Genome sequence of the pea aphid Acyrthosiphon pisum

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

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.

Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution

Background: Chemoreception is a widespread mechanism that is involved in critical biologic processes, including individual and social behavior. The insect peripheral olfactory system comprises three major multigene families: the olfactory receptor (Or), the gustatory receptor (Gr), and the odorant-binding protein (OBP) families. Members of the latter family establish the first contact with the odorants, and thus constitute the first step in the chemosensory transduction pathway.Results: Comparative analysis of the OBP family in 12 Drosophila genomes allowed the identification of 595 genes that encode putative functional and nonfunctional members in extant species, with 43 gene gains and 28 gene losses (15 deletions and 13 pseudogenization events). The evolution of this family shows tandem gene duplication events, progressive divergence in DNA and amino acid sequence, and prevalence of pseudogenization events in external branches of the phylogenetic tree. We observed that the OBP arrangement in clusters is maintained across the Drosophila species and that purifying selection governs the evolution of the family; nevertheless, OBP genes differ in their functional constraints levels. Finally, we detect that the OBP repertoire evolves more rapidly in the specialist lineages of the Drosophila melanogaster group (D. sechellia and D. erecta) than in their closest generalists.Conclusion: Overall, the evolution of the OBP multigene family is consistent with the birth-and-death model. We also found that members of this family exhibit different functional constraints, which is indicative of some functional divergence, and that they might be involved in some of the specialization processes that occurred through the diversification of the Drosophila genus.

Biotecnologia Ambiental. Aplicacions biotecnològiques a la millora del medi ambient

La biotecnología ambiental comprende el conjunto de actividades tecnológicas que facilitan la comprensión y la gestión de los sistemas biológicos en el medio ambiente, con el fin de proveer productos y servicios. Actualmente, la gestión del medio ambiente y de sus recursos naturales no se comprende si no se realiza de manera sostenible. Los avances científicos y tecnológicos le están permitiendo a la biotecnología ambiental, el desarrollo de nuevas herramientas y aplicaciones con los que responder a los principales retos medioambientales actuales. Entre estos debe destacarse la disponibilidad de recursos hídricos y energéticos. El papel esencial de los microorganismos tanto en el ciclo de los elementos como en el funcionamiento de los ecosistemas naturales ha comportado una estrecha relación entre la biotecnología ambiental y la ecología microbiana. Las nuevas técnicas moleculares de genómica, proteómica i metabolómica, han facilitado a la biotecnología ambiental plantearse nuevas perspectivas a partir de los recientes conocimientos estructurales y funcionales de los consorcios microbianos. La comprensión de la biodiversidad y la funcionalidad de los estos consorcios microbianos está introduciendo una nueva forma de gestionar los recursos naturales y el medio ambiente, de manera similar a como actualmente el estudio de los recursos humanos de una empresa resulta una herramienta esencial para la dirección de empresas y el establecimiento de planes estratégicos. Los principales ámbitos de interés actual de la biotecnología ambiental son aquellos aspectos medioambientales relacionados con el cambio climático, la búsqueda de nuevas fuentes energéticas renovables y alternativas, la mejora de los procesos de reciclaje, el aprovechamiento y la gestión de recursos hídricos, y la mejora de las interacciones entre salud y medio ambiente. No obstante, en nuestro ámbito territorial presentan una mayor importancia y demanda social las actividades y metodologías tecnológicas de la biotecnología ambiental relacionadas con los procesos de reciclaje y bioremediación de suelos contaminados, la mejora de la gestión y el control de la calidad de nuestros recursos hídricos y la mejora de aquellas actividades donde interacciona la salud y el medio ambiente. Las aportaciones significativas de la biotecnología ambiental en el desarrollo de energías realmente alternativas y en el control del cambio climático queda relegadas en un segundo término des de un punto de vista de su aplicabilidad actual y futura a corto plazo.

Bioinformatics: making large-scale science happen

Bionformatics is a rapidly evolving research field dedicated toanalyzing and managing biological data with computational resources. This paperaims to overview some of the processes and applications currently implementedat CCiT-UB¿s Bioinformatics Unit, focusing mainly on the areas of Genomics,Transcriptomics and Proteomics

Genomics: more than genes

The fundamentals of Real-time Polymerase Chain Reaction,Automated capillary electrophoresis -Sanger sequencing and Fragmentanalysis- and "Next-generation" sequencing are reviewed. An overview ofapplications is presented using our own examples carried out in our facility.

"Next-generation" Sequencing (NGS): The new genomic revolution

In the past 5 years "Next-generation" Sequencing (NGS) technologies have transformed genomics by delivering fast, inexpensive and accurate genomeinformation changing the way we think about scientific approaches in basic,applied and clinical research. The inexpensive production of large volumes ofsequence data is the main advantage over the automated Sanger method,making this new technology useful for many applications. In this chapter, a brieftechnical review of NGS technologies is given, along with the keys to NGSsuccess and a broad range of applications for NGS technologies.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of such high-quality data is important to design, evaluate and improve novel computational approaches to identify binding motifs on promoter sequences from related genes. ABS (http://genome.imim.es/datasets/abs2005/index.html) is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.

Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of these rearrangement events, we sequenced 24 synteny breakpoint regions in the white-cheeked gibbon (Nomascus leucogenys, NLE) in the form of high-quality BAC insert sequences (4.2 Mbp). While there is a significant deficit of breakpoints in genes, we identified seven human gene structures involved in signaling pathways (DEPDC4, GNG10), phospholipid metabolism (ENPP5, PLSCR2), beta-oxidation (ECH1), cellular structure and transport (HEATR4), and transcription (ZNF461), that have been disrupted in the NLE gibbon lineage. Notably, only three of these genes show the expected evolutionary signatures of pseudogenization. Sequence analysis of the breakpoints suggested both nonclassical nonhomologous end-joining (NHEJ) and replication-based mechanisms of rearrangement. A substantial number (11/24) of human-NLE gibbon breakpoints showed new insertions of gibbon-specific repeats and mosaic structures formed from disparate sequences including segmental duplications, LINE, SINE, and LTR elements. Analysis of these sites provides a model for a replication-dependent repair mechanism for double-strand breaks (DSBs) at rearrangement sites and insights into the structure and formation of primate segmental duplications at sites of genomic rearrangements during evolution.

Diferenciação molecular de cultivares elites de bananeira

Este trabalho teve como objetivo caracterizar molecularmente genótipos elite, e recomendados, de bananeira, por meio de marcadores RAPD e microssatélites. Foram utilizados 47 primers de RAPD e 34 primers de microssatélites. Foi também conduzido um ensaio de contaminação, utilizando-se o primer AGMI 24-25, cuja variedade Tropical foi considerada a amostra-padrão, e as cultivares Caipira e Prata Graúda como contaminantes. Os marcadores permitiram separar as cultivares de acordo com a origem e a constituição genômica e definiram padrões moleculares para algumas cultivares avaliadas. As cultivares Garantida, Preciosa e Pacovan Ken apresentaram alta similaridade genética com ambos marcadores. O primer AGMI 24-25 demonstrou alta capacidade discriminatória de genótipos em ensaios de contaminação.

Estimativa de freqüência de recombinação no mapeamento genético de famílias de irmãos completos

O objetivo deste trabalho foi obter as estimativas de freqüência de recombinação, por meio de simulação, para diferentes situações do mapeamento genético de famílias de irmãos completos. Foi simulado um genoma constituído de três grupos de ligação, em que cada um apresentava 11 marcas moleculares multialélicas, codominantes, distribuídas a cada 10 cM. A partir desse genoma, foram simulados dois cenários: um com genitores completamente informativos e outro com genitores formados aleatoriamente. Após a obtenção de todas as estimativas das freqüências de recombinação, concluiu-se que, para locos completamente informativos, pode-se calcular a freqüência de recombinação entre pares de locos, a partir da freqüência gamética de cada genitor ou a partir da freqüência genotípica da progênie. Para locos parcialmente informativos, a obtenção da freqüência de recombinação a partir da freqüência genotípica conjunta é mais apropriada.

Tamanho de população ideal para mapeamento genético em famílias de irmãos completos

O objetivo deste trabalho foi avaliar o tamanho ótimo de populações de irmãos completos, para estudos de mapas de marcadores moleculares, por meio de simulações de genomas e tamanhos de populações. Foram simulados genomas parentais e amostras de populações de família de irmãos completos do tipo completamente informativas, e também não completamente informativas. As amostras geradas foram de 100, 200, 400 e 600 indivíduos, com três grupos de ligação cada, e 11 marcas moleculares codominantes e multialélicas, espaçadas a dez centimorgans por grupo de ligação. Foram realizadas 100 repetições por amostra. Para populações completamente informativas, o tamanho populacional de 200 indivíduos é suficiente para recuperar as informações originais, contudo, para a população não completamente informativa, é necessária a utilização de uma população maior, de 600 indivíduos.

A new disruption vector (pDHO) to obtain heterothallic strains from both Saccharomyces cerevisiae and Saccharomyces pastorianus

Yeasts are responsible for several traits in fermented beverages, including wine and beer, and their genetic manipulation is often necessary to improve the quality of the fermentation product. Improvement of wild-type strains of Saccharomyces cerevisiae and Saccharomyces pastorianus is difficult due to their homothallic character and variable ploidy level. Homothallism is determined by the HO gene in S. cerevisiae and the Sc-HO gene in S. pastorianus. In this work, we describe the construction of an HO disruption vector (pDHO) containing an HO disruption cassette and discuss its use in generating heterothallic yeast strains from homothallic Saccharomyces species.

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.

Expressão de genes da subfamília HD-Zip I em soja submetida à seca

O objetivo deste trabalho foi identificar genes candidatos da subfamília de fatores transcricionais HD-Zip I que contribuem para a tolerância à seca em soja. Foram avaliados trifólios de soja de cultivar tolerante (Embrapa 48) e suscetível à seca (BR 16), sob três níveis de deficit hídrico: ausência, moderado (-1,5 MPa) e severo (-3,0 MPa). Pela análise dos promotores, foi identificada a presença de possíveis elementos cis-regulatórios relacionados à resposta à seca, nos três genes avaliados (GmHB6, GmHB13 e GmHB21). No entanto, não houve padrão de distribuição específico associado à maior tolerância do genótipo à seca. Com a análise comparativa, foram identificados seis elementos cis-regulatórios potencialmente envolvidos na indução da expressão gênica sob seca. O gene GmHB13 foi exclusivamente induzido pela seca no genótipo tolerante, e o gene GmHB6 apresentou redução da expressão somente no genótipo suscetível. Já o gene GmHB21, apresentou aumento da expressão em ambos os genótipos. O gene GmHB13 é um importante elemento na regulação do mecanismo de tolerância à seca em soja, na cultivar tolerante Embrapa 48.