Biology subjects

Rabanus-Wallace, M. T.

Publications and source records attributed to Rabanus-Wallace, M. T..

4 recordsLinked to original sources

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↗

bioRxiv2023

Replicators, genes, and the C-value enigma: High-quality genome assembly of barley provides directevidence that self-replicating DNA forms 'cooperative' associations with genes in arms races

The C-value enigma--the apparent disjunction between the complexity of organisms and the sizes of their genomes--could be in part resolved if it were definitively shown that tolerance of self-copying DNA elements incurred an occasional selective advantage. We leverage the power of the latest genome assembly of the exceptionally repetitive and well-studied cereal crop barley (Hordeum vulgare L.) to explicitly test the hypothesis that the population of genes that have been repeatedly replicated by the action of replication-inducing sequences has undergone selection, favouring genes involved in co-evolutionary arms races (such as genes implicated in pathogen resistance). This was achieved by algorithmically identifying 1,999 genomic stretches that are locally rich in long repeated units. In these loci, we identified 554 geanes, belonging to 42 gene families. These gene families strongly overlap with a test set of pathogen resistance and other likely evolutionary arms-race genes compiled independently from the literature. By statistically demonstrating that selection has systematically influenced the composition of replicator-associated genes at a genome-wide scale we provide evidence that tolerance of repeat-inducing DNA sequences is an adaptive strategy that may contribute to enigmatically inflated C-values, and invite more detailed research on how particular genes become prone to duplication, to the organisms advantage. To this end, we examined the genomic sequences surrounding several of the candidate gene families, and find a repeated pattern of genomic disperse-and-expand dynamics, but where the repeated genomic unit itself varies between sites of expansion. This suggests that genes effectively form opportunistic relationships with replication-inducing DNA elements. We mention implications for agriculture.

evolutionary biology↗

bioRxiv2022

Genebank genomics allows greatly improved taxonomic correction for Capsicum spp. accessions using a novel automated classification method

To maximise the benefit of exploiting genebank resources, accurate and complete taxonomic assignments are imperative. The rise of genebank genomics allows genetic methods to be used for this task, but these need to be largely automated since the number of samples dealt with is too great for efficient manual recategorisation, but no clearly optimal method has yet arisen. A recent landmark genebank genomic study sequenced over 10,000 accessions of peppers (Capsicum spp.), for which the exploitation of genebank material is of huge commercial, cultural, and scientific importance. This study resulted in precisely the type of dataset that will, in coming decades, be likely be produced for hundreds of plant taxa. The long-appreciated difficulties of pepper taxonomy are evident from the many obvious misclassifications noted in this and other studies, providing a perfect opportunity to simultaneously advance methods development in the area, to correct many genebank taxonomic assignments of pepper accessions, and to provide insights into pepper taxonomy in general. This paper aims to achieve these goals using an approach that combines several ideas from standard classification algorithms to create a highly flexible and customisable classifier that performs favourably when compared with key alternative methods. The various characteristics of different methods are discussed, and possible sensible alterations to pepper taxonomy based on the results are proposed for discussion by the community.

bioinformatics↗

bioRxiv2019

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

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 ryes 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.

genomics↗