Biology subjects

Rocha, S.

Publications and source records attributed to Rocha, S..

3 recordsLinked to original sources

bioRxiv2017

NGSphy: phylogenomic simulation of next-generation sequencing data

MotivationAdvances in sequencing technologies have made it feasible to obtain massive datasets for phylogenomic inference, often consisting of large numbers of loci from multiple species and individuals. The phylogenomic analysis of next-generation sequencing (NGS) data implies a complex computational pipeline where multiple technical and methodological decisions are necessary that can influence the final tree obtained, like those related to coverage, assembly, mapping, variant calling and/or phasing.\n\nResultsTo assess the influence of these variables we introduce NGSphy, an open-source tool for the simulation of Illumina reads/read counts obtained from haploid/diploid individual genomes with thousands of independent gene families evolving under a common species tree. In order to resemble real NGS experiments, NGSphy includes multiple options to model sequencing coverage (depth) heterogeneity across species, individuals and loci, including off-target or uncaptured loci. For comprehensive simulations covering multiple evolutionary scenarios, parameter values for the different replicates can be sampled from user-defined statistical distributions.\n\nAvailabilitySource code, full documentation and tutorials including a quick start guide are available at http://github.com/merlyescalona/ngsphy.\n\nContactmerlyescalona@uvigo.es. dposada@uvigo.es

bioinformatics↗

bioRxiv2017

SINHCAF/FAM60A links SIN3A function to the hypoxia response and its levels are predictive of cancer patient survival

The SIN3A-HDAC complex is a master transcriptional repressor, required for development but often deregulated in disease. Here, we report that the recently identified new component of this complex, SINHCAF/FAM60A, links the SIN3A-HDAC co-repressor complex function to the hypoxia response. SINHCAF Chromatin Immunoprecipitation-sequencing and gene expression analysis reveal a signature associated with the activation of the hypoxia response. We show that SINHCAF specifically repress HIF 2 mRNA and protein expression resulting in functional cellular changes in in-vitro angiogenesis, and proliferation. Analysis of patient datasets demonstrates that SINHCAF and HIF 2 mRNA levels are inversely correlated and predict contrasting outcomes for patient survival in both colon and lung cancer. This relationship is also observed in a mouse model of colon cancer, indicating an evolutionary conserved mechanism. Our analysis reveals an unexpected link between SINHCAF and cancer cell signalling via regulation of the hypoxia response that is predictive of poor patient outcome.

molecular biology↗

bioRxiv2017

Phylogenetic analyses reveal an increase in the speciation rate of raphid pennate diatoms in the Cretaceous

The raphid pennates (order Bacillariales) are a diverse group of diatoms easily recognized by having a slit in the siliceous cell wall, called the raphe, with functions in cell motility. It has been hypothesized that this morphological innovation contributed to the evolutionary success of this relatively young but species-rich group of diatoms. However, owing to the incompleteness of the fossil record this hypothesis remains untested. Using the 18S ribosomal RNA gene, fossil calibrations, and Bayesian phylogenetic and diversification frameworks, we detect a shift in the speciation rate of marine raphid pennate diatoms in the Cretaceous, not detected in other diatom lineages nor previously recognized in the microfossil record. Our results suggest a positive link between the speciation of raphid pennate diatoms and the benefits derived from evolving motility skills, which could account for their outstanding present-day global diversity. The coincidence between the advent of the raphe and the increase in the speciation rate of raphid pennates supports the idea that simple morphological novelties can have important consequences on the evolutionary history of eukaryotic microorganisms.

ecology↗