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Rescooped by Jamilloux from Genomic Parasites: Coevolution between host and parasites
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BMC Genomics | Abstract | Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods

“ Insertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are important components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers.”
Via Gabriel Wallau
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Rescooped by Jamilloux from Genomic Parasites: Coevolution between host and parasites
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PLOS ONE: Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

PLOS ONE: Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes | Sequencing | Scoop.it
“ PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.”
Via Gabriel Wallau
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Rescooped by Jamilloux from Plant Breeding and Genomics News
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Arguments for standardizing transposable element annotation in plant genomes- PubMed - NCBI

AbstractWhole genome sequence assemblies have been generated for many plants. Annotation of transposable elements (TEs), which constitute the major proportion of genomes and play a significant role in epigenome alterations under stress, has not been given equal importance to that of genes. In this opinion article, we argue that the lack of focus dedicated to the fine-scale characterization of repeat fractions and the absence of consistent methods for their annotation impede our ability to critically understand the influence of TEs on the epigenome with implications in gene expression and non-Mendelian inheritance. Major structural changes occur over an evolutionary time scale. However, epigenetic regulation mediated by TEs can happen in a single generation, thus emphasizing the need for their standardized annotation.
Via Plant Breeding and Genomics News
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Transposable Elements, Epigenetics, and Genome Evolution

Transposable genetic elements (TEs) comprise a vast array of DNA sequences, all having the ability to move to new sites in genomes either directly by a cut-and-paste mechanism (transposons) or indirectly through an RNA intermediate (retrotransposons). First discovered in maize plants by the brilliant geneticist Barbara McClintock in the mid-1940s, they were initially considered something of a genetic oddity (1, 2). Several decades later, TEs acquired the anthropomorphic labels of “selfish” and “parasitic” because of their replicative autonomy and potential for genetic disruption (3, 4). However, TEs generally exist in eukaryotic genomes in a reversibly inactive, genetically undetectable form we now call “epigenetically silenced,” whose discovery can also be traced to McClintock's elegant genetic studies (5, 6). As the underlying biochemical mechanisms emerged from obscurity and epigenetics became popular toward the end of the 20th century, it was proposed that epigenetic silencing evolved to control the proliferation of TEs and their perceived destructive potential (5, 6).
Via Jean-Pierre Zryd
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Rescooped by Jamilloux from Plant Breeding and Genomics News
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Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity - Middleton - The Plant Journal - Wiley Online Library

Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity - Middleton - The Plant Journal - Wiley Online Library | Sequencing | Scoop.it
"A 454 sequencing snapshot was utilised to investigate the genome composition and nucleotide diversity of transposable elements for several Triticeae taxa, including T. aestivum, H. vulgare, H. spontaneum, S. cereale together with relatives of the A, B and D genome donors of wheat, T. urartu (A), Ae. speltoides (S), and Ae. tauschii (D). Additional A genome containing taxa T. monococcum and its wild relative T. boeoticum were also included. The main focus of the analysis was on the genomic composition of transposable elements (TEs) as these make up at least 80% of the overall genome content. Although more than 200 TE families were identified in each species, approximately 50% of the overall genome was comprised of 12-15 TE families."
Via Plant Breeding and Genomics News
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Rescooped by Jamilloux from Plant Breeding and Genomics News
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BMC Genomics | Abstract | Whole genome resequencing in tomato reveals variation associated with introgression and breeding events

One of the goals of genomics is to identify the genetic loci responsible for variation in phenotypic traits.
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