Large-scale assignment of orthology: back to phylogenetics?

Automated use of phylogenetic trees to deduce orthology relationships in proteins

Respiratory tract microbiome modifications after lung transplantation and its impact in CLAD

Survival after lung transplantation is limited in large part due to the high incidence of chronic lung allograft dysfunction (CLAD). Infection is a recognized risk factor for the development of CLAD, and both acute infection and chronic lung allograft colonization with microorganisms increase the risk for CLAD. The aim of our study was to analyze respiratory tract microbiome modifications after lung transplantation, with a focus on its relationship with CLAD. Here we used 16S rRNA metabarcoding, observing specific microbiome profiles for both upper and lower respiratory tract and observing lower beta diversity between healthy subjects and patients with NO-CLAD as well as differentially abundant features associated with CLAD

Selection of Marker Genes Using Whole-Genome DNA Polymorphism Analysis

Molecular markers serve to assign individual samples to specific groups. Such markers should be easily identified and have a high discrimination power, being highly conserved within groups while showing sufficient variability between the groups that are to be distinguished. The availability of a large number of complete genomic sequences now enables the informed selection of genes as molecular markers based on the observed patterns of variability. We derived a new scoring system based on observed DNA polymorphic differences, and which uses the Bayes theorem as adapted by Wilcox. For validation, we applied this system to the problem of identifying individual species within a prokaryotic (Vibrio) and a eukaryotic (Diphyllobothrium) genus for validation. Top-scoring candidates genes Chromosome segregation ATPase and ATPase-subunit 6 showed better discrimination power in Vibrio and Diphyllobothrium, respectively, as compared to standard molecular markers (recA, dnaJ and atpA for Vibrio, and 18s rRNA, ITS and COX1 for Diphyllobothrium)

On the Biology, Diversity and Evolution of Nucleariid Amoebae (Amorphea, Obazoa, Opisthokonta

Nucleariids are a small group of free-living heterotrophic amoebae. Although these organisms present a variety of cell sizes and cell coverings, they are mostly spherical cells with radiating filopodia, sometimes with several nuclei. Nuclearia, the genus that gives the name to the group, contains species that are opportunistic consumers of detritus, bacteria, and algae. The beautiful Pompholyxophrys is covered with endogenous siliceous pearls. Lithocolla covers itself with sand particles, or otherwise diatom frustules. The tiny Parvularia exclusively feeds on bacteria, and Fonticula is adapted to solid substrates and presents aggregative multicellular stages. Nucleariids belong to the Opisthokonta, which comprise animals, fungi, and their protist relatives and, form the earliest branch in the holomycotan clade (fungi and closest relatives). Hence, they are key for understanding the origin and diversification of Opisthokonta, an eukaryotic supergroup that contains organisms with different feeding modes, life-styles, and cell organizations. In this review, the reader will find an introduction to nucleariids, from their discovery in the 19th century until the most recent studies. It summarizes available information on their morphology, life history, cell organisation, ecology, diversity, systematics and evolution.The authors acknowledge all researchers who generated the knowledge on filose amoebae that has been introduced in this review, the Biodiversity Heritage Library for providing access to old references, and the reviewers for their thorough and constructive comments. T.G. received funding from the Spanish Ministry of Science and Innovation, cofounded by European Regional Development Fund (ERDF) [grant number PGC2018-099921-B-I00]; from the Catalan Research Agency (AGAUR) [grant number SGR423]; from the European Union’s Horizon 2020 research and innovation programme [grant number ERC-2016-724173]; and from the Gordon and Betty Moore Foundation [grant number GBMF9742]. E.V. thanks Steffen Clauß for imaging. G.T. was supported by 2019 BP 00208, Beatriu de Pinós-3 Postdoctoral Programme (BP3) [grant number: 801370].Peer ReviewedPostprint (author's final draft

PerSVade: personalized structural variant detection in any species of interest

Structural variants (SVs) underlie genomic variation but are often overlooked due to difficult detection from short reads. Most algorithms have been tested on humans, and it remains unclear how applicable they are in other organisms. To solve this, we develop perSVade (personalized structural variation detection), a sample-tailored pipeline that provides optimally called SVs and their inferred accuracy, as well as small and copy number variants. PerSVade increases SV calling accuracy on a benchmark of six eukaryotes. We find no universal set of optimal parameters, underscoring the need for sample-specific parameter optimization. PerSVade will facilitate SV detection and study across diverse organisms.Peer ReviewedPostprint (author's final draft

Exploring the recent evolution of yeast pathogens using the CandidaMine database

Advances in medicine (such as chemotherapy or transplants) have extended the life expectancy of patients at the cost of impairing their immune system. This has generated an increasing population of patients highly susceptible to infections. Among them, fungal infections caused by Candida species have become a major life-threatening issue, with insufficient diagnostic and therapeutic options. Recent studies have used population genomics in clinical Candida isolates to understand their recent evolution, which may also clarify the emergence of phenotypes like drug resistance or virulence. However, there are open questions that hinder our understanding about such evolutionary processes

From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism

Mitochondria are eukaryotic organelles that originated from the endosymbiosis of an alpha-proteobacterium. To gain insight into the evolution of the mitochondrial proteome as it proceeded through the transition from a free-living cell to a specialized organelle, we compared a reconstructed ancestral proteome of the mitochondrion with the proteomes of alpha-proteobacteria as well as with the mitochondrial proteomes in yeast and man. Overall, there has been a large turnover of the mitochondrial proteome during the evolution of mitochondria. Early in the evolution of the mitochondrion, proteins involved in cell envelope synthesis have virtually disappeared, whereas proteins involved in replication, transcription, cell division, transport, regulation, and signal transduction have been replaced by eukaryotic proteins. More than half of what remains from the mitochondrial ancestor in modern mitochondria corresponds to translation, including post-translational modifications, and to metabolic pathways that are directly, or indirectly, involved in energy conversion. Altogether, the results indicate that the eukaryotic host has hijacked the proto-mitochondrion, taking control of its protein synthesis and metabolism