Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups

Although the retrotransposon copia has been studied in the melanogaster group of Drosophila species, very little is known about copia dynamism and evolution in other groups. We analyzed the occurrence and heterogeneity of the copia 5'LTR-ULR partial sequence and their phylogenetic relationships in 24 species of the repleta group of Drosophila. PCR showed that copia occurs in 18 out of the 24 species evaluated. Sequencing was possible in only eight species. The sequences showed a low nucleotide diversity, which suggests selective constraints maintaining this regulatory region over evolutionary time. On the contrary, the low nucleotide divergence and the phylogenetic relationships between the D. willistoni/Zaprionus tuberculatus/melanogaster species subgroup suggest horizontal transfer. Sixteen transcription factor binding sites were identified in the LTR-ULR repleta and melanogaster consensus sequences. However, these motifs are not homologous, neither according to their position in the LTR-ULR sequences, nor according to their sequences. Taken together, the low motif homologies, the phylogenetic relationship and the great nucleotide divergence between the melanogaster and repleta copia sequences reinforce the hypothesis that there are two copia families

Identification of misexpressed genetic elements in hybrids between Drosophila-related species

International audienceCrosses between close species can lead to genomic disorders, often considered to be the cause of hybrid incompatibility, one of the initial steps in the speciation process. How these incompatibilities are established and what are their causes remain unclear. To understand the initiation of hybrid incompatibility, we performed reciprocal crosses between two species of Drosophila (D. mojavensis and D. arizonae) that diverged less than 1 Mya. We performed a genome-wide transcriptomic analysis on ovaries from parental lines and on hybrids from reciprocal crosses. Using an innovative procedure of co-assembling transcriptomes, we show that parental lines differ in the expression of their genes and transposable elements. Reciprocal hybrids presented specific gene categories and few transposable element families misexpressed relative to the parental lines. Because TEs are mainly silenced by piwi-interacting RNAs (piRNAs), we hypothesize that in hybrids the deregulation of specific TE families is due to the absence of such small RNAs. Small RNA sequencing confirmed our hypothesis and we therefore propose that TEs can indeed be major players of genome differentiation and be implicated in the first steps of genomic incompatibilities through small RNA regulation

Plasmodium vivax circumsporozoite genotypes: a limited variation or new subspecies with major biological consequences?

<p>Abstract</p> <p>Background</p> <p><it>Plasmodium vivax </it>circumsporozoite variants have been identified in several geographical areas. The real implication of the genetic variation in this region of the <it>P. vivax </it>genome has been questioned for a long time. Although previous studies have observed significant association between VK210 and the Duffy blood group, we present here that evidences of this variation are limited to the CSP central portion.</p> <p>Methods</p> <p>The phylogenetic analyses were accomplished starting from the amplification of conserved domains of <it>18 SSU RNAr </it>and <it>Cyt B</it>. The antibodies responses against the CSP peptides, MSP-1, AMA-1 and DBP were detected by ELISA, in plasma samples of individuals infected with two <it>P. vivax CS </it>genotypes: VK210 and <it>P. vivax</it>-like.</p> <p>Results</p> <p>These analyses of the two markers demonstrate high similarity among the <it>P. vivax CS </it>genotypes and surprisingly showed diversity equal to zero between VK210 and <it>P. vivax</it>-like, positioning these <it>CS </it>genotypes in the same clade. A high frequency IgG antibody against the N- and C-terminal regions of the <it>P. vivax </it>CSP was found as compared to the immune response to the R- and V- repetitive regions (<it>p </it>= 0.0005, Fisher's Exact test). This difference was more pronounced when the <it>P. vivax</it>-like variant was present in the infection (<it>p </it>= 0.003, Fisher's Exact test). A high frequency of antibody response against MSP-1 and AMA-1 peptides was observed for all <it>P. vivax CS </it>genotypes in comparison to the same frequency for DBP.</p> <p>Conclusions</p> <p>This results target that the differences among the <it>P. vivax CS </it>variants are restrict to the central repeated region of the protein, mostly nucleotide variation with important serological consequences.</p

Scenario of the spread of the invasive species Zaprionus indianus Gupta, 1970 (Diptera, Drosophilidae) in Brazil

Zaprionus indianus was first recorded in Brazil in 1999 and rapidly spread throughout the country. We have obtained data on esterase loci polymorphisms (Est2 and Est3), and analyzed them, using Landscape Shape Interpolation and the Monmonier Maximum Difference Algorithm to discover how regional invasion occurred. Hence, it was apparent that Z. indianus, after first arriving in São Paulo state, spread throughout the country, probably together with the transportation of commercial fruits by way of the two main Brazilian freeways, BR 153, to the south and the surrounding countryside, and the BR 116 along the coast and throughout the north-east

Genetic diversity of NS5A protein from hepatitis C virus genotype 3a and its relationship to therapy response

<p>Abstract</p> <p>Background</p> <p>The quasispecies nature of HCV may have important implications for viral persistence, pathogenicity and resistance to antiviral agents. The variability of one of the viral proteins, NS5A, is believed to be related to the response to IFN therapy, the standard treatment for infection. In this study we analyzed the quasispecies composition of NS5A protein in patients infected with HCV genotype 3a, before IFN therapy.</p> <p>Methods</p> <p>Viral RNA was isolated from samples of 12 patients: four sustained virological responders (SVR), four non-responders (NR), and four end-of-treatment responders (ETR). cDNA was synthesized, the NS5A region was amplified and the fragments obtained were cloned. Fifteen clones from each patient were sequenced with eight primers, generating 179 contigs.</p> <p>Results</p> <p>Higher values for substitution (either synonymous or non-synonymous) and for distance were found in the SVR group. However, the NR group showed relatively more non-synonymous mutations than the other groups, owing to the higher values of dN/dS in complete NS5A and most specific regions. Overall, NS5A protein is undergoing purifying selection, since all dN/dS ratios values are below 0.5.</p> <p>Conclusions</p> <p>Our study provides an overview of the genetic variability of complete NS5A protein in HCV genotype 3a.</p

Estimating genomic instability mediated by Alu retroelements in breast cancer

Alu-PCR is a relatively simple technique that can be used to investigate genomic instability in cancer. This technique allows identification of the loss, gain or amplification of gene sequences based on the analysis of segments between two Alu elements coupled with quantitative and qualitative analyses of the profiles obtained from tumor samples, surgical margins and blood. In this work, we used Alu-PCR to identify gene alterations in ten patients with invasive ductal breast cancer. Several deletions and insertions were identified, indicating genomic instability in the tumor and adjacent normal tissue. Although not associated with specific genes, the alterations, which involved chromosomal bands 1p36.23, 1q41, 11q14.3, 13q14.2, occurred in areas of well-known genomic instability in breast and other types of cancer. These results indicate the potential usefulness of Alu-PCR in identifying altered gene sequences in breast cancer. However, caution is required in its application since the Alu primer can produce non-specific amplification

Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups

Although the retrotransposon copia has been studied in the melanogaster group of Drosophila species, very little is known about copia dynamism and evolution in other groups. We analyzed the occurrence and heterogeneity of the copia 5'LTR-ULR partial sequence and their phylogenetic relationships in 24 species of the repleta group of Drosophila. PCR showed that copia occurs in 18 out of the 24 species evaluated. Sequencing was possible in only eight species. The sequences showed a low nucleotide diversity, which suggests selective constraints maintaining this regulatory region over evolutionary time. On the contrary, the low nucleotide divergence and the phylogenetic relationships between the $D$. willistoni / Zaprionus tuberculatus / melanogaster species subgroup suggest horizontal transfer. Sixteen transcription factor binding sites were identified in the LTR-ULR repleta and melanogaster consensus sequences. However, these motifs are not homologous, neither according to their position in the LTR-ULR sequences, nor according to their sequences. Taken together, the low motif homologies, the phylogenetic relationship and the great nucleotide divergence between the melanogaster and repleta copia sequences reinforce the hypothesis that there are two copia families

Genomic regions harboring insecticide resistance-associated Cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling Drosophila species

International audienceIn the present study, an in silico analysis was performed to identify transposable element (TE) fragments inserted in Cyps with functions associated with resistance to insecticides and developmental regulation as well as in neighboring genes in two sibling species, Drosophila melanogaster and Drosophila simulans. The Cyps associated with insecticide resistance and their neighboring non-Cyp genes have accumulated a greater number of TE fragments than the other Cyps or a random sample of genes, predominantly in the 5'-flanking regions. Most of the insertions were due to DNA transposons, with DNAREP1 fragments being the most common. These fragments carry putative binding sites for transcription factors, which reinforces the hypothesis that DNAREP1 may influence gene regulation and play a role in the adaptation of the Drosophila species

Vertical inheritance and bursts of transposition have shaped the evolution of the BS non-LTR retrotransposon in Drosophila.

International audienceThe history of transposable elements over evolutionary time can often be partially reconstructed on the basis of genome analysis. In this study, we identified and extensively characterized the NLTR BS retrotransposon in 12 sequenced Drosophila genomes, by its sequence diversity within and among genomes, its degeneration pattern and its transcriptional activity. We show that the BS element has a variable copy number and patchy distribution within the Drosophila genus, that it is at distinct stages of the evolutionary cycle in the different Drosophila species and that its evolution is characterized by vertical transmission and by bursts of transposition in certain species