ORCID Profile
0000-0002-6771-6914
Current Organisation
Philipps-Universität Marburg
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Publisher: Oxford University Press (OUP)
Date: 06-2022
Abstract: The genomic landscape of recombination plays an essential role in evolution. Patterns of recombination are highly variable along chromosomes, between sexes, in iduals, populations, and species. In many eukaryotes, recombination rates are elevated in sub-telomeric regions and drastically reduced near centromeres, resulting in large low-recombining (LR) regions. The processes of recombination are influenced by genetic factors, such as different alleles of genes involved in meiosis and chromatin structure, as well as external environmental stimuli like temperature and overall stress. In this work, we focused on the genomic landscapes of recombination in a collection of 916 rye (Secale cereale) in iduals. By analyzing population structure among in iduals of different domestication status and geographic origin, we detected high levels of admixture, reflecting the reproductive biology of a self-incompatible, wind-pollinating grass species. We then analyzed patterns of recombination in overlapping subpopulations, which revealed substantial variation in the physical size of LR regions, with a tendency for larger LR regions in domesticated subpopulations. Genome-wide association scans (GWAS) for LR region size revealed a major quantitative-trait-locus (QTL) at which, among 18 annotated genes, an ortholog of histone H4 acetyltransferase ESA1 was located. Rye in iduals belonging to domesticated subpopulations showed increased synaptonemal complex length, but no difference in crossover frequency, indicating that only the recombination landscape is different. Furthermore, the genomic region harboring rye ScESA1 showed moderate patterns of selection in domesticated subpopulations, suggesting that larger LR regions were indirectly selected during domestication to achieve more homogeneous populations for agricultural use.
Publisher: Oxford University Press (OUP)
Date: 19-01-2021
Abstract: Pan-genomic studies aim at representing the entire sequence ersity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genomes along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this review, we summarize the current approaches to building pan-genomes as an in silico representation of plant sequence ersity and outline relevant methods for their effective utilization in linking structural with phenotypic variation. We propose as future research avenues (i) transcriptomic and epigenomic studies across multiple reference genomes and (ii) the development of user-friendly and feature-rich pan-genome browsers.
Publisher: Springer Science and Business Media LLC
Date: 18-03-2021
DOI: 10.1038/S41588-021-00807-0
Abstract: Rye ( Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a erse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye’s incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye–wheat introgressions.
Publisher: Elsevier BV
Date: 09-2022
DOI: 10.1016/J.TPLANTS.2022.05.005
Abstract: More than half a billion years ago a streptophyte algal lineage began terraforming the terrestrial habitat and the Earth's atmosphere. This pioneering step enabled the subsequent evolution of all complex life on land, and the past decade has uncovered that many traits, both morphological and genetic, once thought to be unique to land plants, are conserved across some streptophyte algae. They provided the common ancestor of land plants with a repertoire of genes, of which many were adapted to overcome the new biotic and abiotic challenges. Exploring these molecular adaptations in non-tracheophyte species may help us to better prepare all green life, including our crops, for the challenges precipitated by the climate change of the Anthropocene because the challenges mostly differ by the speed with which they are now being met.
Publisher: Springer Science and Business Media LLC
Date: 16-11-2018
DOI: 10.1007/S00122-018-3234-Z
Abstract: The concept of a pan-genome refers to intraspecific ersity in genome content and structure, encompassing both genes and intergenic space. Pan-genomic studies employ a combination of de novo sequence assembly and reference-based alignment to discover and genotype structural variants. The large size and complex structure of Triticeae genomes were for a long time an obstacle for genomic research in barley and its relatives. Now that a reference genome is available, computational pipelines for high-quality sequence assembly are in place, and sequence costs continue to drop, investigations into the structural ersity of the barley genome seem within reach. Here, we review the recent progress on pan-genomics in the model grass Brachypodium distachyon, and the cereal crops rice and maize, and devise a multi-tiered strategy for a pan-genome project in barley. Our design involves: (1) the construction of high-quality de novo sequence assemblies for a small core set of representative genotypes, (2) short-read sequencing of a large ersity panel of genebank accessions to medium coverage and (3) the use of complementary methods such as chromosome-conformation capture sequencing and k-mer-based association genetics. The in silico representation of the barley pan-genome may inform about the mechanisms of structural genome evolution in the Triticeae and supplement quantitative genetics models of crop performance for better accuracy and predictive ability.
Publisher: MDPI AG
Date: 09-07-2021
Abstract: Red algae (Rhodophyta) belong to the superphylum Archaeplastida, and are a species-rich group exhibiting erse morphologies. Theory has it that the unicellular red algal ancestor went through a phase of genome contraction caused by adaptation to extreme environments. More recently, the classes Porphyridiophyceae, Bangiophyceae, and Florideophyceae experienced genome expansions, coinciding with an increase in morphological complexity. Transcription-associated proteins (TAPs) regulate transcription, show lineage-specific patterns, and are related to organismal complexity. To better understand red algal TAP complexity and evolution, we investigated the TAP family complement of uni- and multi-cellular red algae. We found that the TAP family complement correlates with gain of morphological complexity in the multicellular Bangiophyceae and Florideophyceae, and that abundance of the C2H2 zinc finger transcription factor family may be associated with the acquisition of morphological complexity. An expansion of heat shock transcription factors (HSF) occurred within the unicellular Cyanidiales, potentially as an adaption to extreme environmental conditions.
Publisher: Springer Science and Business Media LLC
Date: 28-06-2019
DOI: 10.1038/S41588-019-0443-6
Abstract: Genebanks have the long-term mission of preserving plant genetic resources as an agricultural legacy for future crop improvement. Operating procedures for seed storage and plant propagation have been in place for decades, but there is a lack of effective means for the discovery and transfer of beneficial alleles from landraces and wild relatives into modern varieties. Here, we review the prospects of using molecular passport data derived from genomic sequence information as a universal monitoring tool at the single-plant level within and between genebanks. Together with recent advances in breeding methodologies, the transformation of genebanks into bio-digital resource centers will facilitate the selection of useful genetic variation and its use in breeding programs, thus providing easy access to past crop ersity. We propose linking catalogs of natural genetic variation and enquiries into biological mechanisms of plant performance as a long-term joint research goal of genebanks, plant geneticists and breeders.
Publisher: Cold Spring Harbor Laboratory
Date: 12-12-2019
DOI: 10.1101/2019.12.11.869693
Abstract: We present a chromosome-scale annotated assembly of the rye ( Secale cereale L. inbred line ‘Lo7’) genome, which we use to explore Triticeae genomic evolution, and rye’s superior disease and stress tolerance. The rye genome shares chromosome-level organization with other Triticeae cereals, but exhibits unique retrotransposon dynamics and structural features. Crop improvement in rye, as well as in wheat and triticale, will profit from investigations of rye gene families implicated in pathogen resistance, low temperature tolerance, and fertility control systems for hybrid breeding. We show that rye introgressions in wheat breeding panels can be characterised in high-throughput to predict the yield effects and trade-offs of rye chromatin.
Publisher: Cold Spring Harbor Laboratory
Date: 28-01-2022
DOI: 10.1101/2022.01.26.472964
Abstract: This manuscript is discussing the method of Weyrich et al ., 2017, “Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus”. When studying the dietary profile of a Neanderthal specimen from El Sidrón cave (Spain) by sequencing ancient DNA present in calcified dental plaque (calculus) the authors identified a wide-range of potential food sources, including woolly rhinoceros, mushrooms, pine nuts, and moss – namely the less-than-abundant model species Physcomitrium patens . We doubted that Neanderthals were actually eating P. patens . By analyzing the ancient DNA reads using different mapping methods, we show likely a misinterpretation based on the previously used methods. The probability of Neanderthals eating P. patens is the same as eating rice or tomato. However, neither crop was grown in Europe at the time Neanderthals thrived.
Publisher: Springer Science and Business Media LLC
Date: 18-07-2016
DOI: 10.1038/NG.3611
Abstract: The cereal grass barley was domesticated about 10,000 years before the present in the Fertile Crescent and became a founder crop of Neolithic agriculture. Here we report the genome sequences of five 6,000-year-old barley grains excavated at a cave in the Judean Desert close to the Dead Sea. Comparison to whole-exome sequence data from a ersity panel of present-day barley accessions showed the close affinity of ancient s les to extant landraces from the Southern Levant and Egypt, consistent with a proposed origin of domesticated barley in the Upper Jordan Valley. Our findings suggest that barley landraces grown in present-day Israel have not experienced major lineage turnover over the past six millennia, although there is evidence for gene flow between cultivated and sympatric wild populations. We demonstrate the usefulness of ancient genomes from desiccated archaeobotanical remains in informing research into the origin, early domestication and subsequent migration of crop species.
No related grants have been discovered for Mona Schreiber.