El contingut dels introns influeixen en la variació de les proteïnes

La variació en la seqüència d'ADN és la base de la selecció natural i, per tant, l'estudi dels patrons de variació de les seqüències dels gens d'una espècie és imprescindible per entendre els mecanismes de l'evolució a nivell molecular. Els introns són seqüències d'ADN que formen part dels gens però que no codifiquen proteïnes i que, abans, es considerava que eren no funcionals. L'estudi genètic de la mosca del vinagre ha demostrat que el grau de variació de les proteïnes està relacionat inversament amb el tamany dels introns.La variación en la secuencia de ADN es la base de la selección natural y, por lo tanto, el estudio de los patrones de variación de las secuencias de los genes de una especie es imprescindible para entender los mecanismos de la evolución a nivel molecular. Los intrones son secuencias de ADN que forman parte de los genes pero que no codifican proteínas y que, antes, se consideraba que no eran funcionales. El estudio genético de la mosca del vinagre ha demostrado que el grado de variación de las proteínas está relacionado inversamente con el tamaño de los intrones.Variation in DNA sequence is the basis of natural selection, and hence a study of the variation patterns in the gene sequences of a species is essential for the understanding of the mechanisms of evolution at molecular level. Introns are DNA sequences that form part of the genes but do not codify proteins and previously were considered to be non- functional. The genetic study of the vinegar fly has shown that the degree of protein variation is inversely related to intron size

L'eficiència de la selecció natural

Des del Departament de Genètica i Microbiologia de la Universitat Autònoma de Barcelona, s'ha pogut aprofundir una mica més en l'estudi del canvi evolutiu de les espècies. Partint de la teoria quasi neutra de l'evolució molecular, que emfatitza la importància del factor aleatori de les mutacions genètiques que no aporten beneficis a l'espècie, s'ha demostrat que es pot predir l'eficiència de la selecció natural segons el tamany de la població. Per arribar a aquesta conclusió, l'estudi s'ha realitzat a partir d'anàlisis estadístiques d'una base de dades de diferents espècies de Drosophila, tenint en compte la seva diversitat nucleotídica.Desde el Departamento de Genética y Microbiología de la Universitat Autònoma de Barcelona, se ha podido profundizar un poco más en el estudio del cambio evolutivo de las especies. Partiendo de la teoría casi neutra de la evolución molecular, que enfatiza la importancia del factor aleatorio de las mutaciones genéticas que no aportan beneficios a la especie, se ha demostrado que se puede predecir la eficiencia de la selección natural según el tamaño de la población. Para llegar a esta conclusión, el estudio se ha realizado a partir de análisis estadísticos de una base de datos de diferentes especies de Drosophila, teniendo en cuenta su diversidad nucleotídica

Exploring the Phenotypic Space and the Evolutionary History of a Natural Mutation in Drosophila melanogaster

A major challenge of modern Biology is elucidating the functional consequences of natural mutations. Although we have a good understanding of the effects of laboratory-induced mutations on the molecular- and organismal-level phenotypes, the study of natural mutations has lagged behind. In this work, we explore the phenotypic space and the evolutionary history of a previously identified adaptive transposable element insertion. We first combined several tests that capture different signatures of selection to show that there is evidence of positive selection in the regions flanking FBti0019386 insertion. We then explored several phenotypes related to known phenotypic effects of nearby genes, and having plausible connections to fitness variation in nature. We found that flies with FBti0019386 insertion had a shorter developmental time and were more sensitive to stress, which are likely to be the adaptive effect and the cost of selection of this mutation, respectively. Interestingly, these phenotypic effects are not consistent with a role of FBti0019386 in temperate adaptation as has been previously suggested. Indeed, a global analysis of the population frequency of FBti0019386 showed that climatic variables explain well the FBti0019386 frequency patterns only in Australia. Finally, although FBti0019386 insertion could be inducing the formation of heterochromatin by recruiting HP1a (Heterochromatin Protein 1a) protein, the insertion is associated with upregulation of sra in adult females. Overall, our integrative approach allowed us to shed light on the evolutionary history, the relevant fitness effects, and the likely molecular mechanisms of an adaptive mutation and highlights the complexity of natural genetic variants.A.U. is an FPI fellow (BES-2012-052999) and J.G. is a Ramón y Cajal fellow (RYC-2010-07306). This work was supported by grants from the European Comission (Marie Curie CIG PCIG-2011-293860) and from the Spanish Government (Fundamental Research Projects Grant BFU-2011-24397) to J.G.Peer reviewe

Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes

[Background] The rise of the primate lineage is accompanied by an outstanding emergence of microRNAs, small non-coding RNAs with a prominent role in gene regulation. In spite of their biological importance little is known about the way in which natural selection has influenced microRNAs in the human lineage. To study the recent evolutionary history of human microRNAs and to analyze the signatures of natural selection in genomic regions harbouring microRNAs we have investigated the nucleotide substitution rates of 1,872 human microRNAs in the human and chimpanzee lineages.[Results] We produced a depurated set of microRNA alignments of human, chimpanzee and orang-utan orthologs combining BLAT and liftOver and selected 1,214 microRNA precursors presenting optimal secondary structures. We classified microRNAs in categories depending on their genomic organization, duplication status and conservation along evolution. We compared substitution rates of the aligned microRNAs between human and chimpanzee using Tajima’s Relative Rate Test taking orang-utan as out-group and found several microRNAs with particularly high substitution rates in either the human or chimpanzee branches. We fitted different models of natural selection on these orthologous microRNA alignments and compared them using a likelihood ratio test that uses ancestral repeats and microRNA flanking regions as neutral sequences. We found that although a large fraction of human microRNAs is highly conserved among the three species studied, significant differences in rates of molecular evolution exist among microRNA categories. Particularly, primate-specific microRNAs, which are enriched in isolated and single copy microRNAs, more than doubled substitution rates of those belonging to older, non primate-specific microRNA families.[Conclusions] Our results corroborate the remarkable conservation of microRNAs, a proxy of their functional relevance, and indicate that a subset of human microRNAs undergo nucleotide substitutions at higher rates, which may be suggestive of the action of positive selection.This work was supported by the Ministerio de Ciencia e Innovación, España (BFU2012-38236, BFU2010-18477, BFU2009-06974, and CGL2009-09013), Direcció General de Recerca de la Generalitat de Catalunya” (2009SGR-1101, 2014SGR-866 and SGR2014-1311) and European Union Seventh Framework Programme (PIOF-GA-2009-236836 and PIRSES-GA-2013-612583). This publication has been cofinanced by FEDER —European Regional Development Fund “A way to build Europe.” MLV is funded by a Beca per a la Formació de Personal Investigador (FI) fellowship from the Agència de Gestió d’Ajuts Universitaris i de Recerca, Generalitat de Catalunya.Peer reviewe

State-of-the-art of data analyses in environmental DNA approaches towards its applicability to sustainable fisheries management

An increasing number of studies using marine environmental DNA (eDNA) approaches are showing its potential application in marine fisheries management by helping and simplifying some of the labor-intensive traditional surveys required to assess exploited populations and ecosystem status. eDNA approaches (i.e. metabarcoding and targeted) can support to ecosystem-based fisheries management by providing information on species composition; surveillance of invasive, rare and/or endangered species; and providing estimates of species abundance. Due to these potential uses in fisheries and conservation sciences, the number of studies applying eDNA approaches in marine habitats has expanded in the very last few years. However, a lack of consistency across studies when applying pipelines for data analyses, makes results difficult to compare among them. Such lack of consistency is partially caused by poor knowledge in the management of raw sequences data, and analytical methods allowing comparative results. Hence, we review here the essential steps of eDNA data processing and analyses to get sound, reproducible, and comparable results, providing a set of bioinformatics tools useful for each step. Altogether this review presents the state of the art of eDNA data analyses towards a comprehensive application in fisheries management promoting sustainability

Magnetic fields in single late-type giants in the Solar vicinity: How common is magnetic activity on the giant branches?

We present our first results on a new sample containing all single G, K and M giants down to V = 4 mag in the Solar vicinity, suitable for spectropolarimetric (Stokes V) observations with Narval at TBL, France. For detection and measurement of the magnetic field (MF), the Least Squares Deconvolution (LSD) method was applied (Donati et al. 1997) that in the present case enables detection of large-scale MFs even weaker than the solar one (the typical precision of our longitudinal MF measurements is 0.1-0.2 G). The evolutionary status of the stars is determined on the basis of the evolutionary models with rotation (Lagarde et al. 2012; Charbonnel et al., in prep.) and fundamental parameters given by Massarotti et al. (1998). The stars appear to be in the mass range 1-4 M ⊙, situated at different evolutionary stages after the Main Sequence (MS), up to the Asymptotic Giant Branch (AGB). The sample contains 45 stars. Up to now, 29 stars are observed (that is about 64% of the sample), each observed at least twice. For 2 stars in the Hertzsprung gap, one is definitely Zeeman detected. Only 5 G and K giants, situated mainly at the base of the Red Giant Branch (RGB) and in the He-burning phase are detected. Surprisingly, a lot of stars ascending towards the RGB tip and in early AGB phase are detected (8 of 13 observed stars). For all Zeeman detected stars v sin i is redetermined and appears in the interval 2-3 km/s, but few giants with MF possess larger v sin

A waveguide-coupled colloidal quantum dot LED on a silicon nitride platform

Colloidal quantum dots (QDs) have become an attractive light source for visible photonics. Here, we demonstrate the first integrated LED based on CdSe/CdS QDs, with the emission directly coupled to a silicon nitride waveguide. (C) 2020 The Author(s

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

Gazave, Elodie et al.Copy number variants (CNVs) are increasingly acknowledged as an important source of evolutionary novelties in the human lineage. However, our understanding of their significance is still hindered by the lack of primate CNV data. We performed intraspecific comparative genomic hybridizations to identify loci harboring copy number variants in each of the four great apes: bonobos, chimpanzees, gorillas, and orangutans. For the first time, we could analyze differences in CNV location and frequency in these four species, and compare them with human CNVs and primate segmental duplication (SD) maps. In addition, for bonobo and gorilla, patterns of CNV and nucleotide diversity were studied in the same individuals. We show that CNVs have been subject to different selective pressures in different lineages.Evidence for purifying selection is stronger in gorilla CNVs overlapping genes, while positive selection appears to have driven the fixation of structural variants in the orangutan lineage. In contrast, chimpanzees and bonobos present high levels of common structural polymorphism, which is indicative of relaxed purifying selection together with the higher mutation rates induced by the known burst of segmental duplication in the ancestor of the African apes. Indeed, the impact of the duplication burst is noticeable by the fact that bonobo and chimpanzee share more CNVs with gorilla than expected. Finally, we identified a number of interesting genomic regions that present high-frequency CNVs in all great apes, while containing only very rare or even pathogenic structural variants in humans.Financial support was provided by a Beatriu de Pinos postdoctoral Grant to E.G., the Spanish Ministry of Science and Innovation (Grant BFU2009-13409-02-02toA.N.),and the Spanish National Institute for Bioinformatics (INB, www.inab.org).Peer reviewe

A step back on the conservation of a highly threatened species: opposite signs of recovery on Pinna nobilis population from Mar Menor lagoon

The endemic species Pinna nobilis is the most endangered Mediterranean bivalve, facing nearly extinction all over the Mediterranean Sea, hosting its last reservoirs in highly impacted coastal lagoons. Thus, knowledge about the populations' conservation status in these ecosystems is essential. In 2019, the Mar Menor lagoon’s population was considered as a highly vulnerable population (Nebot-Colomer et al., 2021) due to several ecological disasters. The present study represents a continuation of the previous work, which aims to evaluate the resilience of the population, by assessing its reproductive success and maintenance of the population. To do so, between 2019 to 2022, we installed between 23-45 larvae collectors, monitored 13 permanent individual’s plots, and conducted visual searches and censuses. Overall, densities remained stable over years, although the number of individuals alive monitored in permanent plots decrease each year. Moreover, none of the methodologies carried out detected the incorporation of recruits in the population. Our results pointed out to opposite signs of recovery of the species, increasing its vulnerability to future disturbances. Therefore, urgent management and conservation actions focused on restoring the ecosystem and protecting P. nobilis individuals are needed to avoid this population extinction

Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels

International audienceClostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels