Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467

Genetic Information Research Institute, Mountain View, CA 94043, USA.
Cytogenetic and Genome Research (Impact Factor: 1.91). 02/2005; 110(1-4):462-7. DOI: 10.1159/000084979
Source: PubMed

ABSTRACT Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms. Currently, it contains over 3600 annotated sequences representing different families and subfamilies of repeats, many of which are unreported anywhere else. Each sequence is accompanied by a short description and references to the original contributors. Repbase Update includes Repbase Reports, an electronic journal publishing newly discovered transposable elements, and the Transposon Pub, a web-based browser of selected chromosomal maps of transposable elements. Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at

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Available from: Vladimir V Kapitonov, Aug 31, 2015
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    • "). Each cluster aligned was searched against Repbase (Jurka et al., 2005) using BLASTER (Quesneville et al., 2003) and HMMER (Johnson et al., 2010). A consensus feature was detected for each aligned cluster. "
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    ABSTRACT: The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga.
    eLife Sciences 07/2015; 4. · 8.52 Impact Factor
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    • "The second pass also included the EST-and protein-based evidence as described in the first pass. All runs of MAKER included the masking of repetitive regions using REPEATMASKER v4.0.3 (Smit et al. 1996–2010) against the REPBASE v19.07 (Jurka et al. 2005) library. For each gene prediction, we selected the evidence with an annotation edit distance (AED) < 0.75. "
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    ABSTRACT: The single-humped dromedary (Camelus dromedarius), is the most numerous and widespread of domestic camel species and is a significant source of meat, milk, wool, transportation, and sport for millions of people. Dromedaries are particularly well adapted to hot, desert conditions and harbor a variety of biological and physiological characteristics with evolutionary, economic, and medical importance. To understand the genetic basis of these traits, an extensive resource of genomic variation is required. In this study, we assembled at 65x coverage, a 2.06 Gb draft genome of a female dromedary whose ancestry can be traced to an isolated population from the Canary Islands. We annotated 21,167 protein-coding genes and estimated ~33.7% of the genome to be repetitive. A comparison with the recently published draft genome of an Arabian dromedary resulted in 1.91 Gb of aligned sequence with a divergence of 0.095%. An evaluation of our genome with the reference revealed that our assembly contains more error-free bases (91.2%) and fewer scaffolding errors. We identified ~1.4 million single nucleotide polymorphisms with a mean density of 0.71 x 10(-3) per base. An analysis of demographic history indicated that changes in effective population size corresponded with recent glacial epochs. Our de novo assembly provides a useful resource of genomic variation for future studies of the camel's adaptations to arid environments and economically important traits. Furthermore, these results suggest that draft genome assemblies constructed with only two differently sized sequencing libraries can be comparable to those sequenced using additional library sizes; highlighting that additional resources might be better placed in technologies alternative to short-read sequencing to physically anchor scaffolds to genome maps. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 07/2015; DOI:10.1111/1755-0998.12443 · 5.63 Impact Factor
    • "The retrieved scaffolds were subsequently annotated using a combination of tools, including Maker 2.10 (Holt and Yandell 2011) with RepBase 19.5 (Jurka et al. 2005), SNAP, and Augustus trained on Rhodosporidium toruloides NP11 model (PRJNA169538). "
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    ABSTRACT: In most fungi, sexual reproduction is bipolar, that is, two alternate sets of genes at a single mating-type (MAT) locus determine two mating types. However, in the Basidiomycota, a unique (tetrapolar) reproductive system emerged in which sexual identity is governed by two unlinked MAT loci, each of which controls independent mechanisms of self/nonself recognition. Tetrapolar to bipolar transitions have occurred on multiple occasions in the Basidiomycota, resulting for instance, from linkage of the two MAT loci into a single inheritable unit. Nevertheless, owing to the scarcity of molecular data regarding tetrapolar systems in the earliest-branching lineage of the Basidiomycota (subphylum Pucciniomycotina), it is presently unclear if the last common ancestor was tetrapolar or bipolar. Here, we address this question, by investigating the mating system of the Pucciniomycotina yeast Leucosporidium scottii. Using whole-genome sequencing and chromoblot analysis, we discovered that sexual reproduction is gove
    Genetics 07/2015; DOI:10.1534/genetics.115.177717 · 4.87 Impact Factor
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