Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance.

Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease.

Brownian dynamics simulations reveal regulatory properties of higher-order chromatin structures.

A present model of the higher-order chromosome organization suggests the organization of chromosome built up by loops. Here we focus on a single rosette-like part of the fiber and analyse the diffusion behaviour of small particles (corresponding to single proteins/protein complexes) and the accessibility of such particles in relation to the dynamic rosette structure. Surprisingly, although the diffusion pattern of the diffusing particles revealed free diffusion, an area of about 6-12 kbp in the innermost part of these domains becomes visible which is inaccessible even for small particles (corresponding to single proteins/protein complexes). A localisation of a promotor sequence in this area might silence the respective gene by the physical inaccessibility of this area for transcription factors. We conclude that the compartmentalisation of chromatin in domains of a specific dynamical three-dimensional (3D) structure might be of high functional importance.

Dynamic simulation of active/inactive chromatin domains.

In the present study a model for the compactification of the 30 nm chromatin fibre into higher order structures is suggested. The idea is that basically every condensing agent (HMG/SAR, HP1, cohesin, condensin, DNA-DNA interaction …) can be modeled as an effective attractive potential of specific chain segments. This way the formation of individual 1 Mbp sized rosettes from a linear chain could be observed. We analyse how the size of these rosettes depends on the number of attractive segments and on the segment length. It turns out that 8-20 attractive segments per 1 Mbp domain produces rosettes of 300-800 nm in diameter. Furthermore, our results show that the size of the rosettes is relatively insensitive to the segment length.