Additional file 4 of Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats
Octavio M. Palacios‐GimenezJulia KoelmanMarc Palmada‐FloresTessa M. BradfordKarl K. JonesSteven J. CooperTakeshi KawakamiAlexander Suh
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Additional file 4. Repeat consensus sequences of the P24XY sex chromosome race (male) of the of the viatica species group (tar.gz file).Keywords:
Satellite DNA
Grasshopper
Transposons are DNA sequences capable of moving in genomes. Early evidence showed their accumulation in many species and suggested their continued activity in at least isolated organisms. In the past decade, with the development of various genomic technologies, it has become abundantly clear that ongoing activity is the rule rather than the exception. Active transposons of various classes are observed throughout plants and animals, including humans. They continue to create new insertions, have an enormous variety of structural and functional impact on genes and genomes, and play important roles in genome evolution. Transposon activities have been identified and measured by employing various strategies. Here, we summarize evidence of current transposon activity in various plant and animal genomes.
Transposition (logic)
Transposase
Retrotransposon
DNA Transposable Elements
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We have identified and determined the sequence and organization of a new rat satellite DNA in Rattus rattus , the roof rat. This satellite DNA, which we call R. rattus satellite I', consists of tandem arrays of a 185 base pair (bp) repeat unit that we call a' a' is 86% homologous to a 185 bp portion of the 370 bp repeat unit of the previously described rat satellite [Pech et al. (1979) Nucleic Acids Res. 7, 417 -432] present in the common laboratory rat species, R. norvegicus . We can there by distinguish two 185 bp portions of the satellite I 370 bp repeat unit: "a" (homlogous to a') and "b". Satellite I has the structure (a,b) n , and satellite I' has the structure (a') n . Like a, a' is only about 60% homologous to b and fails to hybridize to b. Although R. norvegicus and R. rattus contain about the same total concentration of satellite sequences, R. norvegicus contains essentially only the a, b type (satellite I'), whereas R. rattus contains a' type (satellite I') and lesser amounts of the a, b type( satellite I'). The a,b type (satellite I') in R. rattus is very similar to that in R. norvegicus as judged both by hybridization and by the presence of all but one of the major restriction enzymesites that characterize the R. norvegicus satellite I. In R. rattus the a' and a,b repeat units are not detectably present in the same tandem array. All of the sequence differences between a' ( R. rattus ) and a ( R. norvegicus ) can be accounted for by simple base substitutions, and the implication of this and other features of rat satellite DNA structure for satellite DNA evolution are discussed.
Satellite DNA
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We have studied the genomic distribution of five different families of plant transposable elements by analyzing their location in DNA fractions from maize and tobacco genomes fractionated according to base composition. The results show that each family of elements Is preferentially Integrated In one specific fraction of Its respective host genome. This demonstrates that the distribution of transposable elements In the nuclear genome of plants Is not random but compartimentalized, i.e., the elements are located In specific genomic compartments characterized by having a specific G + C content and representing a small proportion of the genomes. Furthermore, these compartments seem to correspond to the genomic regions where most of the plant genes are also located, suggesting a preferential Integration of transposable elements In the transcriptlonally active regions of the plant genome. The implications of these results on the current applications of transposon tagging techniques are discussed.
Genomic Organization
Genome size
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Eukaryotic organisms have dynamic genomes, with transposable elements (TEs) as a major contributing factor. Although the large autonomous TEs can significantly shape genomic structures during evolution, genomes often harbor more miniature nonautonomous TEs that can infest genomic niches where large TEs are rare. In spite of their cut-and-paste transposition mechanisms that do not inherently favor copy number increase, miniature inverted-repeat transposable elements (MITEs) are abundant in eukaryotic genomes and exist in high copy numbers. Based on the large number of MITE families revealed in previous studies, accurate annotation of MITEs, particularly in newly sequenced genomes, will identify more genomes highly rich in these elements. Novel families identified from these analyses, together with the currently known families, will further deepen our understanding of the origins, transposase sources, and dramatic amplification of these elements.
Transposase
Inverted repeat
Transposition (logic)
Retrotransposon
Insertion sequence
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Satellite DNA
Buoyant density
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Transposons in chloroplast genomes are distributed inhomogeneously among gymnosperms and angiosperms
Abstract An occurrence and specificity of transposons in chloroplast genomes is considered. It is shown that the transposons are met in some genomes, and are nor in others. Rather decreased number of copies is peculiar for transposons found in chloroplast genomes, as well as the prevalence in their location (leading strand). Unique transposon Copia-18_BD-I is found in gymnosperms.
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Transposable elements (TEs) are self-mobilized DNA sequences that constitute a large portion of plant genomes. Being selfish DNA, they utilize different mobilization mechanisms to persist and proliferate in host genomes. It is important that new TE insertions generate de novo variability, most of which is likely to be deleterious, but some can be advantageous. Also, a growing body of evidence shows that TEs were continually recruited by their hosts to provide additional functionality. Here, we review potential ways in which transposable elements can provide novel functions to host genomes, from simple gene knock-outs to complex rewiring of gene expression networks. We discuss possible implications of TE presence and activity in crop genomes for agricultural production.
DNA Transposable Elements
Retrotransposon
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SUMMARY The resolution of antibiotic-CsCl gradients enabled an examination of the satellite DNAs in the nuclear DNA of Drosophila simulans . Of the eight distinct satellite DNAs which were detected, four band at almost the same buoyant density in CsCl but can be resolved in netropsin sulphate-CsCl gradients. Each consists of a repeated sequence which, in five of the satellites, is shown to be arranged in tandem for long regions of the chromosomal DNA. One satellite (1·697 g/ml in CsCl) contains repeated sequences interspersed with other sequences. The satellite DNAs were compared with the satellite DNAs known to be present in the sibling species, D. melanogaster . The two species have different overall complements of satellite DNAs, but one satellite (1·672 g/ml) may be identical.
Satellite DNA
Buoyant density
Netropsin
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plant evolution
Genome size
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