A5069204429- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Plant Virus Research Studies
- Plant Disease Resistance and Genetics
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Genetic diversity and population structure
- Plant and Fungal Interactions Research
- CRISPR and Genetic Engineering
- Plant Reproductive Biology
- Sugarcane Cultivation and Processing
- Plant Pathogens and Resistance
- Saffron Plant Research Studies
- Legume Nitrogen Fixing Symbiosis
- Animal Genetics and Reproduction
- Machine Learning in Bioinformatics
- Hibiscus Plant Research Studies
- Bacterial Genetics and Biotechnology
- Plant tissue culture and regeneration
- Plant Pathogens and Fungal Diseases
- Mycorrhizal Fungi and Plant Interactions
- Advances in Cucurbitaceae Research
- Plant Ecology and Taxonomy Studies
- Plant pathogens and resistance mechanisms
- DNA and Biological Computing
Technische Universität Dresden
2014-2025
RWTH Aachen University
2024-2025
Nawi Graz
2023-2024
University of Graz
2024
University of Oxford
2023
John Wiley & Sons (United Kingdom)
2023
Hudson Institute
2023
John Wiley & Sons (United States)
2023
Institut de Biologie de l'École Normale Supérieure
2012-2014
École Normale Supérieure - PSL
2012
Extrachromosomal circular DNAs (eccDNAs) are ring-like DNA structures physically separated from the chromosomes with 100 bp to several megabasepairs in size. Apart carrying tandemly repeated DNA, eccDNAs may also harbor extra copies of genes or recently activated transposable elements. As occur all eukaryotes investigated so far and likely play roles stress, cancer, aging, they have been prime targets recent research-with their investigation limited by scarcity computational tools.Here, we...
Abstract Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements genetic with not much in common: whereas mainly viewed as housekeeping genes that uphold all prime genome functions, generally portrayed selfish disruptive. These opposing characteristics also mirrored other attributes: organization tandem (ribosomal DNAs) versus a dispersed manner (transposable elements); evolution concerted by diversification activity prolongs genomic stability...
FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve suitability for comparison of consensus error-prone sequences, harbors routines strict relaxed handling ambiguities substitutions. Our shading modules facilitate interpretation motif identification by adding information on sequence annotations similarities. Combined with collage-like outputs, supports simultaneous visual screening large sets, enabling use routine...
Saffron crocus (Crocus sativus) is the source of most expensive spice world, produced from manually harvested stigmas, thus serving as a cash crop for rural communities. However, despite its economic importance, genome and chromosomes are poorly studied. C. sativus sterile triploid species harboring eight chromosome triplets, propagated only clonal lineage by corms. Saffron's evolutionary origin, parental allo- or autotriploidy has been matter discussion almost century. We performed survey...
Summary If two related plant species hybridize, their genomes may be combined and duplicated within a single nucleus, thereby forming an allotetraploid. How the emerging balances co‐evolved is still matter of ongoing research. Here, we focus on satellite DNA (satDNA), fastest turn‐over sequence class in eukaryotes, aiming to trace its emergence, amplification, loss during speciation allopolyploidization. As model, used Chenopodium quinoa Willd. (quinoa), allopolyploid crop with 2 n = 4 x 36...
Abstract Climate change is expected to cause major shifts in boreal forests which are vast areas of Siberia dominated by two species the deciduous needle tree larch ( Larix ). The differ markedly their ecosystem functions, thus respective ranges global relevance. However, drivers distribution not well understood, part because paleoecological data at level lacking. This study tracks time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We...
The saffron-producing Crocus sativus (L.) and its wild relative C. cartwrightianus (Herb.) are key species for understanding genetic evolution in this genus. Molecular-cytogenetic methods, especially fluorescent situ hybridization (FISH), essential exploring the relationships Yet, preparing high-quality chromosomes FISH analysis across remains difficult. A standardized protocol achieving clear well-separated mitotic is still lacking. This study aimed to assess effectiveness of pretreatments...
Chromoviruses are one of the three genera Ty3-gypsy long terminal repeat (LTR) retrotransposons, and present in high copy numbers plant genomes. They widely distributed within kingdom, with representatives even lower plants such as green red algae. Their hallmark is presence a chromodomain at C-terminus integrase. The exhibits structural characteristics similar to proteins heterochromatin protein 1 (HP1) family, which mediate binding each chromovirus type specific histone variants. A...
A large fraction of eukaryotic genomes is made up long interspersed nuclear elements (LINEs). Due to their capability create novel copies via error-prone reverse transcription, they generate multiple families and reach high copy numbers. Although mammalian LINEs have been well described, plant only poorly investigated. Here, we present a systematic cross-species survey in higher shedding light on LINE evolution as diversity, facilitating annotation genome projects. Applying Hidden Markov...
Endogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability replicate through reverse transcription initiate viral infection. Similar closely related retrotransposons, extant were retained often amplified in for several million years. Here, we characterize complete genomic EPRV fraction crop sugar beet (Beta vulgaris,...
Abstract The 5S rRNA genes are among the most conserved nucleotide sequences across all species. Similar to preservation we observe occurrence of 5S-related nonautonomous retrotransposons, so-called Cassandras. Cassandras harbor highly rDNA-related within their long terminal repeats, advantageously providing them with internal promoter. However, dynamics Cassandra retrotransposon evolution in context gene sequence information and structural arrangement still unclear, especially: (1) do...
Despite the many cheap and fast ways to generate genomic data, good exact genome assembly is still a problem, with especially repeats being vastly underrepresented often misassembled. As short reads in low coverage are already sufficient represent repeat landscape of any given genome, read cluster algorithms were brought forward that provide identification classification. But how can trustworthy, reliable representative consensuses be derived from unassembled genomes?
Abstract Background and Aims Ornamental hortensias are bred from a reservoir of over 200 species in the genus Hydrangea s.l. (Hydrangeaceae), valued gardens, households landscapes across globe. The phenotypic diversity hortensia cultivars, hybrids wild relatives is mirrored by their genomic variation, with differences genome size, base chromosome numbers ploidy level. We aim to understand chromosomal basis variation. Therefore, we analysed six different origins setups for repeatome...
Transposable elements (TEs) are DNA sequences that able to move from their location in the genome by cutting or copying themselves another locus. As such, they increasingly recognized as impacting all aspects of function. With dramatic reduction cost sequencing, it is now possible resequence whole genomes order systematically characterize novel TE mobilization a particular individual. However, this task made difficult inherently repetitive nature sequences, which some eukaryotes compose over...
Abstract Background As the major source of sugar in moderate climates, sugar-producing beets ( Beta vulgaris subsp. ) have a high economic value. However, low genetic diversity within cultivated requires introduction new traits, for example to increase their tolerance and resistance attributes – traits that often reside crop wild relatives. For this, information beet relatives phylogenetic placements each other are crucial. To answer this need, we sequenced assembled complete plastome...
Abstract Most crop plants, including sugar beet ( Beta vulgaris subsp. ), suffer from domestication bottlenecks and low genetic diversity caused by extensive selection for few traits. However, wild relatives (CWRs) harbour useful traits relevant improvement, enhanced adaptation to biotic abiotic stresses. Especially polyploids are interesting an evolutionary perspective as genes undergo reorganisation after the polyploidisation event. Through neo-and subfunctionalisation, novel functions...
LTR retrotransposons and retroviruses are closely related. Although a viral envelope gene is found in some all retroviruses, only the latter show infectivity. The identification of Ty3-gypsy-like possessing putative envelope-like open reading frames blurred taxonomical borders led to establishment Errantivirus, Metavirus Chromovirus genera within Metaviridae. Only few plant Errantiviruses have been described, their evolutionary history not well understood. In this study, we investigated 27...
SUMMARY Sugar beet and its wild relatives share a base chromosome number of nine similar morphologies. Yet, interspecific breeding is impeded by sequence divergence that still not fully understood. Since repetitive DNAs are among the fastest evolving parts genome, we investigated, if repeatome innovations losses linked to chromosomal differentiation speciation. We traced genome chromosome‐wide evolution across 13 species comprising all sections genera Beta Patellifolia . For this, combined...
We characterized a novel type of plant non-LTR retrotransposons, identified as the BNR family, in sugar beet (Beta vulgaris) genomes. Although their ORF2 sequences were similar to those previously analysed LINEs (long interspersed nuclear elements) L1 clade, ORF1 differ strongly from most LINEs. Two domains identified, containing conserved secondary motif, known RNA recognition motif (RRM). lacks zinc finger that is typical LINEs, but has an RRM likely have RNA-binding function. are highly...
Abstract Showing a high sequence similarity, the evolutionary closely related bacterial poly(A) polymerases (PAP) and CCA-adding enzymes catalyze quite different reactions—PAP adds tails to RNA 3′-ends, while synthesize CCA at 3′-terminus of tRNAs. Here, two highly conserved structural elements corresponding Escherichia coli were characterized. The first element is set amino acids that was identified in as template region determining enzymes’ specificity for CTP ATP. same also present PAP,...