Sex chromosomes in willows

Sexual reproduction is found in most eukaryotes and has in the majority of animal species led to the evolution of separate sexes. In contrast, only 5-6% of all angiospersms are dioecious with female and male flowers on separate individuals. Interestingly, dioecy has evolved hundreds of times independently and at different timepoints in angiosperms. The development of separate sexes requires a sex determination mechanism, which often is located on sex chromosomes. The independent evolution of numerous sex determination and sex chromosome systems in angiosperms allows for studies of processes involved in different stages of their evolution. The ratio between male and female individuals in a dioecious population is expected to be equal due to frequency dependent selection. Distorted sex ratios are however common in many plant and animal species. The overall aim of my thesis was to investigate the sex chromosome system in the dioecious, perennial willow species Salix viminalis that both in natural populations as well as in lab populations often displays female biased sex ratios. Although dioecy evolved from hermaphroditic ancestors before the split between Salix and its sister genus Populus, we found that the two lineages have different sex chromosomes (Populus: Chr. 19, Salix: Chr. 15). As we found no evidence for translocations between these chromosomes, it is most likely that two different sex determination mechanims are present in the two lineages, meaning that sex chromosome turnover has occurred recently. We furthermore determined that S. viminalis is female heterogametic (females Z/W, males Z/Z) and has a single sex determination locus on chromosome 15. The W homolog of the sex determination region contains hemizygous, female specific sequences and the SNP density in this region is increased in females relative to males, witnessing of lost recombination between the Z/W homologs. We did not find a Fast-Z effect or major degeneration of the W chromosome, suggesting a recent evolution. In fact this sex chromosome system is among the youngest observed so far. Based on our data, the insertion of repetitive sequence and sex specific gene expression appear to be among the first processes to happen in sex chromosome evolution. We also determined that female biased sex ratios in S. viminalis are likely caused by an allelic incompatibility between Z homologs which results in the lack of one expected male genotype, reducing the male frequency in the population. My studies thus extended our knowledge on processes involved in sex chromosome evolution and evolution of biased sex ratios in S. viminalis. However, given how common these phenomena are, results from my research can be applied to most organisms with genetic sex determination

A calibration method for non-overlapping cameras based on mirrored phase target

A novel calibration method for non-overlapping cameras is proposed in this paper. A LCD screen is used as a phase target to display two groups of orthogonal phase-shifted sinusoidal patterns during the calibration process. Through a mirror reflection, the phase target is captured by the cameras respectively. The relations between each camera and the phase target can be obtained according the proposed algorithm. Then the relation between the cameras can be calculated by treating the phase target as an intermediate value. The proposed method is more flexible than conventional mirror-based approach, because it do not require the common identification points and is robust to out-of-focus images. Both simulation work and experimental results show the proposed calibration method has a good result in calibrating a non-overlapping cameras system

Трансформация культуры чтения в цифровую эпоху как показатель цивилизационных сдвигов

Материалы X Международной научной конференции 25–26 мая 2017 г

Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases

Objective Copy number variation of the C4 complement components, C4A and C4B, has been associated with systemic inflammatory autoimmune diseases. This study was undertaken to investigate whether C4 copy number variation is connected to the autoimmune repertoire in systemic lupus erythematosus (SLE), primary Sjögren's syndrome (SS), or myositis. Methods Using targeted DNA sequencing, we determined the copy number and genetic variants of C4 in 2,290 well-characterized Scandinavian patients with SLE, primary SS, or myositis and 1,251 healthy controls. Results A prominent relationship was observed between C4A copy number and the presence of SSA/SSB autoantibodies, which was shared between the 3 diseases. The strongest association was detected in patients with autoantibodies against both SSA and SSB and 0 C4A copies when compared to healthy controls (odds ratio [OR] 18.0 [95% confidence interval (95% CI) 10.2–33.3]), whereas a weaker association was seen in patients without SSA/SSB autoantibodies (OR 3.1 [95% CI 1.7–5.5]). The copy number of C4 correlated positively with C4 plasma levels. Further, a common loss-of-function variant in C4A leading to reduced plasma C4 was more prevalent in SLE patients with a low copy number of C4A. Functionally, we showed that absence of C4A reduced the individuals’ capacity to deposit C4b on immune complexes. Conclusion We show that a low C4A copy number is more strongly associated with the autoantibody repertoire than with the clinically defined disease entities. These findings may have implications for understanding the etiopathogenetic mechanisms of systemic inflammatory autoimmune diseases and for patient stratification when taking the genetic profile into account.publishedVersio

Data from: Single locus sex determination and female heterogamety in the basket willow (Salix viminalis L.)

Most eukaryotes reproduce sexually and a wealth of different sex determination mechanisms have evolved in this lineage. Dioecy or separate sexes are rare among flowering plants but have repeatedly evolved from hermaphroditic ancestors possibly involving male or female sterility mutations. Willows (Salix spp.) and poplars (Populus spp.) are predominantly dioecious and are members of the Salicaceae family. All studied poplars have sex determination loci on chromosome XIX, however, the position differs among species and both male and female heterogametic system exists. In contrast to the situation in poplars, knowledge of sex determination mechanisms in willows is sparse. In the present study, we have for the first time positioned the sex determination locus on chromosome XV in S. viminalis using quantitative trait locus mapping. All female offspring carried a maternally inherited haplotype, suggesting a system of female heterogamety or ZW. We used a comparative mapping approach and compared the positions of the markers between the S. viminalis linkage map and the physical maps of S. purpurea, S. suchowensis and P. trichocarpa. As we found no evidence for chromosomal rearrangements between chromosome XV and XIX between S. viminalis and P. trichocarpa, it shows that the sex determination loci in the willow and the poplar most likely do not share a common origin and has thus evolved separately. This demonstrates that sex determination mechanisms in the Salicaceae family have a high turnover rate and as such it is excellent for studies of evolutionary processes involved in sex chromosome turnover

Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis

Background Sex chromosomes are in some species largely undifferentiated (homomorphic) with restricted sex determination regions. Homomorphic but different sex chromosomes are found in the closely related genera Populus and Salix indicating flexible sex determination systems, ideal for studies of processes involved in sex chromosome evolution. We have performed genome-wide association studies of sex and analysed sex chromosomes in a population of 265 wild collected Salix viminalis accessions and studied the sex determining locus. Results A total of 19,592 markers were used in association analyses using both Fisher's exact tests and a single-marker mixed linear model, which resulted in 48 and 41 sex-associated (SA) markers respectively. Across all 48 SA markers, females were much more often heterozygous than males, which is expected if females were the heterogametic sex. The majority of the SA markers were, based on positions in the S. purpurea genome, located on chromosome 15, previously demonstrated to be the sex chromosome. Interestingly, when mapping the genotyping-by-sequencing sequence tag harbouring the two SA markers with the highest significance to the S. viminalis genomic scaffolds, five regions of very high similarity were found: three on a scaffold that represents a part of chromosome 15, one on a scaffold that represents a part of chromosome 9 and one on a scaffold not anchored to the genome. Based on segregation differences of the alleles at the two marker positions and on differences in PCR amplification between females and males we conclude that females had multiple copies of this DNA fragment (chromosome 9 and 15), whereas males only had one (chromosome 9). We therefore postulate that the female specific sequences have been copied from chromosome 9 and inserted on chromosome 15, subsequently developing into a hemizygous W chromosome linked region. Conclusions Our results support that sex determination in S. viminalis is controlled by one locus on chromosome 15. The segregation patterns observed at the SA markers furthermore confirm that S. viminalis females are the heterogametic sex. We also identified a translocation from chromosome 9 to the W chromosome

Additional file 1: of Allelic incompatibility can explain female biased sex ratios in dioecious plants

Genetic markers with segregation distortion. Table of genetic markers showing segregation distortion in the S5 pedigree population with biased sex ratio. The sequence tag surrounding the marker is given as well as the position of the homologous sequence in P. trichocarpa, the number of individuals in the population with each genotype, separated by their gender and the corrected p-value. (XLS 34 kb

Activation of plasmacytoid dendritic cells and B cells with two structurally different Toll-like receptor 7 agonists

Synthetic Toll-like receptor (TLR) 7 agonists have been suggested as immune modulators in a range of conditions. In contrast, self-derived TLR7 activators, such as RNA-containing immune complexes (RNA-IC), can contribute to autoimmune diseases due to endogenous immune activation. The exact difference in immune cell response between synthetic and endogenous TLR7 triggers is only partly known. An understanding of these differences could aid in the development of new therapeutic agents and provide insights into autoimmune disease mechanisms. We therefore compared the stimulatory capacity of two TLR7 agonists, RNA-IC and a synthetic small molecule DSR-6434, on blood leucocytes, plasmacytoid dendritic cells (pDCs) and B cells from healthy individuals. IFN-α, IL-6, IL-8 and TNF levels were measured by immunoassays, and gene expression in pDCs was analysed by an expression array. DSR-6434 triggered 20-fold lower levels of IFN-α by pDCs, but higher production of IL-6, IL-8 and TNF, compared to RNA-IC. Furthermore, IFN-α and TNF production were increased with exogenous IFN-α2b priming, whereas IL-8 synthesis by B cells was reduced for both stimuli. Cocultivation of pDCs and B cells increased the RNA-IC-stimulated IFN-α and TNF levels, while only IL-6 production was enhanced in the DSR-6434-stimulated cocultures. When comparing pDCs stimulated with RNA-IC and DSR-6434, twelve genes were differentially expressed (log2 fold change >2, adjusted P-value <.05). In conclusion, RNA-IC, which mimics an endogenous TLR7 stimulator, and the synthetic TLR7 agonist DSR-6434 trigger distinct inflammatory profiles in immune cells. This demonstrates the importance of using relevant stimuli when targeting the TLR7 pathway for therapeutic purposes

Genotypes+sex_141013

Genotypes of S3 mapping population in Joinmap infile format. Sex as morphological marker is included in this file too