The 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) is the central enzyme of the shikimate pathway to synthesize three aromatic amino acids in fungi, plants and prokaryotes. Glyphosate is a multi-spectrum herbicide largely utilized to control weeds, which targets the EPSPS enzyme and inhibits the production of these essential amino acids. In most plants and prokaryotes, the EPSPS protein is constituted by a single domain, whereas in fungi contains the EPSPS and several EPSPS-associated domains. Here, we perform a comprehensive analysis of 391 EPSPS proteins of fungi gathered from the Pfam database. We analyze our dataset with a bipartite graph (Cytoscape) and dollon parsimony (Count) to determine the distribution and the evolution of the 22 EPSPS-associated domains in fungi. The EPSPS-associated domains can be classified into four partially overlapping groups: shikimate pathway, other enzymes, gene expression and structural proteins. The most frequent EPSPS-associated domains are shikimate kinase, 3-dehydroquinate synthase, 3-dehydroquinate dehydratase, shikimate dehydrogenase substrate binding domain and shikimate DH. These domains are present in 56% of the proteins analyzed and 34% of proteins contain shikimate DH at the end of sequence. The most common domain architecture of the EPSPS enzyme in fungi contains 5-6 domains. A parsimony analysis suggests that a 6-domain protein is the ancestral form of the EPSPS in fungi and that alternative architectures are due to domain losses (also some gains) and duplications. The results of this study will be useful to determine the impact of glyphosate in fungi and to quantify its putative differential effects on alternative domain architectures.

Prostate cancer (PC) is one of the most prevalent tumors in the world, however, the hereditary (Hereditary PC; HPC) form is a rare pathology (ORPHA: 1331), without exceeding 6%. Despite its very low incidence, a family history of PC in a first-degree relative multiplies the risk to suffer from PC approximately twofold. Therefore, the search for genetic variables associated with detection, monitoring and treatment is unavoidable.

Although the study of the genome and its expression have provided us with valuable information, it has not been able to describe biomarkers that help us resolve the appearance and evolution of the tumor. With this study, we make a deep analysis in data of exome and miRNAs analyzed by Next-generation sequencing (NGS) analysis in search of new biomarkers as variants of aggressiveness of this tumor. We performed this analysis in a family of a high incidence of PC.

Our data revealed that some genes such as HIBCH and DPP4 are just present in all HPC patients. Moreover, high-risk patients have unique additional variants such as FANK1, TUBA3FP and ALDH3B2. These results provide a new set of promising biomarkers in HCP.

Renal Cell Carcinoma (RCC) is the third most common urologic malignancy,remains one of the most lethal urological malignancies, preferably in developed countries. The incidence and mortality rates differ significantly according to sex, race, age and external factors such as smoking, obesity and hypertension increasing RCC risk. The use of novel predictive biomarkers is currently being increased as these improve the diagnosis, progression and prognosis of RCC. Since recent studies have demonstrated a promising association between mitocondrial DNA (mtDNA) copy number alteration in peripheral blood and risk of developing RCC, we conducted a case-control study to determine exosomes mtDNA content in plasma fractions as a potential novel non-invasive biomarker in liquid biopsy in order to monitor the RCC status in patients.

In this way, plasma fractions highly purified in exosomes were obtained from blood samples from controls and RCC cases, and relative mtDNA content was measured by quantitative real-time polymerase chain reaction (qPCR). Our results show fragment size distribution profile and the copy numbers of nuclear regions and mitochondrial genes (in hypervariable and conserved regions) in each plasma fraction.

Conservation biology aims to keep and restore biodiversity on genetic, species and ecosystem levels, prevent species extinction and protect their habitats. One of the important aspects of a conservation is genetic diversity assessed within endangered populations or species. Reduction in sequencing costs facilitated estimation of the genetic diversity in multiple individuals on the whole genome level even with a very limited budget. However, whole genome approach requires generation of reference genome assembly of suitable quality first. Current trend is to use chromosome-level assemblies offering a set of useful advantages.

We compared genetic diversity in endangered species (cheetah, sea otter and others) for both old highly fragmented and recently generated chromosome-level assemblies. New contiguous assemblies allowed to calculate more precisely broadly used indicators of genetic diversity such as length and number of ROHs (runs of homozygosity) and visualize regions of low heterozygosity in the genome. In addition, we located known microsatellite loci previously used in STR-fingerprinting on chromosomes to understand diversity of what regions were estimated in previous diversity studies.

Chromosome level genome assemblies provide better estimates of genetic diversity, better understanding for results of previous studies and new possibilities for visualization of results. Another new opportunity is the simple and cheap procedure for development of comprehensive STR-arrays or microarrays with known localization of each locus to use it for diversity estimates in multiple (hundreds and thousands) individuals and in low quality samples.

Increased levels of insecticide resistance in major malaria vectors such as Anopheles funestus is threatening the continued effectiveness of insecticide-based control programmes. Understanding the ecological factors impacting the spread of resistance alleles in necessary to design suitable resistance management strategies. Here we examined the influence of the highest mountain in West Africa (4,100 meters elevation) on the spread of both metabolic and target-site resistance alleles in An. funestus sensu stricto (s.s) populations. High frequencies of both 296S-Rdl (49% - 90%) and 119F-GSTe2 (67% - 81%) resistance alleles were observed An. funestus s.s. populations across Mount Cameroon. Genetic variability parameters suggested that these resistance markers underwent high levels of polymorphisms with 16 to 12 haplotypes identified respectively. However, neutrality tests were not consistent with recent expansion or resistance genes being under selection. Analysis of the maximum likelihood phylogenetic trees of haplotypes indicated that populations primarily clustered according to resistance patterns, whereas the neighbour joining trees of distances suggested that landscape variations could potentially be associated with the risk of presence and insecticide resistance for malaria vectors. These raise the need for further investigations covering different bioecological zones for a detailed report on current status of insecticide resistance in malaria vectors.