Search results for "phylogeny"
showing 10 items of 1398 documents
Differences in gene activity in a Drosophila species cluster belonging to the Obscura group
1993
The polytene chromosome puffing pattern of Drosophila madeirensis was established and compared with those of the related species D. subobscura and D. guanche. A total of 145 loci, active in some of the 12 developmental stages analysed, were described, 38 of which were found to form the puffing pattern characteristic to this species. Taking into account the number of puffs as well as the mean puff expression, D. madeirensis shows a similar activity level to D. guanche, both species being less active than D. subobscura. The low gene activity of D. madeirensis and D. guanche was explained as a consequence of their ecological characteristics.
Comparative Genomics of Serratia spp.: Two Paths towards Endosymbiotic Life
2012
Symbiosis is a widespread phenomenon in nature, in which insects show a great number of these associations. Buchnera aphidicola, the obligate endosymbiont of aphids, coexists in some species with another intracellular bacterium, Serratia symbiotica. Of particular interest is the case of the cedar aphid Cinara cedri, where B. aphidicola BCc and S. symbiotica SCc need each other to fulfil their symbiotic role with the insect. Moreover, various features seem to indicate that S. symbiotica SCc is closer to an obligate endosymbiont than to other facultative S. symbiotica, such as the one described for the aphid Acirthosyphon pisum (S. symbiotica SAp). This work is based on the comparative genomi…
Genetic Variability of Hepatitis C Virus before and after Combined Therapy of Interferon plus Ribavirin
2008
We present an analysis of the selective forces acting on two hepatitis C virus genome regions previously postulated to be involved in the viral response to combined antiviral therapy. One includes the three hypervariable regions in the envelope E2 glycoprotein, and the other encompasses the PKR binding domain and the V3 domain in the NS5A region. We used a cohort of 22 non-responder patients to combined therapy (interferon alpha-2a plus ribavirin) for which samples were obtained before initiation of therapy and after 6 or/and 12 months of treatment. A range of 25-100 clones per patient, genome region and time sample were sequenced. These were used to detect general patterns of adaptation, t…
Phylogenetic signal and functional categories in Proteobacteria genomes
2007
Abstract Background A comprehensive evolutionary analysis of bacterial genomes implies to identify the hallmark of vertical and non-vertical signals and to discriminate them from the presence of mere phylogenetic noise. In this report we have addressed the impact of factors like the universal distribution of the genes, their essentiality or their functional role in the cell on the inference of vertical signal through phylogenomic methods. Results We have established that supermatrices derived from data sets composed mainly by genes suspected to be essential for bacterial cellular life perform better on the recovery of vertical signal than those composed by widely distributed genes. In addit…
Recombination drives genome evolution in outbreak-related Legionella pneumophila isolates.
2014
Legionella pneumophila is a strictly environmental pathogen and the etiological agent of legionellosis. It is known that non-vertical processes have a major role in the short-term evolution of pathogens, but little is known about the relevance of these and other processes in environmental bacteria. We report the whole-genome sequencing of 69 L. pneumophila strains linked to recurrent outbreaks in a single location (Alcoy, Spain) over 11 years. We found some examples where the genome sequences of isolates of the same sequence type and outbreak did not cluster together and were more closely related to sequences from different outbreaks. Our analyses identify 16 recombination events responsibl…
Phylogenomic Analysis Reveals Deep Divergence and Recombination in an Economically Important Grapevine Virus
2015
The evolutionary history of the exclusively grapevine (Vitis spp.) infecting, grapevine leafroll-associated virus 3 (GLRaV-3) has not been studied extensively, partly due to limited available sequence data. In this study we trace the evolutionary history of GLRaV-3, focussing on isolate GH24, a newly discovered variant. GH24 was discovered through the use of next-generation sequencing (NGS) and the whole genome sequence determined and validated with Sanger sequencing. We assembled an alignment of all 13 available whole genomes of GLRaV-3 isolates and all other publicly available GLRaV-3 sequence data. Using multiple recombination detection methods we identified a clear signal for recombinat…
Deep metazoan phylogeny: When different genes tell different stories
2013
11 páginas, 4 figuras, 1 tabla.
Identification of sapovirus infection among Japanese infants in a day care center.
2005
A total of 921 fecal specimens collected from 44 infants in a day care center in Tokyo, Japan during June 1999 to July 2000 were tested for the presence of sapovirus by reverse transcription-polymerase chain reaction (RT-PCR). Of 88 fecal specimens from infants with acute gastroenteritis, 2.3% (2) were found to be positive for sapovirus. Twenty-two of 833 (2.6%) fecal specimens collected from asymptomatic infants were also infected with this virus. Another interesting feature was the demonstration of high incidence of sapovirus infection (95.5%, 21 of 22) identified in a single day care center, which was not due to viral shedding after the latest acute gastroenteritis. Sapovirus was subject…
Homologous recombination as a mechanism of genetic changes in bovine parainfluenza-3 virus
2021
Bovine parainfluenza-3 virus (BPIV-3) is one of the main viruses associated with bovine respiratory disease complex (BRDC) worldwide. BPIV-3 infect the bovine respiratory tract causing from subclinical infections to severe pneumonia with significant economic losses in the cattle industry. BPIV-3 is a RNA virus with high genetic variability, nevertheless, the contribution of recombination events to its variability has not been assessed so far. In this study the 25 complete genome sequences (CGS) reported so far and 215 partial sequences of different viral genes of BPIV-3 were analyzed to determine their genotypes and subgenotypes, distribution, and the existence of potential recombination ev…
Identification of subdominant sourdough lactic acid bacteria and their evolution during laboratory-scale fermentations
2007
Abstract Presumptive lactic acid bacterial cocci were found in six sourdoughs (out of 20) from the Abruzzo region (central Italy) and subjected to phenotypic and genotypic characterization. A total of 21 isolates, recognized as seven strains by randomly amplified polymorphic DNA (RAPD)–polymerase chain reaction (PCR) typing, were identified by a polyphasic approach, consisting of 16S rRNA gene sequencing, multiplex PCR assays and physiological features, as Enterococcus faecium and Pediococcus pentosaceus. Four strains belonging to those species and previously isolated from wheat kernels were inoculated in sterile flour to verify their capacity to grow in sourdough environment. Doughs with s…