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THE TEMPO AND MODE OF EVOLUTION OF TRANSPOSABLE ELEMENTS AS REVEALED BY MOLECULAR PHYLOGENIES RECONSTRUCTED FROM MOSQUITO GENOMES

STRUCHINER, Claudio J.; MASSAD, Eduardo; TU, Zhijian; RIBEIRO, Jose M. C.
Fonte: WILEY-BLACKWELL PUBLISHING, INC Publicador: WILEY-BLACKWELL PUBLISHING, INC
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
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Although many mathematical models exist predicting the dynamics of transposable elements (TEs), there is a lack of available empirical data to validate these models and inherent assumptions. Genomes can provide a snapshot of several TE families in a single organism, and these could have their demographics inferred by coalescent analysis, allowing for the testing of theories on TE amplification dynamics. Using the available genomes of the mosquitoes Aedes aegypti and Anopheles gambiae, we indicate that such an approach is feasible. Our analysis follows four steps: (1) mining the two mosquito genomes currently available in search of TE families; (2) fitting, to selected families found in (1), a phylogeny tree under the general time-reversible (GTR) nucleotide substitution model with an uncorrelated lognormal (UCLN) relaxed clock and a nonparametric demographic model; (3) fitting a nonparametric coalescent model to the tree generated in (2); and (4) fitting parametric models motivated by ecological theories to the curve generated in (3).; Intramural Research Program of the Division of Intramural Research; National Institute of Allergy and Infectious Diseases (NIAID/NIH); National Institutes of Health (NIH); Regents of the University of California; Foundation for the National Institutes of Health (NIH); Brazilian Research Council (CNPq); FAPESP; FAPERJ

Identificação e caracterização de elementos de transposição no genoma de Rhynchosciara; Identification e characterization of transposable elements in genome of Rhynchosciara

Teixeira, Paula Rezende
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 18/04/2007 PT
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56.59%
Os elementos de transposição são seqüências discretas que são capazes de mover- se de um lócus para outro, constituindo uma parte significante do genoma de eucariotos. São agrupados em duas classes principais, os elementos da Classe I, que se transpõem via um intermediário de RNA (retrotransposon), e os elementos da Classe II, que se transpõem via mecanismo de DNA do tipo corta e cola (transposon). A análise das seqüências de um banco de cDNA construído com RNA mensageiro da glândula salivar de Rhynchosciara americana mostrou a presença de representantes das duas classes de elementos. Nesse trabalho caracteriza-se quarto elementos de transposição tipo mariner, onde as seqüências consenso de nucleotídeos foram derivadas de múltiplas cópias defectivas contendo deleções, mudança no quadro de leitura e códons de terminação. Ramar1, um elemento full-length e Ramar2 um elemento defectivo que contém uma deleção na região interna da ORF da transposase, mas mantém e as extremidades intactas. Ramar3 e Ramar4 são elementos defectivos que apresentam muitas deleções no interior da ORF. As seqüências preditas das transposases demostraram que Ramar1 e Ramar2 estão filogeneticamente muito próximos dos elementos mariner da subfamília mauritiana. Enquanto...

Estudo da influência de elementos transponíveis nos genomas das algas C. reinhardtii e V. carteri; Influence of transposable elements in the genomes of C. reinhardtii and V. carteri algae

Philippsen, Gisele Strieder
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 28/03/2014 PT
Relevância na Pesquisa
66.43%
Elementos transponíveis (TEs) são sequências de DNA que possuem a capacidade de transposição no genoma hospedeiro. O principal objetivo deste trabalho reside na investigação em torno de possíveis contribuições de TEs nos genomas das algas C. reinhardtii e V. carteri, mais especificamente, na arquitetura dos genes ortólogos nestas espécies. Neste contexto, análises em sílico em larga escala foram realizadas, buscando-se identificar associações entre TEs e os genes ortólogos. Os resultados indicaram que os genes em C. reinhardtii tendem a acumular mais cópias de TEs em relação aos seus ortólogos em V. carteri. C. reinhardtii apresentou maior densidade de cópias de TEs para as regiões flanqueadora 5´ , flanqueadora 3´ e intrônica quando comparada a V. carteri; o inverso foi verificado quando analisada a densidade de TEs nas regiões codificantes. Análises para apurar a distribuição dos elementos em regiões intergênicas e intragênicas foram estabelecidas, nas quais a frequência observada dos elementos foi comparada à frequência esperada segundo a distribuição randômica de TEs no genoma, simulada computacionalmente. Foram constatadas regiões em que a presença dos elementos encontra-se significativamente abaixo do esperado...

Cytogenetic Mapping of the Retroelements Rex1, Rex3 and Rex6 among Cichlid Fish: New Insights on the Chromosomal Distribution of Transposable Elements

Valente, G. T.; Mazzuchelli, J.; Ferreira, I. A.; Poletto, A. B.; Fantinatti, B. E. A.; Martins, C.
Fonte: Karger Publicador: Karger
Tipo: Artigo de Revista Científica Formato: 34-42
ENG
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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); To enhance our understanding of the organization of the genome and chromosome evolution of cichlid fish species, we have isolated and physically mapped onto the chromosomes the transposable elements (TEs) Rex1, Rex3 and Rex6, which are conserved in teleost fish, in the chromosomes of African and South American cichlid species. The physical mapping of different Rex elements showed that they are primarily compartmentalized in the pericentromeric heterochromatic regions, although dispersed or clustered signals in euchromatic regions were also observed. The presence of TEs in heterochromatin can be correlated with their role in the structure and organization of heterochromatic areas (such as centromeres) or with the lower selective pressure that act on these gene-poor regions. The Rex elements were also concentrated in the largest chromosome pair of the Nile tilapia, Oreochromis niloticus. This chromosome pair is supposed to have originated by fusions, demonstrating the possible involvement of TEs with chromosome rearrangements. Besides general patterns of chromosomal distribution...

Transposable elements in Coffea (Gentianales : Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants

Lopes, Fabricio Ramon; Carazzolle, Marcelo Falsarella; Guimaraes Pereira, Goncalo Amarante; Colombo, Carlos Augusto; Aparecida Carareto, Claudia Marcia
Fonte: Springer Heidelberg Publicador: Springer Heidelberg
Tipo: Artigo de Revista Científica Formato: 385-401
ENG
Relevância na Pesquisa
56.44%
Transposable elements are major components of plant genomes and they influence their evolution, acting as recombination hot spots, acquiring specific cell functions or becoming part of protein-coding regions. The latter is the subject of the present analysis. This study is a report on the annotation of transposable elements (TEs) in expressed sequences of Coffea arabica, Coffea canephora and Coffea racemosa, showing the occurrence of 383 ESTs and 142 unigenes with TE fragments in these three Coffea species. Based on selected unigenes, it was possible to suggest 26 putative proteins with TE-cassette insertions, demonstrating a likely contribution to protein variability. The genes for two of those proteins, the fertility restorer (FR) and the pyrophosphate-dependent phosphofructokinase (PPi-PFKs) genes, were selected for evaluating the impact of TE-cassettes on host gene evolution of other plant genomes (Arabidopsis thaliana, Oryza sativa and populus trichocarpa). This survey allowed identifying a FR gene in O. sativa harboring multiple insertions of LTR retrotransposons that originated new exons, which however does not necessarily mean a case of molecular domestication. A possible transduction event of a fragment of the PPi-PFK beta-subunit gene mediated by Helitron ATREPX1 in Arabidopsis thaliana was also highlighted.

Ancestral polymorphism and recent invasion of transposable elements in Drosophila species

Dias, Elaine Silva; Aparecida Carareto, Claudia Marcia
Fonte: Biomed Central Ltd. Publicador: Biomed Central Ltd.
Tipo: Artigo de Revista Científica Formato: 12
ENG
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66.55%
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); Processo FAPESP: 10/10731-4; Processo FAPESP: 08/07629-3; Background: During the evolution of transposable elements, some processes, such as ancestral polymorphisms and horizontal transfer of sequences between species, can produce incongruences in phylogenies. We investigated the evolutionary history of the transposable elements Bari and 412 in the sequenced genomes of the Drosophila melanogaster group and in the sibling species D. melanogaster and D. simulans using traditional phylogenetic and network approaches.Results: Maximum likelihood (ML) phylogenetic analyses revealed incongruences and unresolved relationships for both the Bari and 412 elements. The DNA transposon Bari within the D. ananassae genome is more closely related to the element of the melanogaster complex than to the sequence in D. erecta, which is inconsistent with the species phylogeny. Divergence analysis and the comparison of the rate of synonymous substitutions per synonymous site of the Bari and host gene sequences explain the incongruence as an ancestral polymorphism that was inherited stochastically by the derived species. Unresolved relationships were observed in the ML phylogeny of both elements involving D. melanogaster...

Identification and frequency of transposable elements in Eucalyptus

Bacci Jr., Maurício; Soares, Rafael B.S.; Tajara, Eloiza; Ambar, Guilherme; Fischer, Carlos N.; Guilherme, Ivan R.; Costa, Eduardo P.; Miranda, Vitor F.O.
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Artigo de Revista Científica Formato: 634-639
ENG
Relevância na Pesquisa
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Transposable elements (TE) are major components of eukaryotic genomes and involved in cell regulation and organism evolution. We have analyzed 123,889 expressed sequence tags of the Eucalyptus Genome Project database and found 124 sequences representing 76 TE in 9 groups, of which copia, MuDR and FAR1 groups were the most abundant. The low amount of sequences of TE may reflect the high efficiency of repression of these elements, a process that is called TE silencing. Frequency of groups of TE in Eucalyptus libraries which were prepared with different tissues or physiologic conditions from seedlings or adult plants indicated that developing plants experience the expression of a much wider spectrum of TE groups than that seen in adult plants. These are preliminary results that identify the most relevant TE groups involved with Eucalyptus development, which is important for industrial wood production. Copyright by the Brazilian Society of Genetics.

Report of a chimeric origin of transposable elements in a bovine-coding gene

Almeida, L. M.; Amaral, M. E J; Silva, I. T.; Silva, W. A.; Riggs, P. K.; Carareto, C. M.
Fonte: Universidade Estadual Paulista Publicador: Universidade Estadual Paulista
Tipo: Artigo de Revista Científica Formato: 107-116
ENG
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Despite the wide distribution of transposable elements (TEs) in mammalian genomes, part of their evolutionary significance remains to be discovered. Today there is a substantial amount of evidence showing that TEs are involved in the generation of new exons in different species. In the present study, we searched 22,805 genes and reported the occurrence of TE-cassettes in coding sequences of 542 cow genes using the RepeatMasker program. Despite the significant number (542) of genes with TE insertions in exons only 14 (2.6%) of them were translated into protein, which we characterized as chimeric genes. From these chimeric genes, only the FAST kinase domains 3 (FASTKD3) gene, present on chromosome BTA 20, is a functional gene and showed evidence of the exaptation event. The genome sequence analysis showed that the last exon coding sequence of bovine FASTKD3 is ∼85% similar to the ART2A retrotransposon sequence. In addition, comparison among FASTKD3 proteins shows that the last exon is very divergent from those of Homo sapiens, Pan troglodytes and Canis familiares. We suggest that the gene structure of bovine FASTKD3 gene could have originated by several ectopic recombinations between TE copies. Additionally, the absence of TE sequences in all other species analyzed suggests that the TE insertion is clade-specific...

Chromosomal mapping of two Mariner-like elements in the grasshopper Abracris flavolineata (Orthoptera: Acrididae) reveals enrichment in euchromatin

Palacios-Gimenez, Octavio M.; Bueno, Danilo; Cabral-De-Melo, Diogo C.
Fonte: Czech Acad Sci, Inst Entomology Publicador: Czech Acad Sci, Inst Entomology
Tipo: Artigo de Revista Científica Formato: 329-334
ENG
Relevância na Pesquisa
56.34%
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); Processo FAPESP: 11/19481-3; Processo FAPESP: 12/01421-7; Processo FAPESP: 11/180283; The occurrence of transposable elements (TEs) is a ubiquitous characteristic of eukaryotic genomes, and these sequences are highly abundant in some species. Due to their large genomes, grasshoppers (Orthoptera) appear to be potentially good candidates in terms of having genomes that harbour considerable numbers of TEs. In the present study, we have investigated the occurrence of two Mariner-like elements (MLEs) within the genome of the grasshopper, Abracris flavolineata (De Geer, 1773), describing their distribution in both the A (i.e. standard or normal) complement and B chromosomes. PCR amplification followed by cloning and sequencing revealed two Mariner-like elements, which were named Afmar1 and Afmar2. Moreover, subsequent fluorescence in situ hybridization (FISH) assays indicated an abundance of these elements in the euchromatic regions of all the standard complement chromosomes and an absence of such sequences in heterochromatic regions. These sequences were also abundant in the euchromatic B chromosome: Afmar1 was distributed along the entire length of the chromosome...

Identification and frequency of transposable elements in Eucalyptus

Bacci Jr.,Maurício; Soares,Rafael B.S.; Tajara,Eloíza; Ambar,Guilherme; Fischer,Carlos N.; Guilherme,Ivan R.; Costa,Eduardo P.; Miranda,Vitor F.O.
Fonte: Sociedade Brasileira de Genética Publicador: Sociedade Brasileira de Genética
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/01/2005 EN
Relevância na Pesquisa
56.37%
Transposable elements (TE) are major components of eukaryotic genomes and involved in cell regulation and organism evolution. We have analyzed 123,889 expressed sequence tags of the Eucalyptus Genome Project database and found 124 sequences representing 76 TE in 9 groups, of which copia, MuDR and FAR1 groups were the most abundant. The low amount of sequences of TE may reflect the high efficiency of repression of these elements, a process that is called TE silencing. Frequency of groups of TE in Eucalyptus libraries which were prepared with different tissues or physiologic conditions from seedlings or adult plants indicated that developing plants experience the expression of a much wider spectrum of TE groups than that seen in adult plants. These are preliminary results that identify the most relevant TE groups involved with Eucalyptus development, which is important for industrial wood production.

The biology and potential for genetic research of transposable elements in filamentous fungi

Fávaro,Léia Cecilia de Lima; Araújo,Welington Luiz de; Azevedo,João Lúcio de; Paccola-Meirelles,Luzia Doretto
Fonte: Sociedade Brasileira de Genética Publicador: Sociedade Brasileira de Genética
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/12/2005 EN
Relevância na Pesquisa
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Recently many transposable elements have been identified and characterized in filamentous fungi, especially in species of agricultural, biotechnological and medical interest. Similar to the elements found in other eukaryotes, fungal transposons can be classified as class I elements (retrotransposons) that use RNA and reverse transcriptase and class II elements (DNA transposons) that use DNA. The changes (transposition and recombination) caused by transposons can supply wide-ranging genetic variation, especially for species that do not have a sexual phase. The application of transposable elements to gene isolation and population analysis is an important tool for molecular biology and studies of fungal evolution.

Transposable elements from the mesophragmatica group of Drosophila

Germanos,Erika; Mota,Nina R.; Loreto,Elgion L.S.
Fonte: Sociedade Brasileira de Genética Publicador: Sociedade Brasileira de Genética
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/01/2006 EN
Relevância na Pesquisa
66.46%
Transposable elements (TEs) are middle repetitive DNA sequences classified into families according to their sequence similarities, such elements can playing an important role in the evolutionary process of their host genomes. There are many reports on the distribution of TEs in the fruit fly genus Drosophila, although there is relatively little information relating to the Neotropical mesophragmatica group of Drosophila, probably the most typical cluster of species occurring almost exclusively in the Andes mountains. Dot Blot and PCR analyses was used to study the distribution of some TEs (I, mariner, hobo, gypsy, Tom/17.6, micropia and P elements) within the mesophragmatica group of Drosophila. We found gypsy elements in all the mesophragmatica group species studied and mariner elements were absent only from Drosophila pavani but P element homologous sequences were present only in D. pavani and Drosophila gasici and the other TEs (I, hobo, Tom/17.6, micropia) were not found in any of the species investigated.

Dramatic amplification of a rice transposable element during recent domestication

Naito, Ken; Cho, Eunyoung; Yang, Guojun; Campbell, Matthew A; Yano, Kentaro; Okumoto, Yutaka; Tanisaka, Takatoshi; Wessler, Susan R.
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
EN
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Despite the prevalence of transposable elements in the genomes of higher eukaryotes, what is virtually unknown is how they amplify to very high copy numbers without killing their host. Here, we report the discovery of rice strains where a miniature inverted-repeat transposable element (mPing) has amplified from ≈50 to ≈1,000 copies in four rice strains. We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented. Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors: (i) the rapid selection against detrimental insertions, (ii) the neutral or minimal effect of the remaining insertions on gene transcription, and (iii) the continued mobility of mPingelements in strains that already have >1,000 copies. The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice.

Abundance, distribution and potential impact of transposable elements in the genome of Mycosphaerella fijiensis.

SANTANA, M. F.; SILVA, J. C. F.; BATISTA, A. D.; RIBEIRO, L. E.; SILVA, G. F. da; ARAÚJO, E. F. de; QUEIROZ, M. V. de
Fonte: BMC Genomics, v. 13, Dec. 2012. Publicador: BMC Genomics, v. 13, Dec. 2012.
Tipo: Artigo em periódico indexado (ALICE)
EN
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Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated withtransposable elements (TEs). TEs are dispersed repetitive DNA sequences found in a host genome. These elements have the ability to move from one location to another within the genome, and their insertion can cause a wide spectrum of mutations in their hosts. Some of the deleterious effects of TEs may be due to ectopic recombination among TEs of the same family. In addition, some transposons are physically linked to genes and can control their expression. To prevent possible damage caused by the presence of TEs in the genome, some fungi possess TE-silencing mechanisms, such as RIP (Repeat Induced Point mutation). In this study, the abundance, distribution and potential impact of TEs in the genome of M. fijiensis were investigated.; 2012

A major invasion of transposable elements accounts for the large size of the Blumeria graminis f. sp. tritici genome

Parlange, F.; Oberhaensli, S.; Breen, J.; Platzer, M.; Taudien, S.; Šimková, H.; Wicker, T.; Doležel, J.; Keller, B.
Fonte: Springer Verlag Publicador: Springer Verlag
Tipo: Artigo de Revista Científica
Publicado em //2011 EN
Relevância na Pesquisa
66.47%
Powdery mildew of wheat (Triticum aestivum L.) is caused by the ascomycete fungus Blumeria graminis f.sp. tritici. Genomic approaches open new ways to study the biology of this obligate biotrophic pathogen. We started the analysis of the Bg tritici genome with the low-pass sequencing of its genome using the 454 technology and the construction of the first genomic bacterial artificial chromosome (BAC) library for this fungus. High-coverage contigs were assembled with the 454 reads. They allowed the characterization of 56 transposable elements and the establishment of the Blumeria repeat database. The BAC library contains 12,288 clones with an average insert size of 115 kb, which represents a maximum of 7.5-fold genome coverage. Sequencing of the BAC ends generated 12.6 Mb of random sequence representative of the genome. Analysis of BAC-end sequences revealed a massive invasion of transposable elements accounting for at least 85% of the genome. This explains the unusually large size of this genome which we estimate to be at least 174 Mb, based on a large-scale physical map constructed through the fingerprinting of the BAC library. Our study represents a crucial step in the perspective of the determination and study of the whole Bg tritici genome sequence.; Francis Parlange...

Identification and annotation of recombinant repeats in mammals indicates they are experimental products for creating novel transposable element families.

Lim, Sim Lin
Fonte: Universidade de Adelaide Publicador: Universidade de Adelaide
Tipo: Tese de Doutorado
Publicado em //2014
Relevância na Pesquisa
56.62%
About 40-50% of mammalian genomes are made up of repetitive elements, primarily transposable elements. Transposable elements' activities not only drive genome evolution, they contribute to the creation of novel recombinant repeats. Recombinant repeats have largely remained uncharacterized due to their complexity. Initially, I developed a pipeline for the genome wide identification of recombinant repeats in four different mammals: human, mouse, cow and horse. The pipeline identified 1,336,824 copies, but only 37,830 sequences were able to be clustered into 6,116 families. The majority of the recombinant repeats were simple recombinant repeat families and only a small proportion were complex recombinant repeat families. My analysis showed that recombinant repeat families only covered a small fraction of the genomes examined (0.30% in human, 0.13% in mouse, 0.217% in horse and 0.464% in cow), indicating most of the recombinant repeats were singletons. Further analysis has shown that both classes of RR were created via transposon-into-transposon events, indicating that novel transposable elements are likely to be created via this mechanism. I found that simple recombinant repeats were probably retrotranspositionally active because they contained polyA tails and target site duplications...

Mammalian genome evolution as a result of epigenetic regulation of transposable elements

Buckley, R.M.; Adelson, D.L.
Fonte: De Gruyter Publicador: De Gruyter
Tipo: Artigo de Revista Científica
Publicado em //2014 EN
Relevância na Pesquisa
66.37%
Transposable elements (TEs) make up a large proportion of mammalian genomes and are a strong evolutionary force capable of rewiring regulatory networks and causing genome rearrangements. Additionally, there are many eukaryotic epigenetic defense mechanisms able to transcriptionally silence TEs. Furthermore, small RNA molecules that target TE DNA sequences often mediate these epigenetic defense mechanisms. As a result, epigenetic marks associated with TE silencing can be reestablished after epigenetic reprogramming - an event during the mammalian life cycle that results in widespread loss of parental epigenetic marks. Furthermore, targeted epigenetic marks associated with TE silencing may have an impact on nearby gene expression. Therefore, TEs may have driven species evolution via their ability to heritably alter the epigenetic regulation of gene expression in mammals.; Reuben M. Buckley and David L. Adelson

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective

Kaminker, Joshua S.; Bergman, Casey M.; Kronmiller, Brent; Carlson, Joseph; Svirskas, Robert; Patel, Sandeep; Frise, Erwin; Wheeler, David A.; Lewis, Suzanna E.; Rubin, Gerald M.; Ashburner, Michael; Celniker, Susan E.
Fonte: Universidade de Cambridge Publicador: Universidade de Cambridge
Tipo: Article; Published Version
EN
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46.75%
RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.; Abstract Background Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project has provided precise sequence for the repetitive elements in the Drosophila euchromatin. We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species. Results We identified 85 known and eight novel families of transposable element varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence. More than two-thirds of the transposable elements are partial. The density of transposable elements increases an average of 4.7 times in the centromere-proximal regions of each of the major chromosome arms. We found that transposable elements are preferentially found outside genes; only 436 of 1...

Identification of novel non-autonomous CemaT transposable elements and evidence of their mobility within the C. elegans genome

Brownlie, Jeremy; Whyard, S
Fonte: Kluwer Academic Publishers Publicador: Kluwer Academic Publishers
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
66.44%
We describe here two new transposable elements, CemaT4 and CemaT5, that were identified within the sequenced genome of Caenorhabditis elegans using homology based searches. Five variants of CemaT4 were found, all non-autonomous and sharing 26 bp inverted

Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators

Shen Lin; Stefan Haas; Tomasz Zemojtel; Peng Xiao; Martin Vingron; Renhui Li
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Relevância na Pesquisa
46.7%
Background: Transposable elements are widely distributed in archaea, bacteria and eukarya domains. Considerable discrepancies of transposable elements in eukaryotes have been reported; however, the studies focusing on the diversity of transposable systems in prokaryotes were scarce. Understanding the transposable element system in cyanobacteria by the genome-wide analysis will greatly improve the knowledge of cyanobacterial diversity. Results: In this study, the transposable elements of seventeen cyanobacterial genomes were analyzed. The abundance of insertion sequence (IS) elements differs significantly among the cyanobacterial genomes examined. In particular, water bloom forming Microcystis aeruginosa NIES843 was shown to have the highest abundance of IS elements reaching 10.95% of the genome. IS family is a widely acceptable IS classification unit, and IS subfamily, based on probe sequences, was firstly proposed as the basic classification unit for IS element system. Both of IS family and IS subfamily were set as the two hierarchical units for evaluating the IS element system diversity. Totally, 1982 predicted IS elements, within 21 IS families and 133 subfamilies were identified in the examined cyanobacterial genomes. Families IS4...