Search results for "Genome"
showing 10 items of 1913 documents
Differential annotation of tRNA genes with anticodon CAT in bacterial genomes.
2006
We have developed three strategies to discriminate among the three types of tRNA genes with anticodon CAT (tRNA(Ile), elongator tRNA(Met) and initiator tRNA(fMet)) in bacterial genomes. With these strategies, we have classified the tRNA genes from 234 bacterial and several organellar genomes. These sequences, in an aligned or unaligned format, may be used for the identification and annotation of tRNA (CAT) genes in other genomes. The first strategy is based on the position of the problem sequences in a phenogram (a tree-like network), the second on the minimum average number of differences against the tRNA sequences of the three types and the third on the search for the highest score value …
Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story
2006
Buchnera aphidicola, the primary endosymbiont of aphids, has undergone important genomic and biochemical changes as an adaptation to intracellular life. The most important structural changes include a drastic genome reduction and the amplification of genes encoding key enzymes for the biosynthesis of amino acids by their translocation to plasmids. Molecular characterization through different aphid subfamilies has revealed that the genes involved in leucine and tryptophan biosynthesis show a variable fate, since they can be located on plasmids or on the chromosome in different lineages. This versatility contrasts with the genomic stasis found in three distantly related B. aphidicola strains …
Genetics of hepatocellular carcinoma.
2007
The completely assembled human genome has made it possible for modern medicine to step into an era rich in genetic information and high-throughput genomic analysis. These novel and readily available genetic resources and analytical tools may be the key to unravel the molecular basis of hepatocellular carcinoma (HCC). Moreover, since an efficient treatment for this disease is lacking, further understanding of the genetic background of HCC will be crucial in order to develop new therapies aimed at selected targets. We report on the current status and recent developments in HCC genetics. Special emphasis is given to the genetics and regulation of major signalling pathways involved in HCC such …
The Minimal Gene-Set Machinery
2014
All known living beings are made of cells, each one of which stores in its genome all of the information required for its correct functioning. The advent of high-throughput sequencing technologies and improvements in bioinformatics tools have allowed the complete sequencing, functional analysis and comparison of thousands of genomes from different species, helping research groups to delineate the minimal set of functions necessary to keep a cell alive under defined environmental conditions. This knowledge can not only be used to obtain a better understanding of the phenomenon of life, but also has many direct biotechnological and biomedical implications. Keywords: minimal genome; orthologou…
Ty3/Gypsy Retrotransposons: Description of New Arabidopsis thaliana Elements and Evolutionary Perspectives Derived from Comparative Genomic Data
2000
We performed a comprehensive analysis of the evolution of the Ty3/GYPSY: group of long-terminal-repeat retrotransposons (also known as METAVIRIDAE:). Exhaustive database searches allowed us to detect novel elements of this group. In particular, the Arabidopsis thaliana and Drosophila melanogaster genome sequencing projects have recently disclosed a large number of new Ty3/GYPSY: sequences. So far, elements of three different Ty3/GYPSY: lineages had been described for A. thaliana. Here, we describe six new lineages, which we have called Tit-for-tat1, Tit-for-tat2, Gimli, Gloin, Legolas, and Little Athila. We confirm that plant Ty3/GYPSY: elements form two main monophyletic groups. Moreover, …
A single type of cadherin is involved inBacillus thuringiensistoxicity inPlutella xylostella
2015
Cadherins have been described as one the main functional receptors for the toxins of the entomopathogenic bacterium, Bacillus thuringiensis (Bt). With the availability of the whole genome of Plutella xylostella, different types of cadherins have been annotated. In this study we focused on determining those members of the cadherin-related proteins that potentially play a role in the mode of action of Bt toxins. For this, we mined the genome of P. xylostella to identify these putative cadherins. The genome screening revealed 52 genes that were annotated as cadherin or cadherin-like genes. Further analysis revealed that six of these putative cadherins had three motifs common to all Bt-related …
SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models
2015
The discovery of single nucleotide variants (SNVs) from next-generation sequencing (NGS) data typically works by aligning reads to a given genome and then creating an alignment map to interpret the presence of SNVs. Various approaches have been developed to call whether germline SNVs (or SNPs) in normal cells or somatic SNVs in cancer/tumor cells. Nonetheless, efficient callers for both germline and somatic SNVs have not yet been extensively investigated. In this paper, we present SNVSniffer, an integrated caller for germline and somatic SNVs from NGS data based on Bayesian probabilistic models. In SNVSniffer, our germline SNV calling models allele counts per site as a multinomial condition…
Tirant: A new retrotransposon-like element inDrosophila melanogaster
1996
In this paper we report a new retrotransposon-like element of Drosophila melanogaster called Tirant. This sequence is moderately repeated in the genome of this species and it has been found to be widely dispersed throughout its distribution area. From Southern blot and in situ analyses, this sequence appears to be mobile in D. melanogaster, since its chromosome location and the hybridization patterns vary among the different strains analyzed. In this way, partial sequencing of Tirant ends suggests that it is a retrotransposon, since it is flanked by two LTRs. The presence of sequences homologous to Tirant has been also investigated in 28 species of the genus Drosophila by means of Southern …
A genome-wide association study identifies Arabidopsis thaliana genes that contribute to differences in the outcome of infection with two Turnip mosa…
2021
Viruses lie in a continuum between generalism and specialism depending on their ability to infect more or less hosts. While generalists are able to successfully infect a wide variety of hosts, specialists are limited to one or a few. Even though generalists seem to gain an advantage due to their wide host range, they usually pay a pleiotropic fitness cost within each host. On the contrary, a specialist has maximal fitness within its own host. A relevant yet poorly explored question is whether viruses differ in the way they interact with their hosts’ gene expression depending on their degree of specialization. Using a genome-wide association study approach, we have identified host genes whos…
Sequences homologous to the hobo transposable element in E strains of Drosophila melanogaster.
2001
Hobo is one of the three Drosophila melanogaster transposable elements, together with the P and I elements, that seem to have recently invaded the genome of this species. Surveys of the presence of hobo in strains from different geographical and temporal origins have shown that recently collected strains contain complete and deleted elements with high sequence similarity (H strains), but old strains lack hobo elements (E strains). Besides the canonical hobo sequences, both H and E strains show other poorly known hobo-related sequences. In the present work, we analyze the presence, cytogenetic location, and structure of some of these sequences in E strains of D. melanogaster. By in situ hybr…