Biology subjects

Haberer, G.

Publications and source records attributed to Haberer, G..

8 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↗

bioRxiv2024

A pangenome and pantranscriptome of hexaploid oat

Oat grain is a traditional human food rich in dietary fiber that contributes to improved human health. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogs. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here, we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oats along with an atlas of gene expression across six tissues of different developmental stages in 23 accessions. We describe the interplay of gene expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory up-regulation of the remaining homeologs, but this process is constrained by subgenome divergence. Chromosomal rearrangements have significantly impacted recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semidwarf mutant has risen to prominence in Australian elite varieties. The oat pangeome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

genomics↗

bioRxiv2024

Adaptive diversification through structural variation in barley

Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here, we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that have become hot spots of gene copy number variation in evolutionarily recent times. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release, and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that rapid evolution at structurally complex loci may have helped crop plants adapt to new selective regimes in agricultural ecosystems.

plant biology↗

bioRxiv2019

The de novo reference genome and transcriptome assemblies of the wild tomato species Solanum chilense

BackgroundWild tomato species, like Solanum chilense, are important germplasm resources for enhanced biotic and abiotic stress resistance in tomato breeding. In addition, S. chilense serves as a model system to study adaptation of plants to drought and to investigate the evolution of seed banks. However to date, the absence of a well annotated reference genome in this compulsory outcrossing, very diverse species limits in-depth studies on the genes involved.\n\nFindingsWe generated [~]134 Gb of DNA and 157 Gb of RNA sequence data of S chilense, which yielded a draft genome with an estimated length of 914 Mb in total encoding 25,885 high-confidence (hc) predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% (18,290) of the hc gene models are additionally supported by RNA-seq data derived from leaf tissue samples. A benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% BUSCO genes, which is in the current range of high-quality genomes for non-inbred plants. To further verify the genome annotation completeness and accuracy, we manually inspected the NLR resistance gene family and assessed its assembly quality. We revealed the existence of unique gene families of NLRs to S. chilense. Comparative genomics analyses of S. chilense, cultivated tomato S. lycopersicum and its wild relative S. pennellii revealed similar levels of highly syntenic gene clusters between the three species.\n\nConclusionsWe generated the first genome and transcriptome sequence assembly for the wild tomato species Solanum chilense and demonstrated its value in comparative genomics analyses. We make these genomes available for the scientific community as an important resource for studies on adaptation to biotic and abiotic stress in Solanaceae, on evolution of self-incompatibility, and for tomato breeding.

plant biology↗

bioRxiv2017

A small subset of NLR genes drives local adaptation to pathogens in wild tomato

O_LINucleotide binding site, Leucine-rich repeat Receptors (NLRs), are canonical resistance (R) genes in plants, fungi and animals, functioning as central (helper) and peripheral (sensor) genes in a signalling network. We investigate NLR evolution during the colonisation of novel habitats in a model tomato species, Solanum chilense.\nC_LIO_LIWe used R-gene enrichment sequencing (RENSeq) to obtain polymorphism data at NLRs of 140 plants sampled across 14 populations covering the whole species range. We inferred the past demographic history of habitat colonisation by resequencing whole genomes from three S. chilense plants from three key populations, and performing Approximate Bayesian Computation using data from the 14 populations.\nC_LIO_LIUsing these parameters we simulated the genetic differentiation statistics distribution expected under neutral NLR evolution, and identified small subsets of outlier NLRs exhibiting signatures of selection across populations.\nC_LIO_LINLRs under selection between habitats are more often helper genes, while those showing signatures of adaptation in single populations are more often sensor-NLRs. Thus, centrality in the NLR network does not constrain NLR evolvability, and new mutations in central genes in the network are key for R gene adaptation during colonisation of different habitats.\nC_LI

evolutionary biology↗

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↗