Biology subjects

Spannagl, M.

Publications and source records attributed to Spannagl, M..

14 recordsLinked to original sources

bioRxiv2026

Evolutionary dynamics of the Timopheevii wheat lineage

Wheat, the most widely cultivated crop globally, includes multiple species with varying ploidy levels1. Globally cultivated species such as pasta and bread wheat belong to the Emmer lineage. In contrast, the Timopheevii lineage is of negligible agricultural significance2, yet it harbours genetic diversity of potential value for wheat improvement. Here, we present genomic resources for the Timopheevii wheat lineage. Our analyses uncovered extensive homoeologous exchange and genome instability in zhukovskys wheat, the hexaploid representative of the Timopheevii lineage. Population genomic analyses reveal a mosaic-like haplotype composition of domesticated tetraploid timopheevs wheat, suggesting it was once cultivated across a broader geographic range. This is further supported by the discovery of fossil haplotype segments in bread wheat landraces, likely derived from now-extinct domesticated timopheevs wheat populations. By examining the Timopheevii lineage, we provide new insights into the evolutionary dynamics of wheat, discovering previously underexplored and potentially useful genetic diversity for wheat improvement.

genomics↗

bioRxiv2026

Selecting genomes that matter: haplotype-based prioritization for iterative pangenome expansion

BackgroundAs pangenomes approach saturation, identifying additional genomes that contribute novel sequence information becomes increasingly difficult. Current sample-selection strategies often rely on global diversity metrics or variant counts and do not explicitly account for the composition of an existing pangenome, a limitation that becomes increasingly relevant as pangenomes mature. Here, we present SelHap, a haplotype-based pipeline that uses whole-genome sequencing (WGS) data to prioritize accessions based on their contribution of novel haplotypes relative to a defined background, enabling targeted and iterative pangenome expansion. ResultsWe applied SelHap to the barley pangenome, using 76 assembled genomes as a background to select new accessions from a large WGS panel. Using this approach, we generated chromosome-scale genome assemblies from 19 accessions selected with SelHap and from 17 elite lines selected based on their relevance in historical barley breeding. Across multiple benchmarking scenarios, SelHap-based selection consistently resulted in a greater increase in non-redundant (single-copy) pangenome sequence, demonstrating that prioritizing haplotype novelty relative to an existing background maximizes unrepresented sequence content. ConclusionsBy transforming complex haplotype-clustering outputs into interpretable summaries and ranked candidate lists, SelHap provides a practical framework for targeted pangenome expansion. Beyond sample selection, SelHap can facilitate ancestry and germplasm comparisons across diverse panels. As WGS data become more accessible, SelHap offers a scalable and interpretable solution for extending mature pangenomes by explicitly targeting previously unrepresented sequence space.

genomics↗

bioRxiv2025

Post-Domestication selection of MKK3 Shaped Seed Dormancy and End-Use Traits in Barley

Anthropogenic selection of grain traits such as dormancy has shaped the developmental trajectories of crop plants (1). In cereals, shortening dormancy provides rapid and even post-harvest germination, but increases the risk of weather-induced pre-harvest sprouting (PHS) with harvest losses estimated at beyond 1 billion USD a year (2, 3, 4). Our understanding of how, why, when and where diversification of cereal dormancy arose is fragmentary. Here, we show in the founder cereal crop barley (Hordeum vulgare) that the Mitogen-Activated Protein Kinase (MAPK) pathway regulates dormancy primarily through a mosaic of locus haplotypes comprising copy-number variation and inherent kinase activity of Mitogen-activated protein kinase kinase 3 (MKK3). We provide evidence supporting the historical selection of specific MKK3 haplotypes that shape dormancy levels according to changing climatic pressures. Understanding the regulatory landscape of MKK3 provides a genetic framework to balance short grain dormancy and PHS-avoidance during a period of rapid climate change.

plant biology↗

bioRxiv2024

Multiomics plasticity in seed traits of pan-genome wheat cultivars

The molecular basis of cultivar-level variations in polyploid wheat that enables environmental adaptation while maintaining yield and quality in polyploid wheat remains poorly understood. We conducted a detailed phenotypic assessment and multiomics analysis of nine pan-genome polyploid wheat cultivars grown under control and drought conditions. We aimed to investigate the subgenome-level variations, cultivar differences and biochemical mechanisms affecting plant fitness under moderate drought stress. Intrinsic water use efficiency, grain yield, and grain protein content and quality differed among cultivars, supporting the plasticity of drought stress responses. Biased proteome and metabolome abundance changes in response to moderate drought stress during the vegetative stage indicate different strategies for the utilization of homeologous protein isoforms assigned to the A, B, and D subgenomes. Drought effects were detected at the protein level, but significant changes were observed in central carbon pathway metabolites and micronutrient profiles. The subgenomic localization of seed storage proteins highlight differences in nutrient reservoir accumulation and emphasizes the enhanced role of S-rich prolamins in the stress response. Subgenomic variations define cultivar phenotypes by producing molecules that accumulate and enable the underlying trade-offs between environmental adaptation and yield- or quality-related traits. These variations can be used to select crops with increased stress resistance without compromising yield.

plant biology↗

bioRxiv2024

De novo annotation of the wheat pangenome reveals complexity and diversity of the hexaploid wheat pan-transcriptome

Wheat is the most widely cultivated crop in the world with over 215 million hectares grown annually. However, to meet the demands of a growing global population, breeders face the challenge of increasing wheat production by approximately 60% within the next 40 years. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome level the genomes of nine wheat cultivars to develop our understanding of genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars, across multiple different tissues and whole seedlings sampled at dusk/dawn. Analysis of these de novo annotations facilitated the discovery of genes absent from the Chinese Spring reference, identified genes specific to particular cultivars and defined the core and dispensable genomes. Expression analysis across cultivars and tissues revealed conservation in expression between a large core set of homeologous genes, but also widespread changes in subgenome homeolog expression bias between cultivars. Co-expression network analysis revealed the impact of divergence of sub-genome homeolog expression and identified cultivar-specific expression profiles. In a case study utilising both the newly constructed wheat pan-genome and pan-transcriptome we demonstrate prevalent variation in the prolamin superfamily and immune-reactive proteins across the pan-cultivars.In summary, this work provides both a valuable resource for the wider wheat community and reveals diversity in gene content and expression patterns between global wheat cultivars.

genomics↗

bioRxiv2022

Chromosome-scale assembly of the lablab genome - A model for inclusive orphan crop genomics

Orphan crops (also described as underutilised and neglected crops) hold the key to diversified and climate-resilient food systems. After decades of neglect, the genome sequencing of orphan crops is gathering pace, providing the foundations for their accelerated domestication and improvement. Recent attention has however turned to the gross under-representation of researchers in Africa in the genome sequencing efforts of their indigenous orphan crops. Here we report a radically inclusive approach to orphan crop genomics using the case of Lablab purpureus (L.) Sweet (syn. Dolichos lablab, or hyacinth bean) - a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led South-North plant genome collaboration produced a high-quality chromosomescale assembly of the lablab genome - the first chromosome-scale plant genome assembly locally sequenced in Africa. We also re-sequenced cultivated and wild accessions of lablab from Africa confirming two domestication events and examined the genetic diversity in lablab germplasm conserved in Africa. Our approach provides a valuable resource for lablab improvement and also presents a model that could be explored by other researchers sequencing indigenous crops particularly from Low and middle income countries (LMIC).

genomics↗

bioRxiv2021

Genome sequences of Aegilops species of section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement

Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Ae. longissima and Ae. speltoides. Whole-genome comparative analysis, along with the recently sequenced Ae. sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly similar and most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides is the closest ancestor of the wheat B subgenome and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding site leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement. TeaserGenome sequences of Aegilops species provides a key for efficient exploitation of this rich genetic resource in wheat improvement.

plant biology↗

bioRxiv2019

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We have developed TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluated the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and constructed an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

genomics↗

bioRxiv2018

Impact of transposable elements on genome structure and evolution in bread wheat

BackgroundTransposable elements (TEs) are ubiquitous components of genomes and they are the main contributors to genome evolution. The reference sequence of the hexaploid bread wheat (Triticum aestivum L.) genome enabled for the first time a comprehensive genome-wide view of the dynamics of TEs that have massively proliferated in the A, B, and D subgenomes.\n\nResultsTEs represent 85% of the genome. We traced back TE amplification dynamics in the evolutionary history of wheat and did not find large bursts in the wake of either the tetra- or the hexaploidization. Despite the massive turnover of TEs since A, B, and D diverged, 76% of TE families are present in similar proportions in the three subgenomes. Moreover, spacing between homeologous genes was also conserved. TE content around genes is very different from the TE space comprising large intergenic regions and families that are enriched or depleted from gene promoters are the same in the three subgenomes.\n\nConclusionsThe chromosome-scale assembly of the wheat genome provided an unprecedented genome-wide view of the organization and impact of TEs in such a complex genome. Our results suggest that TEs play a role at the structural level and that the overall chromatin structure is likely under selection pressure.

genomics↗

bioRxiv2018

The genome and metabolome of the tobacco tree, Nicotiana glauca: a potential renewable feedstock for the bioeconomy

BackgroundGiven its tolerance to stress and its richness in particular secondary metabolites, the tobacco tree, Nicotiana glauca, has been considered a promising biorefinery feedstock that would not be competitive with food and fodder crops.\n\nResultsHere we present a 3.5 Gbp draft sequence and annotation of the genome of N. glauca spanning 731,465 scaffold sequences, with an N50 size of approximately 92 kbases. Furthermore, we supply a comprehensive transcriptome and metabolome analysis of leaf development comprising multiple techniques and platforms.\n\nThe genome sequence is predicted to cover nearly 80% of the estimated total genome size of N. glauca. With 73,799 genes predicted and a BUSCO score of 94.9%, we have assembled the majority of gene-rich regions successfully. RNA-Seq data revealed stage-and/or tissue-specific expression of genes, and we determined a general trend of a decrease of tricarboxylic acid cycle metabolites and an increase of terpenoids as well as some of their corresponding transcripts during leaf development.\n\nConclusionThe N. glauca draft genome and its detailed transcriptome, together with paired metabolite data, constitute a resource for future studies of valuable compound analysis in tobacco species and present the first steps towards a further resolution of phylogenetic, whole genome studies in tobacco.

plant biology↗

bioRxiv2018

Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars

BackgroundRecent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the evolutionary dynamics of wheat genomes on a megabase-scale.\n\nResultsHere, we provide a comparative sequence analysis of the ~700-megabase chromosome 2D between two bread wheat genotypes - the old landrace Chinese Spring and the elite Swiss spring wheat line CH Campala Lr22a. There was a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations revealed four large insertions/deletions (InDels) of >100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the evolutionary mechanisms that caused these InDels. Three of the large InDels affected copy number of NLRs, a gene family involved in plant immunity. Analysis of single nucleotide polymorphism (SNP) density revealed three haploblocks of ~8 Mb, ~9 Mb and ~48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome.\n\nConclusionsThis comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.

genomics↗

bioRxiv2017

Epigenomic variation across a polyploid wheat diversity collection

Wheat has been domesticated into a large number of agricultural environments and has a remarkable ability to adapt to diverse environments. To understand this process, we survey genotype, repeat content and DNA methylation across a bread wheat landrace collection representing global genetic diversity. We identify independent variation in methylation, genotype and transposon copy number. We show that these, so far unexploited, sources of variation have had a massive impact on the wheat genome and that ancestral methylation states become preferentially hard coded as SNPs via 5-methylcytosine deamination. These mechanisms also drive local adaption, impacting important traits such as heading date and salt tolerance. Methylation and transposon diversity could therefore be used alongside single nucleotide polymorphism (SNP) based markers for breeding.

genomics↗

bioRxiv2017

European Flint reference sequences complement the maize pan-genome

The genomic diversity of maize is reflected by a large number of SNPs and substantial structural variation. Here, we report the de novo assembly of two European Flint maize lines to remedy the scarcity of sequence resources for the Flint pool. EP1 and F7 are important founder lines of European hybrid breeding programs. The lines were sequenced on an Illumina platform at 320X and 225X coverage. Using NRGene{acute}s DeNovoMAGIC 2.0 technology, pseudochromosomes were assembled encompassing a total of 2,463 Mb for EP1 and 2,405 Mb for F7. Structural and functional annotation of the two genomes is currently in progress. The two high-quality de novo assemblies complement the existing maize pan-genome and will pave the way for future functional and comparative studies.

genomics↗

bioRxiv2016

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Advances in genome sequencing and assembly technologies are generating many high quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimised data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents more than 78% of the genome with a scaffold N50 of 88.8kbp that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNAseq and PacBio full-length cDNAs to identify 104,091 high confidence protein-coding genes and 10,156 non-coding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop. [Supplemental material is available for this article.]

genomics↗