Search results for "phylogeny"

Outbreak of sapovirus infection among infants and children with acute gastroenteritis in Osaka City, Japan during 2004–2005

2006

One hundred and twenty five fecal specimens were collected from sporadic cases of acute gastroenteritis in a pediatric clinic in Osaka City, Japan from July 2004 to June 2005 and tested for the presence of rotavirus, norovirus, sapovirus, astrovirus, and adenovirus by RT-multiplex PCR. Among diarrheal viruses detected, norovirus was the most prevalent (19.2%, 24 of 125), followed by group A rotavirus (18.4%, 23 of 125), astrovirus (1.6%, 2 of 125), and adenovirus (0.8%, 1 of 125), respectively. Interestingly, sapovirus infection was identified with high incidence of 17.6% (22 of 125). Sapovirus was subjected to molecular genetic analysis by sequencing. It was found that sapovirus detected i…

Prevalence and genetic diversity of Aichi virus strains in stool samples from community and hospitalized patients.

2008

ABSTRACT Aichi virus has been proposed as a causative agent of gastroenteritis. A total of 457 stool specimens from children hospitalized with acute diarrhea and 566 stool specimens from adults and children involved in 110 gastroenteritis outbreaks were screened for the presence of Aichi virus by reverse transcription-PCR (RT-PCR) amplification of the genomic region of the 3C and 3D (3CD) nonstructural proteins. Our results show a low incidence of Aichi virus in pediatric samples and the existence of mixed infections with other microbiological agents in some cases. From the outbreak survey, it appears that the presence of Aichi virus is an indicator of mixed infections causing gastroenterit…

Phylogeny of the autumn-flowering species of A. sect. Codonoprasum from the Mediterranean region.

2009

Mycotoxin Profile and Phylogeny of Pathogenic Alternaria Species Isolated from Symptomatic Tomato Plants in Lebanon

2021

The tomato is one of the most consumed agri-food products in Lebanon. Several fungal pathogens, including Alternaria species, can infect tomato plants during the whole growing cycle. Alternaria infections cause severe production and economic losses in field and during storage. In addition, Alternaria species represent a serious toxicological risk since they are able to produce a wide range of mycotoxins, associated with different toxic activities on human and animal health. Several Alternaria species were detected on tomatoes, among which the most important are A. solani, A. alternata, and A. arborescens. A set of 49 Alternaria strains isolated from leaves and stems of diseased tomato plant…

Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l.

2019

AbstractGene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-base…

Evolutionary History and Functional Characterization of the Amphibian Xenosensor CAR

2011

AbstractThe xenosensing constitutive androstane receptor (CAR) is widely considered to have arisen in early mammals via duplication of the pregnane X receptor (PXR). We report that CAR emerged together with PXR and the vitamin D receptor from an ancestral NR1I gene already in early vertebrates, as a result of whole-genome duplications. CAR genes were subsequently lost from the fish lineage, but they are conserved in all taxa of land vertebrates. This contrasts with PXR, which is found in most fish species, whereas it is lost from Sauropsida (reptiles and birds) and plays a role unrelated to xenosensing in Xenopus. This role is fulfilled in Xenopus by CAR, which exhibits low basal activity a…

Microcrinoids from the lower and middle Albian of the Anglo-Paris Basin (southern England, UK, Seine Maritime, Pas de Calais and Aube, France).

2021

16 pages; International audience; Microcrinoids of the family Roveacrinidae Peck, 1943 are described from lower and middle Albian clays of the Anglo-Paris Basin (Seine Maritime, Pas de Calais and Aube, France; Kent and Bedfordshire, UK). They are referred to two subfamilies - the Orthogonocrininae Gale, 2019 and the Plotocrininae Gale, 2020. Orthogonocrinines include the long-ranging (middle Albian-lower Cenomanian) species Orthogonocrinus apertus Peck, 1943, and Styracocrinus peracutus (Peck, 1955), known from Texas, USA, Morocco, the UK and France, and two stratigraphically successive species of the genus Hyalocrinus, H. magniezii Destombes, 1984 and H. bulliensis Destombes, 1984, known o…

Ancestral Reconstruction and Investigations of Genomic Recombination on some Pentapetalae Chloroplasts

2019

Abstract In this article, we propose a semi-automated method to rebuild genome ancestors of chloroplasts by taking into account gene duplication. Two methods have been used in order to achieve this work: a naked eye investigation using homemade scripts, whose results are considered as a basis of knowledge, and a dynamic programming based approach similar to Needleman-Wunsch. The latter fundamentally uses the Gestalt pattern matching method of sequence matcher to evaluate the occurrences probability of each gene in the last common ancestor of two given genomes. The two approaches have been applied on chloroplastic genomes from Apiales, Asterales, and Fabids orders, the latter belonging to Pe…

Transcriptome data reveal syndermatan relationships and suggest the evolution of endoparasitism in acanthocephala via an epizoic stage

2014

The taxon Syndermata comprises the biologically interesting wheel animals ("Rotifera": Bdelloidea + Monogononta + Seisonidea) and thorny-headed worms (Acanthocephala), and is central for testing superordinate phylogenetic hypotheses (Platyzoa, Gnathifera) in the metazoan tree of life. Recent analyses of syndermatan phylogeny suggested paraphyly of Eurotatoria (free-living bdelloids and monogononts) with respect to endoparasitic acanthocephalans. Data of epizoic seisonids, however, were absent, which may have affected the branching order within the syndermatan clade. Moreover, the position of Seisonidea within Syndermata should help in understanding the evolution of acanthocephalan endoparas…

Contribution of sponge genes to unravel the genome of the hypothetical ancestor of Metazoa (Urmetazoa)

2001

Recently the term Urmetazoa, as the hypothetical metazoan ancestor, was introduced to highlight the finding that all metazoan phyla including the Porifera (sponges) are derived from one common ancestor. Sponges as the evolutionarily oldest, still extant phylum, are provided with a complex network of structural and functional molecules. Analyses of sponge genomes from Demospongiae (Suberites domuncula and Geodia cydonium), Calcarea (Sycon raphanus) and Hexactinellida (Aphrocallistes vastus) have contributed also to the reconstruction of the evolutionary position of Metazoa with respect to Fungi. Furthermore, these analyses have provided evidence that the characteristic evolutionary novelties…