Search results for "Phylogenetic analysi"
showing 10 items of 56 documents
Molecular analysis suggests that recent Citrus tristeza virus outbreaks in Italy were originated by at least two independent introductions
2005
Citrus tristeza virus (CTV) is the causal agent of the most important virus disease of citrus. Numerous CTV isolates differing in biological and molecular characteristics have been reported worldwide. Recently, CTV was detected in Italy in several citrus crops from three separate areas: (1) Cassibile, province of Syracuse; (2) Massafra, province of Taranto; and (3) Belpasso, province of Catania. CTV isolates from Massafra and Cassibile were mild, whereas isolates from Belpasso induced severe symptoms. To study the genetic variation of CTV populations of these areas, 150 samples per area were examined by single strand conformation polymorphism (SSCP) and nucleotide sequence analysis of CTV g…
Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae.
2020
In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain in…
The migratory birds: novel ecological niche of fungal diversity?
2015
Francesca et al (2010) studied the ecology of wine yeasts associated to birds caught in vineyards. The same authors were able to prove that migratory birds might carry living pro-technological yeasts for about 12 hours from the ingestion of inoculated feed (Francesca et al 2012). In subsequent studies, they tried to demonstrate that microorganisms are not only transported for a short period by birds, but microorganisms might be adapted to the specific conditions (body temperature about 42 °C and low pH) of the intestinal tract of birds. Hence, it was demonstrated that the majority of isolates carried by birds are thermotolerant. The most interesting results were the isolation of two new spe…
One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.
2020
Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species…
Evolutionary morphology in shape and size of haptoral anchors in 14 Ligophorus spp. (Monogenea: Dactylogyridae).
2017
The search for phylogenetic signal in morphological traits using geometric morphometrics represents a powerful approach to estimate the relative weights of convergence and shared evolutionary history in shaping organismal form. We assessed phylogenetic signal in the form of ventral and dorsal haptoral anchors of 14 species of Ligophorus occurring on grey mullets (Osteichthyes: Mugilidae) from the Mediterranean, the Black Sea and the Sea of Azov. The phylogenetic relationships among these species were mapped onto the morphospaces of shape and size of dorsal and ventral anchors and two different tests were applied to establish whether the spatial positions in the morphospace were dictated by …
Evaluation of HIV transmission clusters among natives and foreigners living in Italy
2020
We aimed at evaluating the characteristics of HIV-1 molecular transmission clusters (MTCs) among natives and migrants living in Italy, diagnosed between 1998 and 2018. Phylogenetic analyses were performed on HIV-1 polymerase (pol) sequences to characterise subtypes and identify MTCs, divided into small (SMTCs, 2&ndash
The genomic history of the Aegean palatial civilizations
2021
Summary The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as e…
Genetic diversity and phylogenetic relationships among four breeds reared in Sicily using β-lactoglobulin promoter region polymorphisms
2011
The aim of this work was to analyze the genetic diversity and the phylogenetic relationships among the Valle del Belice (VDB) breed and the other sheep breeds considered as ancestors, using -lactoglobulin (BLG) promoter region polymorphisms. The BLG promoter region of 50 randomly chosen animals from the four breeds (VDB n=20; Comisana (COM) n=10; Pinzirita (PIN) n=10; Sarda (SAR) n=10) were sequenced and aligned, and results showed the presence of 36 single nucleotide polymorphisms (SNPs) and one deletion. The number of polymorphic sites identified showed high variability within breeds. Nucleotide (π) and haplotype (Hd) diversity were estimated with DnaSP software, whereas PHASE software w…
Application of molecular markers to investigate genetic diversity in Sicilian livestock
2014
La diversità genetica delle specie e razze di interesse zootecnico, rappresenta un’importante risorsa in tutti i sistemi di allevamento . Per lo studio della diversità genetica, nel corso dei decenni sono stati sviluppati diversi metodi che si basano su informazioni del pedigree o su dati molecolari (microsatelliti e SNPs, Single Nucleotide Polymorphisms). Con l’aumento della disponibilità di marcatori molecolari per la maggior parte delle specie di interesse zootecnico, e con lo sviluppo di sofisticate tecniche analitiche, sta crescendo la capacità di caratterizzare la variabilità genetica delle razze. Inoltre, ad oggi, poche sono le informazioni sulla diversità genetica delle razze e dell…
Topological congruence between phylogenies of Anacanthorus spp. (Monogenea: Dactylogyridae) and their Characiformes (Actinopterygii) hosts: A case of…
2017
Cophylogenetic studies aim at testing specific hypotheses to understand the nature of coevolving associations between sets of organisms, such as host and parasites. Monogeneans and their hosts provide and interesting platform for these studies due to their high host specificity. In this context, the objective of the present study was to establish whether the relationship between Anacanthorus spp. with their hosts from the upper Paraná River and its tributaries can be explained by means of cospeciation processes. Nine fish species and 14 monogenean species, most of them host specific, were studied. Partial DNA sequences of the genes RAG1, 16S and COI of the fish hosts and of the genes ITS2, …