Identification and characterization of regions of difference between the Salmonella Gallinarum biovar Gallinarum and the Salmonella Gallinarum biovar Pullorum genomes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The genomes of two key bumblebee species with primitive eusocial organization

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Chromosomal location of retrotransposable REX 1 in the genomes in five Prochilodus (Teleostei: Characiformes)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Variabilidade genética da raça Brahman no Brasil detectada por meio de análise de pedigree

O objetivo deste trabalho foi analisar a variabilidade genética da raça Brahman no Brasil, por meio da análise de 15.851 pedigrees. O arquivo de dados foi dividido em dois períodos: 1998-2001 e 2002-2005. A variabilidade genética foi avaliada por parâmetros baseados na probabilidade de origem do gene: número efetivo de ancestrais, número efetivo de fundadores, número efetivo de genomas remanescentes e coeficientes de parentesco e de endogamia. Os valores encontrados quanto ao número de fundadores mostraram que a população está em expansão, embora o número efetivo de fundadores tenha diminuído de um período para outro. Os resultados foram diferentes em relação ao número de ancestrais e genomas remanescentes, que apresentaram crescimento de 23% nos períodos avaliados. O coeficiente de endogamia diminuiu nos períodos estudados, porém o coeficiente de parentesco inter se cresceu. Poucos ancestrais apresentaram grande contribuição genética para a população, o que evidencia a utilização de poucos indivíduos na reprodução. A raça Brahman, no Brasil, encontra-se em expansão, caracterizada pela diminuição do coeficiente de endogamia e aumento nos números efetivos de fundadores e de genótipos remanescentes. Entretanto, a variabilidade genética da raça mostra aumento do parentesco inter se e grande concentração do patrimônio genético de poucos indivíduos na população.

Análise da variabilidade genética de acessos dePsidium spp. (Myrtaceae) avaliados quanto à reação a Meloidogyne enterolobii

This study aimed to characterize molecular of 13 accessions of Psidium spp. (Myrtaceae) that was been identified for the reaction to rootknot guava nematode. The DNA extraction of the samples was carried according to the protocol of Shillito & Saul (1988). The molecular markers type fAFLP, were obtained from fAFLP Regular Plant Genomes Fingerprinting Kit' (Applied Biosystems from Brasil Ltda.) and were tested 24 selectives combinations of primers, of which 18 showed amplification that produced 272 polymorphic markers. To the analysis of the markers were employed the softwares GeneScan (ABI Prism versao 1.0) and Genotyper (ABI Prism version 1.03), and the data collected were transformed into a binary matrix that was analyzed in the software PAUP (Phylogenetic Analysis Using Parcimony - version 3.01). Were calculated genetic distance index intra and interespecific between the genotipes. It was found that the AFLP markers were efficient in the discrimination between accessions, as well as in showing genetic similarity among accessions identified as resistant to the nematode Meloidogyne enterolobii, which could be discussed in the future.

Whole-genome expression profiling of Xylella fastidiosa in response to growth on glucose

Xylella fastidiosa is the etiologic agent of diseases in a wide range of economically important crops including citrus variegated chlorosis, a major threat to the Brazilian citrus industry. The genomes of several strains of this phytopathogen have been completely sequenced enabling large-scale functional studies. In this work we used whole-genome DNA microarrays to investigate the transcription profile of X. fastidiosa grown in defined media with different glucose concentrations. Our analysis revealed that while transcripts related to fastidian gum production were unaffected, colicin-V-like and fimbria precursors were induced in high glucose medium. Based on these results, we suggest a model for colicin-defense mechanism in X. fastidiosa.

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in Two Corynebacterium pseudotuberculosis Strains

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Further characterization of two sequiviruses infecting lettuce and development of specific RT-PCR primers

Lettuce mottle virus (LeMoV) and dandelion yellow mosaic virus (DaYMV) infect lettuce in South America and Europe, respectively. LeMoV and DaYMV possess isometric particles, occur at low concentrations in plants and have narrow host ranges. Partial genome sequences of both viruses were obtained using purified viral preparations and universal primers for members of the family Sequiviridae. DaYMV and LeMoV sequences were analyzed and showed identity with other members of the family. Universal primers that detect both viruses and specific primers for LeMoV and DaYMV were designed and used in RT-PCR-based diagnostic assays. These results provide the first molecular data on the LeMoV and DaYMV genomes and suggest that LeMoV is a member of the genus Sequivirus, probably distinct from DaYMV.

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Population dynamics of DENV-1 genotype V in Brazil is characterized by co-circulation and strain/lineage replacement

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Comparative genomics analyses of citrus-associated bacteria

Xylella fastidiosa 9a5c (XF-9a5c) and Xanthomonas axonopodis pv. citri (XAC) are bacteria that infect citrus plants. Sequencing of the genomes of these strains is complete and comparative analyses are now under way with the genomes of other bacteria of the same genera. In this review, we present an overview of this comparative genomic work. We also present a detailed genomic comparison between XF-9a5a and XAC. Based on this analysis, genes and operons were identified that might be relevant for adaptation to citrus. XAC has two copies of a type II secretion system, a large number of cell wall-degrading enzymes and sugar transporters, a complete energy metabolism, a whole set of avirulence genes associated with a type III secretion system, and a complete flagellar and chemotatic system. By contrast, XF-9a5c possesses more genes involved with type IV pili biosynthesis than does XAC, contains genes encoding for production of colicins, and has 4 copies of Type I restriction/modification system while XAC has only one.

Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp aurantifolii

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Chicken skeletal muscle-associated macroarray for gene discovery

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Comparison between RT-PCR and the mouse inoculation test for detection of rabies virus in samples kept for long periods under different conditions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.