ec32 has been established as a genomic model for brown algae. Here we present the genome and metabolic network of the closely related species, Ectocarpus subulatus Kutzing, which is characterized by high abiotic stress tolerance. Since their separation, both strains show new traces of viral sequences and the activity of large retrotransposons, which may also be related to the expansion of a family of chlorophyll-binding proteins. Further features suspected to contribute to stress tolerance include an expanded family of heat shock proteins, the reduction of genes involved in the production of halogenated defence compounds, and the presence of fewer cell wall polysaccharide-modifying enzymes. Overall, E. subulatus has mainly lost members of gene families down-regulated in low salinities, and conserved those that were up-regulated in the same condition. However, 96% of genes that differed between the two examined Ectocarpus species, as well as all genes under positive selection, were found to encode proteins of unknown function. This underlines the uniqueness of brown algal stress tolerance mechanisms as well as the significance of establishing E. subulatus as a comparative model for future functional studies.

genomics↗

bioRxiv2017

nextPARS: Parallel probing of RNA structures in Illumina

RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation of in-vitro parallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing.

genomics↗