Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, modifications. The combinatorial complexity can be reduced to nine that describe with high resolution robustness. Each state has a strong propensity associate subset other defining discrete number motifs. These topographical relationships revealed an...

A coordinated transition from cell proliferation to differentiation is crucial for organogenesis. We found that extensive chromatin reorganization, shown here histone H3 proteins, characterizes population dynamics in the root developmental compartments. The canonical H3.1 protein, incorporated during S-phase, maintained at high levels cells dividing a rate but massively evicted undergoing their last cycle before exit differentiation. similar pattern was observed quadruple mutant...

Horizontal gene transfer mediated by plasmid conjugation plays a significant role in the evolution of bacterial species, as well dissemination antibiotic resistance and pathogenicity determinants. Characterization their regulation is important for gaining insights into these features. Relatively little known about how Gram-positive plasmids regulated. We have characterized native Bacillus subtilis pLS20. Contrary to enterococcal plasmids, pLS20 not activated recipient-produced pheromones but...

Leishmania parasites are the causative of leishmaniasis, a group potentially fatal human diseases. Control strategies for leishmaniasis can be enhanced by genome based investigations. The publication in 2005 major sequence, and two years later genomes species braziliensis infantum were milestones. Since then, L. genome, although highly fragmented incomplete, has been used widely as reference to address whole transcriptomics proteomics studies. Here, we report sequencing NGS methodologies...

Abstract RNA viruses exist as complex mixtures of genotypes, known quasispecies, where the evolution potential resides in whole community related genotypes. Quasispecies structure and dynamics have been studied detail for virus infecting animals plants but remain unexplored those micro‐organisms environmental samples. We report first metagenomic study an Antarctic lake (Lake Limnopolar, Livingston Island). Similar to low‐latitude aquatic environments, this harbours virome dominated by...

Knowledge of population structure and genetic diversity within between wild farmed populations gilthead sea bream (Sparus aurata) European seabass (Dicentrarchus labrax) is important to achieve sustainable aquaculture production these species assess the risk impacts fish escaped from farms. Previous studies on have been based a limited number markers samples. In this study, features were assessed using samples 24 seabream 25 distributed throughout Mediterranean Sea, 3 Atlantic populations....

The low pregnancy rate by artificial insemination in sheep represents a fundamental challenge for breeding programs. In this species, oestrus synchronization is carried out manipulating hormonal regimens through the insertion of progestogen intravaginal devices. This reproductive strategy may alter vaginal microbiota affecting outcome.In study, we analyzed microbiome 94 swabs collected from 47 ewes with alternative treatments applied to progesterone-releasing devices (probiotic,...

Abstract Leishmania donovani is a unicellular parasite that causes visceral leishmaniasis, fatal disease in humans. In this study, complete assembly of the genome L . provided. Apart from being first published strain (HU3), constitutes best for an attained to date. The use combination sequencing platforms enabled assemble, without any sequence gap, 36 chromosomes species. Additionally, based on and using RNA-seq reads derived poly-A + RNA, transcriptome species, not yet available, was...

The Cu(+) pump ATP7B plays an irreplaceable role in the elimination of excess by hepatocyte into bile. trafficking and site action are subjects controversy. One current proposal is that increase intracellular results translocation to lysosomes excretion through lysosomal-mediated exocytosis at bile canaliculus. Here, we show transported from trans-Golgi network (TGN) canaliculus basolateral sorting endocytosis, microtubule-mediated transcytosis subapical compartment. Trafficking not...

Leishmania braziliensis is the etiological agent of American mucosal leishmaniasis, one most severe clinical forms leishmaniasis. Here, we report assembly L. (M2904) genome into 35 continuous chromosomes. Also, annotation 8395 genes provided. The public availability this information will contribute to a better knowledge pathogen and help in search for vaccines novel drug targets aimed control disease caused by species.

NGS long-reads sequencing technologies (or third generation) such as Pacific BioSciences (PacBio) have revolutionized the field over last decade improving multiple genomic applications like de novo genome assemblies. However, their error rate, mostly involving insertions and deletions (indels), is currently an important concern that requires special attention to be solved. Multiple algorithms are available fix these errors using short reads (such Illumina), although they require long...

Genomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands DNA replication origins (ORIs) scattered throughout genome. The and chromatin features determining ORI specification are not presently known. We have generated a high-resolution genome-wide map 3230 ORIs in cultured Arabidopsis thaliana cells. Here, we focused defining associated with heterochromatin. In pericentromeric gene-poor domains associate almost exclusively...

A high level of transposon-mediated genome rearrangement is a common trait among microorganisms isolated from thermal environments, probably contributing to the extraordinary genomic plasticity and horizontal gene transfer (HGT) observed in these habitats. In this work, active inactive insertion sequences (ISs) spanning sequenced members genus Thermus were characterized, with special emphasis on three T. thermophilus strains: HB27, HB8, NAR1. large number full ISs fragments derived different...

Eukaryotic genome replication depends on thousands of DNA origins (ORIs). A major challenge is to learn ORI biology in multicellular organisms the context growing organs understand their developmental plasticity. We have identified a set ORIs Arabidopsis thaliana and chromatin landscape at two stages post-embryonic development. associate with multiple signatures including transcription start sites (TSS) but also proximal distal regulatory regions heterochromatin, where colocalize...

Abstract Next‐generation sequencing ( NGS ) has been proposed as a suitable tool for liquid biopsy in colorectal cancer CRC ), although most studies to date have focused almost exclusively on of panels potential clinically actionable genes. We evaluated the clinical value whole‐exome WES cell‐free DNA (cf circulating plasma, with goal identifying differential profiles patients . To this end, we applied an original concept, “differential presence exons” DPE ). determined differences levels...

Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection obtain a high density of markers along the genome. It requires low sequencing depth be cost effective, which may increase error at genotype assigment. Third generation nanopore technology offers and possibility detect genome methylation, provides added value genotype-by-sequencing. The aim this study was evaluate performance genotype-by-low pass for estimating direct dairy cattle,...

Abstract Genomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands DNA replication origins (ORIs) scattered throughout genome. In spite multiple efforts, and chromatin features that determine ORI specification are not presently known. We have generated a high-resolution genome-wide map ORIs in cultured Arabidopsis thaliana cells rendered collection 3230 ORIs. this study we focused defining associated with heterochromatin. found while...

Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection obtain a high density of markers along the genome. It requires low sequencing depth be cost effective, which may increase error at genotype assigment. Third generation Nanopore technology offers and possibility detect genome methylation, provides added value genotype-by-sequencing. The aim this study was evaluate performance genotype-by-LowPass for estimating direct dairy cattle,...

Epigenetic marks could potentially explain a portion of the phenotypic variance related to traits interest in animal breeding models. DNA methylation is most studied epigenetic mark, involving addition methyl group fifth carbon cytosine, which transforms it into 5-methylcytosine. This mark commonly associated with inhibiting gene expression without altering nucleotide sequence, particularly when located within promoter regions. While bisulphite sequencing gold standard for detecting marks,...

Differential presence of exons (DPE) is a method interpretation exome sequencing, which has been proposed to design predictive algorithm with clinical value in patients colorectal cancer (CRC). The goal the present study was examine reproducibility rat model metastatic colon cancer. DHD/K12-TRb cells were injected syngenic immunocompetent BD-IX rats. Cells from two stocks low and normal potential, into separate groups Five ten weeks after injection, blood samples taken prior euthanasia whole...