Search results for "phylogeny"

Effects of cadmium exposure on sea urchin development assessed by SSH and RT-qPCR: metallothionein genes and their differential induction

2012

In order to study the defense strategies activated by Paracentrotus lividus embryos in response to sub-lethal doses of CdCl2, we compared the induced transcripts to that of control embryos by suppression subtractive hybridization technique. We isolated five metallothionein (MT) cDNAs and other genes related to detoxification, to signaling pathway components, to oxidative, reductive and conjugative biotransformation, to RNA maturation and protein synthesis. RT-qPCR analysis revealed that two of the five P. lividus MT (PlMT7 and PlMT8) genes appeared to be constitutively expressed and upregulated following cadmium treatment, whereas the other three genes (PlMT4, PlMT5, PlMT6) are specifically…

Lactobacillus bobalius sp. nov., a lactic acid bacterium isolated from Spanish Bobal grape must

2008

A Lactobacillus strain, designated 203(T), previously isolated from Bobal grape must was characterized phylogenetically, genotypically and phenotypically in order to establish whether it represents a novel species. On the basis of the 16S rRNA gene sequence, strain 203(T) was shown to belong to the genus Lactobacillus, falling within the Lactobacillus alimentarius-Lactobacillus farciminis group and being closely related to the type strains of L. alimentarius, Lactobacillus kimchii and Lactobacillus paralimentarius. DNA-DNA hybridization results confirmed the separate status of strain 203(T) at the species level. To establish the similarities and differences between 203(T) and the three afor…

A Na+-coupled C4-dicarboxylate transporter (Asuc_0304) and aerobic growth of Actinobacillus succinogenes on C4-dicarboxylates

2014

Actinobacillus succinogenes, which is known to produce large amounts of succinate during fermentation of hexoses, was able to grow on C4-dicarboxylates such as fumarate under aerobic and anaerobic conditions. Anaerobic growth on fumarate was stimulated by glycerol and the major product was succinate, indicating the involvement of fumarate respiration similar to succinate production from glucose. The aerobic growth on C4-dicarboxylates and the transport proteins involved were studied. Fumarate was oxidized to acetate. The genome of A. succinogenes encodes six proteins with similarity to secondary C4-dicarboxylate transporters, including transporters of the Dcu (C4-dicarboxylate uptake), Dcu…

Ribosomal DNA 18S-28S sequence Probe Mapping on Primate Genome: evolutionary insights

2017

Redescription and phylogenetic analysis of the type species of the genus Panagrellus Thorne, 1938 (Rhabditida, Panagrolaimidae), P. pycnus Thorne, 19…

2021

Abstract The identity of Panagrellus pycnus, the type species of the genus Panagrellus, is discussed after studying specimens from a cultured population collected in Italy that fits the original material of the species. A new characterization is consequently provided as follows: body 0.93–1.32 mm long, lip region continuous with the adjoining body, stoma with gymnostom very reduced, pharynx with not swollen metacorpus, neck 161–203 µm long, excretory pore at level of the metacorpus, post-vulval uterine sac 99–162 µm long or 2.6–3.8 times as long as the body diameter divided in a short tubular proximal part and a long swollen distal part, vulva post-equatorial (V = 63–69), female tail conica…

Differential Greek and northern African migrations to Sicily are supported by genetic evidence from the Y chromosome

2009

The presence or absence of genetic heterogeneity in Sicily has long been debated. Through the analysis of the variation of Y-chromosome lineages, using the combination of haplogroups and short tandem repeats from several areas of Sicily, we show that traces of genetic flows occurred in the island, due to ancient Greek colonization and to northern African contributions, are still visible on the basis of the distribution of some lineages. The genetic contribution of Greek chromosomes to the Sicilian gene pool is estimated to be about 37% whereas the contribution of North African populations is estimated to be around 6%. In particular, the presence of a modal haplotype coming from the southern…

Reconstructing the ancestor of Mycobacterium leprae: The dynamics of gene loss and genome reduction

2007

We have reconstructed the gene content and order of the last common ancestor of the human pathogens Mycobacterium leprae and Mycobacterium tuberculosis. During the reductive evolution of M. leprae, 1537 of 2977 ancestral genes were lost, among which we found 177 previously unnoticed pseudogenes. We find evidence that a massive gene inactivation took place very recently in the M. leprae lineage, leading to the loss of hundreds of ancestral genes. A large proportion of their nucleotide content (∼89%) still remains in the genome, which allowed us to characterize and date them. The age of the pseudogenes was computed using a new methodology based on the rates and patterns of substitution in the…

Evolution of arginine deiminase (ADI) pathway genes

2002

We have analyzed the evolution of the three genes encoding structural enzymes of the arginine deiminase (ADI) pathway, arginine deiminase (ADI), ornithine transcarbamoylase (OTC), and carbamate kinase (CK) in a wide range of organisms, including Archaea, Bacteria, and Eukarya. This catabolic route was probably present in the last common ancestor to all the domains of life. The results obtained indicate that these genes have undergone a complex evolutionary history, including horizontal transfer events, duplications, and losses. Therefore, these genes are not adequate to infer organismal relationships at deep branching levels, but they provide an insight into how catabolic genes evolved and …

Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability

2015

Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aega…

Multiple overseas dispersal in amphibians

2003

Amphibians are thought to be unable to disperse over ocean barriers because they do not tolerate the osmotic stress of salt water. Their distribution patterns have therefore generally been explained by vicariance biogeography. Here, we present compelling evidence for overseas dispersal of frogs in the Indian Ocean region based on the discovery of two endemic species on Mayotte. This island belongs to the Comoro archipelago, which is entirely volcanic and surrounded by sea depths of more than 3500 m. This constitutes the first observation of endemic amphibians on oceanic islands that did not have any past physical contact to other land masses. The two species of frogs had previously been tho…