Characterization of a single clonal lineage of Fusarium oxysporum f. sp. albedinis causing Bayoud disease of date palm in Morocco

Bayoud, the #Fusarium wilt of date palm, was first detectd in southern Morocco (Draa Valley), after which it spread to most of the Moroccan pal groves. To assess whether the epidemic results from the spread of a single virulent clone, 42 isolats of #Fusarium oxysporum f. sp. #albedinis were collected from several cultivars of wilted palms at different locations in Morocco ; two isolates were included from Algeria, where the disease also occurs. The isolates were tested for vegetative compatibility group (VCG), restriction fragment length polymorphism (RFLP), and random amplified polymorphic DNA (RAPD). No polymorphism was observed either in RFLP studies on mitochondrial DNA or in RAPD analysis, and all strains belonged to a single VCG (0170). Sequences homologous to the DNA transposable element Fot1 were found in the genome of the #F. oxysporum f. sp. #albedinis$strains. Repetitive DNA patterns were produced when EcoRI-digested DNA of the isolates was probed with Fot1 ; 23 distinct hybridization patterns were established among the 44 isolates. Of these patterns, 4 accounted for more than 50$ f. sp. #albedinis strains at a genetic distance of 0.11. Such close genetic relationships between the isolates provides evidence that Moroccan #F. oxysporum f. sp. #albedinis$ populations may belong to a single clonal lineage that originated in Moroccan palm groves and eventually reached the Algerian oases. (Résumé d'auteur

Expression of DNA transposable elements during nervous system development: A discussion about its possible functions

Transposable elements (retrotransposons and DNA transposons) comprise a large proportion of animal genomes, for example 20% in D. melanogaster, 36% in X. tropicalis and 45% in humans. After invading a new genome, the transposable element increases its copy number and subsequently accumulates mutations. These may eventually result in inactive copies. Until recent days transposons have been considered “junk” DNA and no clear function have been assigned for this important amount of information on genomes

Are the Available DNA Sequence Alignments and Search Tools Reliable for Alu Research?

The results of most bioinformatics and microbiology research studies that use SINEs depend entirely on the mechanism used to detect and count these element instances in the genome. Hence, the reliability and accuracy of the DNA sequence alignment and search tool is vital for genetic researches. This research report presents the findings from testing the reliability of some popular DNA Sequence alignment and search (SA&S) tools using a test/known genomic sequence. The findings reveal the need for novel tool design

Recent translational research: Oncogene discovery by insertional mutagenesis gets a new boost

Knowledge of the genes and genetic pathways involved in onco-genesis is essential if we are to identify novel targets for cancer therapy. Insertional mutagenesis in mouse models is among the most efficient tools to detect novel cancer genes. Retrovirus-mediated insertional mutagenesis received a tremendous boost by the availability of the mouse genome sequence and new PCR methods. Application of such advances were limited to lympho-magenesis but are now also being applied to mammary tumourigenesis. Novel transposons that allow insertional muta-genesis studies to be conducted in tumors of any mouse tissue may give cancer gene discovery a further boost

Functional divergence of the rapidly evolving miR-513 subfamily in primates

BACKGROUND: The miR-513 subfamily belongs to an X-linked primate-specific miR506-514 cluster. Across primate species, there have been several duplication events and different species each possess a variety of miR-513 copies, indicating it underwent rapid evolution. Evidence suggests that this subfamily is preferentially expressed in the testis, but otherwise, to date, the evolutionary history and functional significance of this miRNA subfamily has remained largely unexplored. RESULTS: We analyzed the evolutionary pattern of gene duplications and their functional consequence for the miR-513 subfamily in primates. Sequence comparisons showed that the duplicated copies of miR-513 were derived from transposable element (MER91C). Moreover, duplication events of the miR-513 subfamily seem to have occurred independently in Platyrrhini (New World monkeys) and Catarrhini (Old World monkeys, apes and humans) after they diverged. Different copies of the miR-513 subfamily (miR-513a/b/c) have different seed sequences, due to after-duplication sequence divergences, which eventually led to functional divergences. The results of functional assays indicated that miR-513b could inhibit the expression of its target gene, the down-regulator of transcription 1 (DR1) at both the mRNA and protein levels. In the developing testis of rhesus macaques, we observed a temporal coupling of expression levels between miR-513b and DR1, suggesting that miR-513b could affect male sexual maturation by negatively regulating the development-stage related functioning of DR1. CONCLUSIONS: The miR-513 subfamily underwent multiple independent gene duplications among five different lineages of primates. The after-duplication sequence divergences among the different copies of miR-513 led to functional divergence of these copies in primates

Transposon-mediated BAC transgenesis in zebrafish and mice

<p>Abstract</p> <p>Background</p> <p>Bacterial artificial chromosomes (BACs) are among the most widely used tools for studies of gene regulation and function in model vertebrates, yet methods for predictable delivery of BAC transgenes to the genome are currently limited. This is because BAC transgenes are usually microinjected as naked DNA into fertilized eggs and are known to integrate as multi-copy concatamers in the genome. Although conventional methods for BAC transgenesis have been very fruitful, complementary methods for generating single copy BAC integrations would be desirable for many applications.</p> <p>Results</p> <p>We took advantage of the precise cut-and-paste behavior of a natural transposon, <it>Tol2</it>, to develop a new method for BAC transgenesis. In this new method, the minimal sequences of the <it>Tol2 </it>transposon were used to deliver precisely single copies of a ~70 kb BAC transgene to the zebrafish and mouse genomes. We mapped the BAC insertion sites in the genome by standard PCR methods and confirmed transposase-mediated integrations.</p> <p>Conclusion</p> <p>The <it>Tol2 </it>transposon has a surprisingly large cargo capacity that can be harnessed for BAC transgenesis. The precise delivery of single-copy BAC transgenes by <it>Tol2 </it>represents a useful complement to conventional BAC transgenesis, and could aid greatly in the production of transgenic fish and mice for genomics projects, especially those in which single-copy integrations are desired.</p

Dynamics of transposable elements generates structure and symmetries in genetic sequences

Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a common origin for both features. However, the mechanism leading to this relationship is unknown. Here we investigate a biologically motivated dynamics for the evolution of genetic sequences. We show that a metastable (long-lived) regime emerges in which sequences have symmetry and structure interlaced in a way that matches that of extant genomes.Comment: 6 pagesm 4 figure