900 resultados para Assembly vectors


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Information Paper, No 19

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This report indicates the main advances of the past 20 years based on the information provided by the region’s countries on implementation of the Beijing Declaration and Platform for Action, in response to the recommendations made in the final document of the twenty-third special session of the General Assembly (2000) for the regional and global reviews that would take place in 2015, on the twentieth anniversary of the Beijing Conference (Beijing+20). The subregional report on the Caribbean (ECLAC, 2014c) has also been taken into account, which includes data from the country gender assessments prepared by the Caribbean Development Bank, the country poverty assessments and information provided by the Caribbean Community (CARICOM).

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Bacterial artificial chromosomes (BAC) have been widely used for fluorescence in situ hybridization (FISH) mapping of chromosome landmarks in different organisms, including a few in teleosts. In this study, we used BAC-FISH to consolidate the previous genetic and cytogenetic maps of the turbot (Scophthalmus maximus), a commercially important pleuronectiform. The maps consisted of 24 linkage groups (LGs) but only 22 chromosomes. All turbot LGs were assigned to specific chromosomes using BAC probes obtained from a turbot 5x genomic BAC library. It consisted of 46,080 clones with inserts of at least 100 kb and < 5 % empty vectors. These BAC probes contained gene-derived or anonymous markers, most of them linked to quantitative trait loci (QTL) related to productive traits. BAC clones were mapped by FISH to unique marker-specific chromosomal positions, which showed a notable concordance with previous genetic mapping data. The two metacentric pairs were cytogenetically assigned to LG2 and LG16, and the nucleolar organizer region (NOR)-bearing pair was assigned to LG15. Double-color FISH assays enabled the consolidation of the turbot genetic map into 22 linkage groups by merging LG8 with LG18 and LG21 with LG24. In this work, a first-generation probe panel of BAC clones anchored to the turbot linkage and cytogenetical map was developed. It is a useful tool for chromosome traceability in turbot, but also relevant in the context of pleuronectiform karyotypes, which often show small hardly identifiable chromosomes. This panel will also be valuable for further integrative genomics of turbot within Pleuronectiformes and teleosts, especially for fine QTL mapping for aquaculture traits, comparative genomics, and whole-genome assembly.

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

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

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

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High throughput sequencing (HTS) provides new research opportunities for work on non-model organisms, such as differential expression studies between populations exposed to different environmental conditions. However, such transcriptomic studies first require the production of a reference assembly. The choice of sampling procedure, sequencing strategy and assembly workflow is crucial. To develop a reliable reference transcriptome for Triatoma brasiliensis, the major Chagas disease vector in Northeastern Brazil, different de novo assembly protocols were generated using various datasets and software. Both 454 and Illumina sequencing technologies were applied on RNA extracted from antennae and mouthparts from single or pooled individuals. The 454 library yielded 278 Mb. Fifteen Illumina libraries were constructed and yielded nearly 360 million RNA-seq single reads and 46 million RNA-seq paired-end reads for nearly 45 Gb. For the 454 reads, we used three assemblers, Newbler, CAP3 and/or MIRA and for the Illumina reads, the Trinity assembler. Ten assembly workflows were compared using these programs separately or in combination. To compare the assemblies obtained, quantitative and qualitative criteria were used, including contig length, N50, contig number and the percentage of chimeric contigs. Completeness of the assemblies was estimated using the CEGMA pipeline. The best assembly (57,657 contigs, completeness of 80 %, < 1 % chimeric contigs) was a hybrid assembly leading to recommend the use of (1) a single individual with large representation of biological tissues, (2) merging both long reads and short paired-end Illumina reads, (3) several assemblers in order to combine the specific advantages of each.

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Prevotella is one of the most abundant genera in bovine rumen, although no genome has yet been assembled by a metagenomics approach applied to Brazilian Nelore. We report the draft genome sequence of Prevotella sp., comprising 2,971,040 bp, obtained using the Illumina sequencing platform. This genome includes 127 contigs and presents a low 48% GC.

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Myxobolus cerebralis, the cause of whirling disease in salmonids, has dispersed to waters in 25 states within the USA, often by an unknown vector. Its incidence in Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri within the highly protected environment of Yellowstone Lake, Yellowstone National Park, is a prime example. Given the local abundances of piscivorous birds, we sought to clarify their potential role in the dissemination of M. cerebralis. Six individuals from each of three bird species (American white pelican Pelecanus erythrorhynchos, double-crested cormorant Phalacrocorax auritus, and great blue heron Ardea herodias) were fed known-infected or uninfected rainbow trout O. mykiss. Fecal material produced during 10-d periods before and after feeding was collected to determine whether M. cerebralis could be detected and, if so, whether it remained viable after passage through the gastrointestinal tract of these birds. For all (100%) of the nine birds fed known-infected fish, fecal samples collected during days 1–4 after feeding tested positive for M. cerebralis by polymerase chain reaction. In addition, tubificid worms Tubifex tubifex that were fed fecal material from known-infected great blue herons produced triactinomyxons in laboratory cultures, confirming the persistent viability of the parasite. No triactinomyxons were produced from T. tubifex fed fecal material from known-infected American white pelicans or double-crested cormorants, indicating a potential loss of parasite viability in these species. Great blue herons have the ability to concentrate and release viable myxospores into shallow-water habitats that are highly suitable for T. tubifex, thereby supporting a positive feedback loop in which the proliferation of M. cerebralis is enhanced. The presence of avian piscivores as an important component of aquatic ecosystems should continue to be supported. However, given the distances traveled by great blue herons between rookeries and foraging areas in just days, any practices that unnaturally attract them may heighten the probability of M. cerebralis dispersal and proliferation within the Greater Yellowstone Ecosystem.