Divergent evolution and molecular adaptation in the Drosophila odorant-binding protein family: inferences from sequence variation at the OS-E and OS-F genes

<p>Abstract</p> <p>Background</p> <p>The <it>Drosophila </it>Odorant-Binding Protein (<it>Obp</it>) genes constitute a multigene family with moderate gene number variation across species. The <it>OS-E </it>and <it>OS-F </it>genes are the two phylogenetically closest members of this family in the <it>D. melanogaster </it>genome. In this species, these genes are arranged in the same genomic cluster and likely arose by tandem gene duplication, the major mechanism proposed for the origin of new members in this olfactory-system family.</p> <p>Results</p> <p>We have analyzed the genomic cluster encompassing <it>OS-E </it>and <it>OS-F </it>genes (<it>Obp83 </it>genomic region) to determine the role of the functional divergence and molecular adaptation on the <it>Obp </it>family size evolution. We compared nucleotide and amino acid variation across 18 <it>Drosophila </it>and 4 mosquito species applying a phylogenetic-based maximum likelihood approach complemented with information of the OBP three-dimensional structure and function. We show that, in spite the <it>OS-E </it>and <it>OS-F </it>genes are currently subject to similar and strong selective constraints, they likely underwent divergent evolution. Positive selection was likely involved in the functional diversification of new copies in the early stages after the gene duplication event; moreover, it might have shaped nucleotide variation of the <it>OS-E </it>gene concomitantly with the loss of functionally related members. Besides, molecular adaptation likely affecting the functional OBP conformational changes was supported by the analysis of the evolution of physicochemical properties of the OS-E protein and the location of the putative positive selected amino acids on the OBP three-dimensional structure.</p> <p>Conclusion</p> <p>Our results support that positive selection was likely involved in the functional differentiation of new copies of the OBP multigene family in the early stages after their birth by gene duplication; likewise, it might shape variation of some members of the family concomitantly with the loss of functionally related genes. Thus, the stochastic gene gain/loss process coupled with the impact of natural selection would influence the observed OBP family size.</p

Unique Features of Odorant-Binding Proteins of the Parasitoid Wasp Nasonia vitripennis Revealed by Genome Annotation and Comparative Analyses

Insects are the most diverse group of animals on the planet, comprising over 90% of all metazoan life forms, and have adapted to a wide diversity of ecosystems in nearly all environments. They have evolved highly sensitive chemical senses that are central to their interaction with their environment and to communication between individuals. Understanding the molecular bases of insect olfaction is therefore of great importance from both a basic and applied perspective. Odorant binding proteins (OBPs) are some of most abundant proteins found in insect olfactory organs, where they are the first component of the olfactory transduction cascade, carrying odorant molecules to the olfactory receptors. We carried out a search for OBPs in the genome of the parasitoid wasp Nasonia vitripennis and identified 90 sequences encoding putative OBPs. This is the largest OBP family so far reported in insects. We report unique features of the N. vitripennis OBPs, including the presence and evolutionary origin of a new subfamily of double-domain OBPs (consisting of two concatenated OBP domains), the loss of conserved cysteine residues and the expression of pseudogenes. This study also demonstrates the extremely dynamic evolution of the insect OBP family: (i) the number of different OBPs can vary greatly between species; (ii) the sequences are highly diverse, sometimes as a result of positive selection pressure with even the canonical cysteines being lost; (iii) new lineage specific domain arrangements can arise, such as the double domain OBP subfamily of wasps and mosquitoes.Rothamsted Research receives grant-aided support from the BBSRC of the UK. The authors thank Prof. David M. Shuker, University of Edinburgh, UK, who provided us with N. vitripennis. FGV was supported by a predoctoral fellowship SFRH/BD/22360/2005 from the ‘Fundac¸a˜o para a Cieˆncia e a Tecnologı´a’ (Portugal). This work was funded by grants BFU2007-62927 and BFU2010-15484 from the ‘Direccio´n General de Investigacio´n Cientı´fica y Te´cnica’ (Spain) to JR. JR was partially supported by ICREA Academia (Generalitat de Catalunya). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Genome-wide DNA polymorphism analyses using VariScan

BACKGROUND: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. RESULTS: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers. CONCLUSION: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data

Análisis de la variabilidad a nivel nucleotídico de la región rp49 en Drosophila subobscura

[spa] Se ha analizado la variabilidad existente en una región de 1.6 KB. que incluye al locus RP49 (Ribosome Protein 49) en distintas ordenaciones cromosómicas de Drosophila subobscura. El estudio se ha efectuado mediante comparación de mapas de restricción según la técnica "Four-Cutter Analysis". Se han estudiado las siguientes poblaciones naturales: Barcelona (49 líneas), Ter Apel -Holanda- (58 líneas), Tenerife (54 líneas) y Santiago de Chile (54 líneas). Tras el análisis de los mapas de restricción se han detectado un total de 19 polimorfismos por substitución nucleotídica y 8 por inserción/deleción y un total de 96 haplotipos. La heterozigosidad por nucleótido fue de 0.0045 en las poblaciones europeas, de 0.0028 en la población de Tenerife y de 0.0056 en la población de Santiago de Chile. Las principales conclusiones del trabajo han sido: 1) No existencia de heterogeneidad entre las dos poblaciones europeas para ninguna de las 3 ordenaciones cromosómicas que se consideraron (OST' 03+4 Y 03+4+8). 2) Existencia de un importante intercambio genético entre distintas ordenaciones cromosómicas. 3) Mayor antigüedad de la ordenación cromosómica 03+4 respecto a la de la ordenación OST. 4) Gran diferenciación genética de la población de Tenerife respecto a las poblaciones europeas. 5) Gran reducción del número de haplotipos en la población de Santiago de Chile. 6) Evidencia de que los haplotipos de la región RP49 que se hallan en la actualidad en Santiago de Chile son descendientes por réplica de únicamente 6 a 8 cromosomas

BadiRate Software

Podeu consultar l'article relacionat a: http://hdl.handle.net/2445/53350Podeu consultar la pàgina de desenvolupament del programari: http://www.ub.edu/softevol/badirate/BadiRate is a software package to estimate, within a phylogenetic context and by likelihood-based methods (or parsimony): (1) the gain, birth, death and innovation family turnover rates (2) most likely number of family members in internal nodes (3) families with turnover rates higher or lower than that estimated for the whole dat

Bioinformática y evolución molecular

Aunque la bioinformática y la evolución molecular pueden parecer disciplinas científicas muy heterogéneas, comparten gran parte de sus intereses y fundamentos, concretamente, el mismo interés por el estudio y análisis de secuencias de DNA y proteínas; no sólo eso: estos estudios son el núcleo central de ambas disciplina

The genetic variability of pigs is greater than was thought

L'espècie porcina és molt més variable del que es pensava. Els investigadors han trobat una variabilitat genètica per al gen FABP4 (que està implicat en la quantitat de grasa que deposita l'animal) deu vegades superior a la trobada a l'espècie humana i similar a la de les espècies silvestres, no domesticades. A més, han descobert que el porc ibèric és molt variable.La especie porcina es mucho más variable de lo que se pensaba. Los investigadores han encontrado una variabilidad genética para el gen FABP4 (que está implicado en la cantidad de grasa que deposita el animal) diez veces superior a la encontrada en la especie humana y similar a la de las especies silvestres, no domesticadas. Además, han descubierto que el cerdo Ibérico es muy variable.The porcine species is much more variable than was once thought. Researchers have found a genetic variability for the gene FABP4 (which is involved in the quantity of fat that the animal deposits) ten times greater than that found in humans and similar to that of wild, undomesticated species. In addition they have discovered that the Iberian pig is very variable

Comment on 'The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway'

Letter to the Editor on Wang M, Wang Q, Wang Z, Zhang X, Pan Y. The molecular evolutionary patterns of the insulin/FOXO signaling pathwa

Comparative genomics reveals thousands of novel chemosensory genes and massive changes in chemoreceptor repertories across chelicerates

Chemoreception is a widespread biological function that is essential for the survival, reproduction, and social communication of animals. Though the molecular mechanisms underlying chemoreception are relatively well known in insects, they are poorly studied in the other major arthropod lineages. Current availability of a number of chelicerate genomes constitutes a great opportunity to better characterize gene families involved in this important function in a lineage that emerged and colonized land independently of insects. At the same time, that offers new opportunities and challenges for the study of this interesting animal branch in many translational research areas. Here, we have performed a comprehensive comparative genomics study that explicitly considers the high fragmentation of available draft genomes and that for the first time included complete genome data that cover most of the chelicerate diversity. Our exhaustive searches exposed thousands of previously uncharacterized chemosensory sequences, most of them encoding members of the gustatory and ionotropic receptor families. The phylogenetic and gene turnover analyses of these sequences indicated that the whole-genome duplication events proposed for this subphylum would not explain the differences in the number of chemoreceptors observed across species. A constant and prolonged gene birth and death process, altered by episodic bursts of gene duplication yielding lineage-specific expansions, has contributed significantly to the extant chemosensory diversity in this group of animals. This study also provides valuable insights into the origin and functional diversification of other relevant chemosensory gene families different from receptors, such as odorant-binding proteins and other related molecules