A new gypsy-like retroelement family in Vitis vinifera

As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to unforeseen transposition activities.We had performed in silico analysis of the Vitis vinifera 'Pinot Noir' genome to search for gypsy type retroelements homologues to the one identified in Pinus radiata (IFG7) and P. pinaster (PpRT1) and in Quercus suber (Corky). We intended to see the existence and structure of gypsy-like retroelements homologues in the Vitis genome as well as the existence of integration site preference. From all data and to perform a deeper analysis we chose 36 complete sequences copies in the Vitis genome. We used three genetic distance corrections, additional to p-distance to estimate retroelements insertion time and reverse transcriptase, integrase and LTR (Long Terminal Repeat) sequences to establish a phylogeny and to see the contributions of different regions according to the evolutionary rates. We found three elements with identical LTRs and two old elements that revealed recent and very old insertions as well as insertions inside other retroelements. Additionally, we found no preference for the integration site as shown by the different target site repeat for each element.

Genome restructuring in rye affects the expression, organization and disposition of homologous rDNA loci

Research ArticleThe standard rye cultivar ‘Imperial’ and a structural variant carrying an intact 1R chromosome and two telocentric 1R chromosomes (short and long arms) were used to investigate expression patterns of homologous rDNA loci, and the influence of chromosome structural change on their interphase organisation and relative disposition. Sequential silver staining and in situ hybridization with the rDNA probe pTa71, established a correspondence between the expression and organization patterns of rDNA domains in metaphase and interphase cells. In most cells of the cultivar Imperial, nucleolar organizer region (NOR) silver staining on metaphase chromosomes with equivalent numbers of rDNA genes revealed a size heteromorphism between homologousrDNA loci, resulting from their differential expression. NOR heteromorphism in the structural variant line was significantly reduced. The preferential activity of one NOR over its homologue was found to be random within cells and independent of parental origin. Nucleotypic modifications mediated by changes in the 1R chromosome structure include increased proximity between homologous rDNA loci in interphase, and an increase in the frequency of cells with intra-nucleolar ribosomal condensed chromatin. These results seem to indicate a ‘sequence recognition’ process for the regulation of homologous loci

Ribosomal DNA heterochromatin in plants

The aim of this review is to integrate earlier results and recent findings to present the current state-of-the art vision concerning the dynamic behavior of the ribosomal DNA (rDNA) fraction in plants. The global organization and behavioral features of rDNA make it a most useful system to analyse the relationship between chromatin topology and gene expression patterns. Correlations between several heterochromatin fractions and rDNA arrays demonstrate the heterochromatic nature of the rDNA and reveal the importance of the genomic environment and of developmental controls in modulating its dynamicsFCT - Fundação para a Ciência e Tecnologi

Master of Computational Biology & Bioinformatics

XIX ENBE Annual Meeting of the Portuguese Association for Evolutionary Biology, 18-19 December 2023, Lisboninfo:eu-repo/semantics/publishedVersio

Transcriptionally active heterochromatin in rye B chromosomes

B chromosomes (Bs) are dispensable components of the genomes of numerous species. Thus far, there is a lack of evidence for any transcripts of Bs in plants, with the exception of some rDNA sequences. Here, we show that the Giemsa bandingpositive heterochromatic subterminal domain of rye (Secale cereale) Bs undergoes decondensation during interphase. Contrary to the heterochromatic regions of A chromosomes, this domain is simultaneously marked by trimethylated H3K4 and by trimethylated H3K27, an unusual combination of apparently conflicting histone modifications. Notably, both types of B-specific high copy repeat families (E3900 and D1100) of the subterminal domain are transcriptionally active, although with different tissue type–dependent activity. No small RNAs were detected specifically for the presence of Bs. The lack of any significant open reading frame and the highly heterogeneous size of mainly polyadenylated transcripts indicate that the noncoding RNA may function as structural or catalytic RNA

Mood Disorder Due to a General Medical Condition with Manic Features

This case report describes a patient with manic and psychotic symptoms who had a history of neurocysticercosis and presented with an episode of hypertensive hydrocephalus in 2003. Despite her history, she was initially treated for primary psychiatric disease