Search results for "phylogeny"
showing 10 items of 1398 documents
Genome interdependence in insect-bacterium symbioses
2001
Symbioses between unicellular and multicellular organisms have contributed significantly to the evolution of life on Earth. As exemplified by several studies of bacterium-insect symbioses, modern genomic techniques are providing exciting new information about the molecular basis and the biological roles of these complex relationships, revealing for instance that symbionts have lost many genes for functions that are provided by the host, but that they can provide amino acids that the host cannot synthesize.
A novel putative insect chitinase with multiple catalytic domains: hormonal regulation during metamorphosis
2002
0264-6021 (Print) Journal Article Research Support, Non-U.S. Gov't; We have used differential display to identify genes that are regulated by juvenile hormone in the epidermis of the beetle Tenebrio molitor. One of the genes encodes T. molitor chitinase 5 (TmChit5), a chitinase possessing an unusual structure. Sequence analysis of TmChit5 identified five 'chitinase units' of approx. 480 amino acids with similarity to chitinase family 18. These units are separated by less conserved regions containing putative PEST (rich in proline, glutamic acid, serine and threonine) sequences, putative chitin-binding domains and mucin domains. Northern-blot analysis identified a single transcript of approx…
From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case.
2007
The increasing availability of complete genome sequences and the development of new, faster methods for phylogenetic reconstruction allow the exploration of the set of evolutionary trees for each gene in the genome of any species. This has led to the development of new phylogenomic methods. Here, we have compared different phylogenetic and phylogenomic methods in the analysis of the monophyletic origin of insect endosymbionts from the gamma-Proteobacteria, a hotly debated issue with several recent, conflicting reports. We have obtained the phylogenetic tree for each of the 579 identified protein-coding genes in the genome of the primary endosymbiont of carpenter ants, Blochmannia floridanus…
The respiratory proteins of insects
2007
For a long time, respiratory proteins have been considered unnecessary in most insects because the tracheal system was thought to be sufficient for oxygen supply. Only a few species that survive under hypoxic conditions were known exceptions. However, recently it has become evident that (1) intracellular hemoglobins belong to the standard repertoire of insects and (2) that hemocyanin is present in many "lower" insects. Intracellular hemoglobins have been identified in Drosophila, Anopheles, Apis and many other insects. In all investigated species, hemoglobin is mainly expressed in the fat body and the tracheal system. The major Drosophila hemoglobin binds oxygen with high affinity. This hem…
The Gypsy Database (GyDB) of mobile genetic elements.
2007
In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by t…
Structure and evolution of the leucine plasmids carried by the endosymbiont (Buchnera aphidicola) from aphids of the family Aphididae.
1998
In all examined species of the family Aphididae, the bacterial endosymbiont Buchnera aphidicola carries a plasmid encoding the genes leuABCD (involved in leucine biosynthesis) along with repA1, repA2 and ORF1. The gene organisation of the leucine plasmids was conserved, except in Buchnera isolated from Pterocomma populeum, where ORF1 was located in a different position. An inverted repeat (LIR1) located between repA2 and leuA is found in all of the Buchnera leucine plasmids examined. The predicted secondary structure of the LIR1 transcript conforms to a long hairpin loop, suggesting an involvement in transcription termination or messenger stability. Phylogenetic reconstruction based on repA…
Phylogenetic affinities of the Italian population of Eastern Montpellier snake, Malpolon insignitus (Serpentes: Lamprophiidae)
2022
The only Italian population of the Eastern Montpellier snake is found on Lampedusa, a small island in the Strait of Sicily, Mediterranean Sea. This population is currently attributed to Malpolon insignitus based only on morphology. Here, we present the first genetic data on this population, based on mitochondrial cytochrome b and 12S ribosomal RNA data. Our results confirm that the population on Lampedusa belongs to M. insignitus, falling within a clade that also includes Tunisian populations, and presents private haplotypes for both markers. Their slight differentiation from the Tunisian populations suggests an origin linked to natural expansion from Africa, during the latest glaciation ev…
18S rRNA gene sequences and phylogenetic relationships of European hard-tick species (Acari: Ixodidae)
1998
The complete 18S rRNA gene sequences of the following six European hard-tick species were obtained by direct PCR cycle sequencing and silver-staining methods: Rhipicephalus pusillus, Boophilus annulatus, Dermacentor marginatus, Hyalomma lusitanicum, Haemaphysalis punctata, and Ixodes ricinus. Differences observed in the sequence alignment of these six species together with the 18S rRNA gene sequences of 13 other hard-tick species demonstrate that this gene is a good marker for supraspecific differentiation as well as genus grouping among hard ticks. Phylogenetic analyses strongly support that Hyalomma species share a common ancestor with Rhipicephalinae and, consequently, Hyalomminae should…
Proteomic Analyses Reveal an Acidic Prime Side Specificity for the Astacin Metalloprotease Family Reflected by Physiological Substrates
2011
Astacins are secreted and membrane-bound metalloproteases with clear associations to many important pathological and physiological processes. Yet with only a few substrates described their biological roles are enigmatic. Moreover, the lack of knowledge of astacin cleavage site specificities hampers assay and drug development. Using PICS (proteomic identification of protease cleavage site specificity) and TAILS (terminal amine isotopic labeling of substrates) degradomics approaches >3000 cleavage sites were proteomically identified for five different astacins. Such broad coverage enables family-wide determination of specificities N- and C-terminal to the scissile peptide bond. Remarkably, me…
Phylogeny and prevalence of kobuviruses in dogs and cats in the UK
2013
AbstractThe kobuviruses represent an emerging genus in the Picornaviridae. Here we have used next generation sequencing and conventional approaches to identify the first canine kobuvirus (CaKoV) from outside the USA. Phylogenetic analysis suggests that a single lineage genotype of CaKoV now exists in Europe and the USA with 94% nucleotide similarity in the coding region. CaKoV was only identified in a single case from a case–control study of canine diarrhoea, suggesting this virus was not a frequent cause of disease in this population. Attempts to grow CaKoV in cell culture failed. Sequence analysis suggested CaKoV was distinct from human Aichi virus (AiV), and unlikely to pose a significan…