RESUMO
Building de novo genome assemblies for complex genomes is possible thanks to long-read DNA sequencing technologies. However, maximizing the quality of assemblies based on long reads is a challenging task that requires the development of specialized data analysis techniques. We present new algorithms for assembling long DNA sequencing reads from haploid and diploid organisms. The assembly algorithm builds an undirected graph with two vertices for each read based on minimizers selected by a hash function derived from the k-mer distribution. Statistics collected during the graph construction are used as features to build layout paths by selecting edges, ranked by a likelihood function. For diploid samples, we integrated a reimplementation of the ReFHap algorithm to perform molecular phasing. We ran the implemented algorithms on PacBio HiFi and Nanopore sequencing data taken from haploid and diploid samples of different species. Our algorithms showed competitive accuracy and computational efficiency, compared with other currently used software. We expect that this new development will be useful for researchers building genome assemblies for different species.
Assuntos
Algoritmos , Sequenciamento de Nucleotídeos em Larga Escala , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos , Genoma , SoftwareRESUMO
The mother-child relationship is fundamental to the establishment and maintenance of synaptic networks and physiological and emotional development. Animal models including maternal separation have been used to study changes at behavioral and neurobiochemical levels. Due to the relevance of glial cells during development, our aim was to determine if short periods of maternal separation during breastfeeding induce permanent changes in a number of astrocytes labeled with the glial fibrillary acidic protein in different brain areas. Wistar rats were housed under standard laboratory conditions with reversed light/dark cycle; food and water ad libitum. Pups were separated from their mothers for 6 h daily during breastfeeding period. On day 22, pups were separately housed according to gender and treatment. At day 60, subjects were evaluated in the elevated plus maze and, after processing for immunohistochemistry, 20-μm sections were made. Prefrontal cortex, paraventricular nucleus, preoptic area, hippocampus and amygdala were localized. Labeled cells were quantified using Image-J program. Results showed that separated females had more entries into open arms and spend more time as compared with the control groups. In the prefrontal cortex we identified a decrease in staining cells in separated females, whereas there was an increase in staining cells in separated males. In the hippocampus and preoptic area, we observed a decrease only in separated males. We did not find any differences in the paraventricular nucleus or amygdala. Our results indicate that maternal separation during breastfeeding induces permanent changes in the number of astrocytes in different brain areas of both males and females.
Assuntos
Astrócitos , Imuno-Histoquímica , Neuroglia , Transmissão Sináptica , Desmame , Modelos Animais , Plasticidade NeuronalRESUMO
The mother-child relationship is fundamental to the establishment and maintenance of synaptic networks and physiological and emotional development. Animal models including maternal separation have been used to study changes at behavioral and neurobiochemical levels. Due to the relevance of glial cells during development, our aim was to determine if short periods of maternal separation during breastfeeding induce permanent changes in a number of astrocytes labeled with the glial fibrillary acidic protein in different brain areas. Wistar rats were housed under standard laboratory conditions with reversed light/dark cycle; food and water ad libitum. Pups were separated from their mothers for 6 h daily during breastfeeding period. On day 22, pups were separately housed according to gender and treatment. At day 60, subjects were evaluated in the elevated plus maze and, after processing for immunohistochemistry, 20-μm sections were made. Prefrontal cortex, paraventricular nucleus, preoptic area, hippocampus and amygdala were localized. Labeled cells were quantified using Image-J program. Results showed that separated females had more entries into open arms and spend more time as compared with the control groups. In the prefrontal cortex we identified a decrease in staining cells in separated females, whereas there was an increase in staining cells in separated males. In the hippocampus and preoptic area, we observed a decrease only in separated males. We did not find any differences in the paraventricular nucleus or amygdala. Our results indicate that maternal separation during breastfeeding induces permanent changes in the number of astrocytes in different brain areas of both males and females.(AU)