Cyclophosphamide in Drosophila promotes genes and transposable elements differential expression and mitochondrial dysfunction

Cyclophosphamide (CPA) is an alkylating agent used for cancer chemotherapy, organ transplantation, and autoimmune disease treatment. Here, mRNA sequencing and high-resolution respirometry were performed to evaluate the alterations of Drosophila melanogaster gene expression fed with CPA under acute (0.1 mg/mL, for 24 h) and chronic (0.05 mg/mL, for 35 days) treatments. Differential expression analysis was performed using Cufflinks-Cuffdiff, DESeq2, and edgeR software. CPA affected genes are involved in several biological functions, including stress response and immune-related pathways, oxi-reduction and apoptotic processes, and cuticle and vitelline membrane formation. In particular, this is the first report of CPA-induced mitochondrial dysfunction caused by the downregulation of genes involved with mitochondria constituents. CPA treatment also changed the transcription pattern of transposable elements (TEs) from the gypsy and copia superfamilies. The results presented here provided evidence of CPA mitochondrial toxicity mechanisms and that CPA can modify TEs transcription in Drosophila flies

DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics.

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics

Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets

Unraveling the evolutionary scenario of the hobo element in populations of Drosophila melanogaster and D. simulans in South America using the TPE repeats as markers

Abstract Transposable elements (TEs) are nucleotide sequences found in most studied genomes. These elements are highly diversified and have a large variation in nucleotide structure and mechanisms of transposition. hobo is a member of class II, belonging to hAT superfamily, described inDrosophila melanogaster, and it presents in its Open Reading Frame, a repetitive region encoding the amino acids threonine-proline-glutamic acid (TPE), which shows variability in the number of repeats in some regions of the world. Due to this variability some evolutionary scenarios of the hobo element are discussed, such as the scenario of the invasion of hobo element in populations ofD. melanogaster. In the present study, we investigated 22 DNA sequences of D. melanogaster and seven sequences ofD. simulans, both from South America, to check the number of repetitions of TPE, in order to clarify the evolutionary scenario of thehobo element in these populations. Our results showed a monomorphism in populations of both species in South America, with only three TPE repeats. Hence, we discuss and propose an evolutionary scenario of the invasion of the hobo element in populations of D. melanogaster and D. simulans

Mar, a MITE family of hAT transposons in Drosophila

Submitted by Manoel Barata ([email protected]) on 2018-09-21T19:06:10Z No. of bitstreams: 1 MobileDNA8753-3-13.pdf: 1967837 bytes, checksum: 1303d81cceabd983a3a7c01b4044d3d2 (MD5)Approved for entry into archive by Manoel Barata ([email protected]) on 2018-09-24T18:06:09Z (GMT) No. of bitstreams: 1 MobileDNA8753-3-13.pdf: 1967837 bytes, checksum: 1303d81cceabd983a3a7c01b4044d3d2 (MD5)Made available in DSpace on 2018-09-24T18:06:10Z (GMT). No. of bitstreams: 1 MobileDNA8753-3-13.pdf: 1967837 bytes, checksum: 1303d81cceabd983a3a7c01b4044d3d2 (MD5) Previous issue date: 2012Universidade Federal do Rio Grande do Sul. Departamento de Genética. Programa de Pós-Graduação em Genética e Biologia Molecular. Porto Alegre, RS, Brasil / Universidade Federal do Rio Grande do Sul. Departamento de Zoologia. Programa de Pós-Graduação em Biologia Animal. Porto Alegre, RS, Brasil.Universidade Federal do Rio Grande do Sul. Departamento de Genética. Programa de Pós-Graduação em Genética e Biologia Molecular. Porto Alegre, RS, Brasil / Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil / Pontifícia Universidade Católica do Paraná. Curitiba, PR, Brasil.Universidade Federal do Rio Grande do Sul. Departamento de Genética. Programa de Pós-Graduação em Genética e Biologia Molecular. Porto Alegre, RS, Brasil / Universidade Federal do Rio Grande do Sul. Departamento de Zoologia. Programa de Pós-Graduação em Biologia Animal. Porto Alegre, RS, Brasil.Universidade Federal do Rio Grande do Sul. Departamento de Genética. Programa de Pós-Graduação em Genética e Biologia Molecular. Porto Alegre, RS, Brasil / Universidade Federal de Santa Maria. Departamento de Biologia. Santa Maria, RS, Brasil.Miniature inverted-repeat transposable elements (MITEs) are short, nonautonomous DNA elements flanked by subterminal or terminal inverted repeats (TIRs) with no coding capacity. MITEs were originally recognized as important components of plant genomes, where they can attain extremely high copy numbers, and are also found in several animal genomes, including mosquitoes, fish and humans. So far, few MITEs have been described in Drosophila. As results, here in we describe the distribution and evolution of Mar, a MITE family of hAT transposons, in Drosophilidae species. In silico searches and PCR screening showed that Mar distribution is restricted to the willistoni subgroup of the Drosophila species, and a phylogenetic analysis of Mar indicates that this element may have originated prior to the diversification of these species. Most of the Mar copies in D. willistoni present conserved target site duplications and TIRs, indicating recent mobilization of these sequences. We also identified relic copies of potentially full-length Mar transposon in D. tropicalis and D. willistoni. The phylogenetic relationship among transposases from the putative full-length Mar and other hAT superfamily elements revealed that Mar is placed into the recently determined Buster group of hAT transposons. We have as conclusion that on the basis of the obtained data, we can suggest that the origin of these Mar MITEs occurred before the subgroup willistoni speciation, which started about 5.7 Mya. The Mar relic transposase existence indicates that these MITEs originated by internal deletions and suggests that the full-length transposon was recently functional in D. willistoni, promoting Mar MITEs mobilization

Is the evolutionary history of the O-type P element in the saltans and willistoni groups of Drosophila similar to that of the canonical P element?

We studied the occurrence of O-type P elements in at least one species of each subgroup of the saltans group, in order to better understand the phylogenetic relationships among the elements within the saltans group and with those of species belonging to the willistoni group. We found that the O-type subfamily has a patchy distribution within the saltans group (it does not occur in D. neocordata and D. emarginata), low sequence divergence among species of the saltans group as well as in relation to species of the willistoni group, a lower rate of synonymous substitution for coding sequences compared to Adh, and phylogenetic incongruities. These findings suggest that the evolutionary history of the O-type subfamily within the saltans and willistoni groups follows the same model proposed for the canonical subfamily of P elements, i.e., events of horizontal transfer between species of the saltans and willistoni groups

Detection of P element transcripts in embryos of Drosophila melanogaster and D. willistoni

Submitted by Sandra Infurna ([email protected]) on 2018-12-20T13:30:51Z No. of bitstreams: 1 rafaelav_bruno_etal_IOC_2009.pdf: 1409373 bytes, checksum: 39eef486097d649fce38ed8d35c046a1 (MD5)Approved for entry into archive by Sandra Infurna ([email protected]) on 2018-12-20T13:42:15Z (GMT) No. of bitstreams: 1 rafaelav_bruno_etal_IOC_2009.pdf: 1409373 bytes, checksum: 39eef486097d649fce38ed8d35c046a1 (MD5)Made available in DSpace on 2018-12-20T13:42:15Z (GMT). No. of bitstreams: 1 rafaelav_bruno_etal_IOC_2009.pdf: 1409373 bytes, checksum: 39eef486097d649fce38ed8d35c046a1 (MD5) Previous issue date: 2009Universidade do Estado de Mato Grosso. Departamento de Ciências Biológicas. Tangará da Serra, MT, Brasil / Universidade Federal do Rio Grande do Sul. Instituto de Biociências. Departamento de Genética. Laboratório de Drosophila. Porto Alegre, RS, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Molecular de Instos. Rio de Janeiro, RJ. Brasil.Instituto Nacional de Câncer. Centro de Transplante de Medula Óssea. Rio de Janeiro, RJ, Brasil.Universidade Federal do Rio Grande do Sul. Instituto de Biociências. Departamento de Genética. Laboratório de Drosophila. Porto Alegre, RS, Brasil / Universidade Federal de Santa Maria. Centro de Ciências Naturais e Exatas. Departamento de Biologia. Santa Maria, RS, Brasil.Universidade Federal do Rio Grande do Sul. Instituto de Biociências. Departamento de Genética. Laboratório de Drosophila. Porto Alegre, RS, Brasil / Universidade Federal de Santa Maria. Centro de Ciências Naturais e Exatas. Departamento de Biologia. Santa Maria, RS, Brasil.The P element is one of the most thoroughly studied transposable elements (TE). Its mobilization causes the hybrid dysgenesis that was first described in Drosophila melanogaster. While studies of the P element have mainly been done in D. melanogaster, it is believed that Drosophila willistoni was the original host species of this TE and that P was transposed to the D. melanogaster genome by horizontal transfer. Our study sought to compare the transcriptional behavior of the P element in embryos of D. melanogaster, which is a recent host, with embryos of two strains of D. willistoni, a species that has contained the P element for a longer time. In both species, potential transcripts of transposase, the enzyme responsible for the TE mobilization, were detected, as were transcripts of the 66-kDa repressor, truncated and antisense sequences, which can have the ability to prevent TEs mobilization. The truncated transcripts reveal the truncated P elements present in the genome strains and whose number seems to be related to the invasion time of the genome by the TE. No qualitative differences in antisense transcripts were observed among the strains, even in the D. willistoni strain with the highest frequency of heterochromatic P elements