Genome-wide analysis of LTR retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.)

Background: Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels. Results: After determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species. Conclusions: This large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial habit of that species

Specific LTR-Retrotransposons Show Copy Number Variations between Wild and Cultivated Sunflowers

The relationship between variation of the repetitive component of the genome and domestication in plant species is not fully understood. In previous work, variations in the abundance and proximity to genes of long terminal repeats (LTR)-retrotransposons of sunflower (Helianthus annuus L.) were investigated by Illumina DNA sequencingtocompare cultivars and wild accessions. In this study, we annotated and characterized 22 specific retrotransposon families whose abundance varies between domesticated and wild genotypes. These families mostly belonged to the Chromovirus lineage of the Gypsy superfamily and were distributed overall chromosomes. They were also analyzed in respect to their proximity to genes. Genes close to retrotransposon were classified according to biochemical pathways, and differences between domesticated and wild genotypes are shown. These data suggest that structural variations related to retrotransposons might have occurred to produce phenotypic variation between wild and domesticated genotypes, possibly by affecting the expression of genes that lie close to inserted or deleted retrotransposons and belong to specific biochemical pathways as those involved in plant stress responses

Nonlinear response of single-molecule nanomagnets: equilibrium and dynamical

We present an experimental study of the {\em nonlinear} susceptibility of Mn$_{12}$ single-molecule magnets. We investigate both their thermal-equilibrium and dynamical nonlinear responses. The equilibrium results show the sensitivity of the nonlinear susceptibility to the magnetic anisotropy, which is nearly absent in the linear response for axes distributed at random. The nonlinear dynamic response of Mn$_{12}$ was recently found to be very large and displaying peaks reversed with respect to classical superparamagnets [F. Luis {\em et al.}, Phys. Rev. Lett. {\bf 92}, 107201 (2004)]. Here we corroborate the proposed explanation -- strong field dependence of the relaxation rate due to the detuning of tunnel energy levels. This is done by studying the orientational dependence of the nonlinear susceptibility, which permits to isolate the quantum detuning contribution. Besides, from the analysis of the longitudinal and transverse contributions we estimate a bound for the decoherence time due to the coupling to the phonon bath.Comment: 13 pages, 8 figures, resubmitted to Phys. Rev. B with minor change

Comparative genome-wide analysis of repetitive DNA in the genus Populus L.

Genome skimming was performed, using Illumina sequence reads, in order to obtain a detailed comparative picture of the repetitive component of the genome of Populus species. Read sets of seven Populus and two Salix species (as outgroups) were subjected to clustering using RepeatExplorer (Novák et al. BMC Bioinformatics 11:378 2010). The repetitive portion of the genome ranged from 33.8 in Populus nigra to 46.5% in Populus tremuloides. The large majority of repetitive sequences were long terminal repeat-retrotransposons. Gypsy elements were over-represented compared to Copia ones, with a mean ratio Gypsy to Copia of 6.7:1. Satellite DNAs showed a mean genome proportion of 2.2%. DNA transposons and ribosomal DNA showed genome proportions of 1.8 and 1.9%, respectively. The other repeat types accounted for less of 1% each. Long terminal repeat-retrotransposons were further characterized, identifying the lineage to which they belong and studying the proliferation times of each lineage in the different species. The most abundant lineage was Athila, which showed large differences among species. Concerning Copia lineages, similar transpositional profiles were observed among all the analysed species; by contrast, differences in transpositional peaks of Gypsy lineages were found. The genome proportions of repeats were compared in the seven species, and a phylogenetic tree was built, showing species separation according to the botanical section to which the species belongs, although significant differences could be found within sections, possibly related to the different geographical origin of the species. Overall, the data indicate that the repetitive component of the genome in the poplar genus is still rapidly evolving

Eating Disorders

Anorexia and bulimia are diseases known since ancient times, but in recent years their frequency has been continuously increasing in most industrialized countries. The etiology of these disorders can be traced back to the interaction between genetic predisposition, childhood experiences, and cultural pressures. As regards the course, a certain tendency to chronicity can be observed, and in extreme cases, they can cause death. According to the diagnostic classification of the DSM-5, eating disorders include anorexia nervosa, bulimia nervosa, binge eating disorder (which, compared to DSM-IV, becomes a diagnostic category in its own right), and other specified feeding and eating disorders (OSFED). Both anorexia and bulimia cause potentially serious medical complications. To maximize the chances of good outcomes a multidisciplinary intervention is necessary with staff including professionally heterogeneous figures: a psychiatrist, a psychologist, and a nutritionist. Therapeutic success for these patients is limited. Eating disorders require, among psychiatric disorders, the greatest possible collaboration between different professional figures with different specializations

Small-scale swirl events in the quiet Sun chromosphere

Recent progress in instrumentation enables solar observations with high resolution simultaneously in the spatial, temporal, and spectral domains. We use such high-resolution observations to study small-scale structures and dynamics in the chromosphere of the quiet Sun. We analyze time series of spectral scans through the Ca II 854.2nm spectral line obtained with the CRISP instrument at the Swedish 1-m Solar Telescope. The targets are quiet Sun regions inside coronal holes close to disc-centre. The line core maps exhibit relatively few fibrils compared to what is normally observed in quiet Sun regions outside coronal holes. The time series show a chaotic and dynamic scene that includes spatially confined "swirl" events. These events feature dark and bright rotating patches, which can consist of arcs, spiral arms, rings or ring fragments. The width of the fragments typically appears to be on the order of only 0.2", which is close to the effective spatial resolution. They exhibit Doppler shifts of -2 to -4 km/s but sometimes up to -7 km/s, indicating fast upflows. The diameter of a swirl is usually of the order of 2". At the location of these swirls, the line wing and wide-band maps show close groups of photospheric bright points that move with respect to each other. A likely explanation is that the relative motion of the bright points twists the associated magnetic field in the chromosphere above. Plasma or propagating waves may then spiral upwards guided by the magnetic flux structure, thereby producing the observed intensity signature of Doppler-shifted ring fragments.Comment: 4 pages, 3 figures, A&A Letter, accepted (final version

Gene expression in Rhizoglomus irregulare at two different time points of mycorrhiza establishment in Helianthus annuus roots, as revealed by RNA-seq analysis

Arbuscular mycorrhizal fungi (AMF) play a fundamental role in plant growth and nutrition in natural and agricultural ecosystems. Despite the importance of such symbionts, the different developmental changes occurring during the AMF life cycle have not been fully elucidated at the molecular level. Here, the RNA-seq approach was used to investigate Rhizoglomus irregulare specific and common transcripts at two different time points of mycorrhizal establishment in Helianthus annuus in vivo. Four days after inoculation, transcripts related to cellular remodeling (actin and tubulin), cellular signaling (calmodulin, serine/threonine protein kinase, 14-3-3 protein, and calcium transporting ATPase), lipid metabolism (fatty acid desaturation, steroid hormone, and glycerophospholipid biosynthesis), and biosynthetic processes were detected. In addition to such transcripts, 16 days after inoculation, expressed genes linked to binding and catalytic activities; ion (K+, Ca2+, Fe2+, Zn2+, Mn2+, Pi, ammonia), sugar, and lipid transport; and those involved in vacuolar polyphosphate accumulation were found. Knowledge of transcriptomic changes required for symbiosis establishment and performance is of great importance to understand the functional role of AMF symbionts in food crop nutrition and health, and in plant diversity in natural ecosystems

Repetitive DNA and plant domestication: variation in copy number and proximity to genes of LTR-retrotransposons among wild and cultivated sunflower (Helianthus annuus) genotypes.

The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next generation sequencing technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes - 7 wild accessions and 8 cultivars - of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis we mapped Illumina paired reads to two sets of sequences, i.e. long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was ascertained also for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower