Search results for "Tree"
showing 10 items of 1841 documents
pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment
2007
Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the -ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pai…
Molecular phylogeny of parabasalids with emphasis on the order Cristamonadida and its complex morphological evolution
2009
1055-7903 doi: DOI: 10.1016/j.ympev.2009.03.011; Parabasalia represents a complex assemblage of species, which recently received extensive reorganization. The newly created order Cristamonadida unites complex hypermastigids belonging to the Lophomonadida like the joeniids, the multinucleate polymonad Calonymphidae, and well-developed trichomonads in the Devescovinidae. All these protists exclusively occur in the guts of termites and related insects. In this study, small subunit rRNA and glyceraldehyde-3-phosphate dehydrogenase genes were identified without cultivation from 14 species in Cristamonadida including previously unstudied genera such as Joenina, Joenia, Joenoides, Macrotrichomonas…
Phylogenetics of Anthyllis (Leguminosae: Papilionoideae: Loteae): Partial incongruence between nuclear and plastid markers, a long branch problem and…
2010
Abstract Phylogenetic relationships in the genus Anthyllis (Leguminosae: Papilionoideae: Loteae) were investigated using data from the nuclear ribosomal internal transcribed spacer regions (ITS) and three plastid regions (psbA–trnH intergenic spacer, petB–petD region and rps16 intron). Bayesian and maximum parsimony (MP) analysis of a concatenated plastid dataset recovered well-resolved trees that are topologically similar, with many clades supported by unique indels. MP and Bayesian analyses of the ITS sequence data recovered trees that have several well-supported topological differences, both among analyses, and to trees inferred from the plastid data. The most substantial of these concer…
Comparative phylogeography of the Veronica alpina complex in Europe and North America
2006
The Veronica alpina complex comprises eight species of alpine habitats over a wide range of mountain systems in the Northern Hemisphere. The occurrence of sympatric species in the European and North American mountain systems allowed us not only to investigate the effect of the ice ages on intraspecific phylogeographical patterns and genetic diversity in different continents of the Northern Hemisphere, but also to compare these patterns in closely related species. Plastid DNA trnL-F sequences and AFLP (amplified fragment length polymorphism) fingerprints were used to infer the phylogenetic history of the group and phylogeographical patterns within species. Hybrid origin of tetraploid eastern…
Local old olive landrace varieties in Israel—Valuable plant genetic resources in olive cultivation
2008
It is assumed that the cultivation of olive trees started in the East Mediterranean in the third millennia BCE. Throughout history and until recently, successful olive clones were maintained vegetatively and were grafted either on seedlings or on spheroblasts removed from the base of the trunk. It therefore can be hypothesized that local old olive trees, older than 500 years might represent an ancient gene pool. Modern terminology categorizes local genotypes into four main variety groups. However, in traditional terminology these were further differentiated into 27 cultivars according to their phenotypic traits. This genetic diversity, along with the fact that olive trees have been cultivat…
Genetic similarity among Tunisian cultivated olive estimated through SSR markers
2013
Olive (Olea europaea L. subsp. europaea var. europaea) is one of the oldest fruit tree in the Mediterranean basin, and is cultivated for oil and canned fruit. Part of this interest is driven by the economic importance of olive oil which is increasing throughout the world due to its beneficial effect to human health. In Tunisia, olive has great socio-economic importance, with more than 60 millions olive trees cultivated for olive oil production including a wide range of cultivars which are widely extended from the north to the south regions of the country for its high economic value. Here, we applied microsatellites (SSRs) molecular markers to assess the genetic variability of the most impor…
Insensitivity of Tree-Ring Growth to Temperature and Precipitation Sharpens the Puzzle of Enhanced Pre-Eruption NDVI on Mt. Etna (Italy)
2017
On Mt. Etna (Italy), an enhanced Normalized Difference in Vegetation Index (NDVI) signature was detected in the summers of 2001 and 2002 along a distinct line where, in November 2002, a flank eruption subsequently occurred. These observations suggest that pre-eruptive volcanic activity may have enhanced photosynthesis along the future eruptive fissure. If a direct relation between NDVI and future volcanic eruptions could be established, it would provide a straightforward and low-cost method for early detection of upcoming eruptions. However, it is unclear if, or to what extent, the observed enhancement of NDVI can be attributed to volcanic activity prior to the subsequent eruption. We conse…
A novel methodology for large-scale phylogeny partition
2011
Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. The method has been applied to identify transmission clusters of a phylogeny …
Genetic Variability and Phylogenetic Relationships within Trypanosoma cruzi I Isolated in Colombia Based on Miniexon Gene Sequences
2010
Phylogenetic studies ofTrypanosoma cruzihave identified the existence of two groups:T. cruziI andT. cruziII. There are aspects that still remain unknown about the genetic variability within theT. cruziI group. Given its epidemiological importance, it is necessary to have a better understanding ofT. cruzitransmission cycles. Our purpose was to corroborate the existence of haplotypes within theT. cruziI group and to describe the genetic variability and phylogenetic relationships, based on single nucleotide polymorphisms (SNPs) found in the miniexon gene intergenic region, for the isolates from different hosts and epidemiological transmission cycles in Colombian regions. 31T. cruziisolates wer…
Sequence analyses of S10-spcoperon among 16SrV group phytoplasmas: phylogenetic relationships and identification of discriminating single nucleotide …
2012
Phytoplasmas are cell-wall less, uncultivable bacteria, belonging to the class Mollicutes. They parasitise both plant hosts and insect vectors, but knowledge of their biological and molecular properties is limited. In particular, analyses of 16S rDNA nucleotide sequences revealed that 16SrV group phytoplasma strains identified in grapevine plants are closely related, but associated with distinct ecologies. In this work, we investigated the evolutionary relationships of eight representative 16SrV phytoplasma strains by sequencing 15 ribosomal protein (rp) genes positioned within the S10-spc operon. Phylogenetic analyses of concatenated nucleotide and amino acid sequences underscored that 16S…