Search results for "Phylogeny"
showing 10 items of 1398 documents
Comparative Sequence Analysis ofMycobacterium lepraeand the New Leprosy-CausingMycobacterium lepromatosis
2009
ABSTRACTMycobacterium lepromatosisis a newly discovered leprosy-causing organism. Preliminary phylogenetic analysis of its 16S rRNA gene and a few other gene segments revealed significant divergence fromMycobacterium leprae, a well-known cause of leprosy, that justifies the status ofM. lepromatosisas a new species. In this study we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides). Overall, the level of matching of these sequences withM. lepraesequences was 90.9%, which substantiated the species-level difference; the levels of matching for the 16S rRNA genes and 14 protein-encoding genes were 98.0% and 93.1%, respectively, but the level of matching for five pseudogenes…
Taxas de substituições das Annonaceas: uma perspectiva do modelo códon
2014
The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these…
Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern.
2014
Background Novosphingobium sp. strain PP1Y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. It exploits the aromatic fraction of fuel oils as a carbon and energy source. PP1Y is able to grow on a wide range of mono-, poly- and heterocyclic aromatic hydrocarbons. Here, we report the complete functional annotation of the whole Novosphingobium genome. Results PP1Y genome analysis and its comparison with other Sphingomonadal genomes has yielded novel insights into the molecular basis of PP1Y’s phenotypic traits, such as its peculiar ability to encapsulate and degrade the aromatic fraction of fuel oils. In particular, we have identified and dissected several highly …
Natural hybrids fromSaccharomyces cerevisiae,Saccharomyces bayanusandSaccharomyces kudriavzeviiin wine fermentations
2006
Several wine isolates of Saccharomyces were analysed for six molecular markers, five nuclear and one mitochondrial, and new natural interspecific hybrids were identified. The molecular characterization of these Saccharomyces hybrids was performed based on the restriction analysis of five nuclear genes ( CAT8 , CYR1 , GSY1 , MET6 and OPY1 , located in different chromosomes), the ribosomal region encompassing the 5.8S rRNA gene and the two internal transcribed spacers, and sequence analysis of the mitochondrial gene COX2 . This method allowed us to identify and characterize new hybrids between Saccharomyces cerevisiae and Saccharomyces kudriavzevii , between S. cerevisiae and Saccharomyces ba…
Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants.
2006
The internal transcribed spacers (ITS) of the nuclear ribosomal 18S–5.8S–26S cistron continue to be the most popular non-plastid region for species-level phylogenetic studies of plant groups despite the early warnings about their potential Xaws, which may ultimately result in incorrect assumptions of orthology. It has been gradually realized that the alternative target regions in the nuclear genome (lowcopy nuclear genes, LCNG) are burdened with similar problems. The consequence is that, to date, developing useful LCNG for nonmodel organisms requires an investment in time and eVort that hinders its use as a real practical alternative for many labs. It is here argued that ITS sequences, desp…
Grape and environmental mycoflora monitoring in old, traditionally-cultivated vineyards on Mount Etna, southern Italy
2015
BACKGROUND: Grape contamination by several fungal species occurs during a vineyard's preharvest and harvest. Agronomic management and microclimatic conditions can affect fungi occurrence and epidemiology, thus explaining qualitative differences in mycoflora composition, including the presence of phytopathogenic or mycotoxigenic fungi. In this study a two-year grape, air and soil mycoflora monitoring programme was undertaken in vineyards on Mount Etna (eastern Sicily, Italy). The mycoflora composition was investigated at pea berry and veraison phenological phases from air and soil and at ripening from sample grapes. RESULTS: Mycoflora in air and soil varied according to the phenological stag…
Prima filogenesi del genere Nyctereutes (Canidae, Carnivora): conferme e implicazioni
2019
Il cane procione, Nyctereutes procyonoides (Gray, 1834), è un canide di piccola taglia originario dell’Asia orientale e Giappone, diffusosi anche in Europa centro-orientale in seguito a introduzioni. La tassonomia di questo canide e le sue affinità filogenetiche rispetto ad altri membri della stessa famiglia sono state una fonte di dibattito scientifico. Ad esempio, recenti analisi cromosomiche suggeriscono la possibilità di separare le popolazioni del Giappone da quelle del continente in una specie diversa, N. viverrinus. Inoltre, sebbene filogenesi morfologiche basate su campioni attuali indicavano possibili relazioni tra Nyctereutes ed alcuni canidi sudamericani, p.e. Cerdocyon Hamilton-…
A PHYLOGENY OF THE GENUS NYCTEREUTES TEMMINCK, 1838 (MAMMALIA: CARNIVORA: CANIDAE), INCLUDING A NEW SPECIES FROM ÇALTA (TURKEY)
2019
The phylogenetic relationships of the raccoon-dog, Nyctereutes procyonoides, were matter of debate in the last decades. Morphological phylogenies recognized some affinities between Nyctereutes and some South American canids, e.g. Cerdocyon, whereas more recent molecular studies support the inclusion of the raccoon-dog in the tribe Vulpini together with the genera Vulpes and Otocyon. The present study reports the first most-parsimonious analysis on extant and fossil species of Nyctereutes using a dataset of 115 ad hoc selected cranial, dentognatic, cerebral and postcranial characters, analyzed through the freeware software TNT v. 1.5. The resulting strict consensus tree (tested with bootstra…
Prevalence of tick-borne pathogens in ticks collected from migratory birds in Latvia.
2014
Migratory birds act as hosts and long-distance vectors for several tick-borne infectious agents. Here, feeding Ixodes ticks were collected from migratory birds during the autumn migration period in Latvia and screened for the presence of epidemiologically important non-viral pathogens. A total of 93 DNA samples of ticks (37 larvae and 56 nymphs) removed from 41 birds (order Passeriformes, 9 species) was tested for Lyme borreliosis spirochaetes, Anaplasma phagocytophilum, Rickettsia spp., and Babesia spp. Borrelia burgdorferi DNA was detected in 18% of the tick samples, and a majority of infected ticks were from thrush (Turdus spp.) birds. Among the infected ticks, Borrelia valaisiana was de…
Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes
2021
ABSTRACT The vertical structuring of methanotrophic communities and its genetic controllers remain understudied in the water columns of oxygen-stratified lakes. Therefore, we used 16S rRNA gene sequencing to study the vertical stratification patterns of methanotrophs in two boreal lakes, Lake Kuivajärvi and Lake Lovojärvi. Furthermore, metagenomic analyses were performed to assess the genomic characteristics of methanotrophs in Lovojärvi and the previously studied Lake Alinen Mustajärvi. The methanotroph communities were vertically structured along the oxygen gradient. Alphaproteobacterial methanotrophs preferred oxic water layers, while Methylococcales methanotrophs, consisting of putative…