It takes two transposons to tango:transposable-element-mediated chromosomal rearrangements

Gray, Yasmine H. M.

doi:10.1016/s0168-9525(00)02104-1

Cited by 272 publications

(216 citation statements)

References 44 publications

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“…When an inversion has been generated by a TE, copies of this element will be flanking the inverted segment in the chromosome with the inversion (Lim and Simmons 1994;Gray 2000). If the inversion succeeds and goes to fixation, these TE insertions will be brought to fixation as well.…”

Section: Discussionmentioning

confidence: 99%

Testing Chromosomal Phylogenies and Inversion Breakpoint Reuse in Drosophila

González¹,

Casals²,

Ruíz

2007

Genetics

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A combination of cytogenetic and bioinformatic procedures was used to test the chromosomal phylogeny relating Drosophila buzzatii with D. repleta. Chromosomes X and 2, harboring most of the inversions fixed between these two species, were analyzed. First, chromosomal segments conserved during the divergence of the two species were identified by comparative in situ hybridization to the D. repleta chromosomes of 180 BAC clones from a BAC-based physical map of the D. buzzatii genome. These conserved segments were precisely delimited with the aid of clones containing inversion breakpoints. Then GRIMM software was used to estimate the minimum number of rearrangements necessary to transform one genome into the other and identify all possible rearrangement scenarios. Finally, the most plausible inversion trajectory was tested by hybridizing 12 breakpoint-bearing BAC clones to the chromosomes of seven other species in the repleta group. The results show that chromosomes X and 2 of D. buzzatii and D. repleta differ by 12 paracentric inversions. Nine of them are fixed in chromosome 2 and entail two breakpoint reuses. Our results also show that the cytological relationship between D. repleta and D. mercatorum is closer than that between D. repleta and D. peninsularis, and we propose that the phylogenetic relationships in this lineage of the repleta group be reconsidered. We also estimated the rate of rearrangement between D. repleta and D. buzzatii and conclude that rates within the genus Drosophila vary substantially between lineages, even within a single species group.

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Section: Discussionmentioning

confidence: 99%

Testing Chromosomal Phylogenies and Inversion Breakpoint Reuse in Drosophila

González¹,

Casals²,

Ruíz

2007

Genetics

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“…More structural changes (deletions) were found in the two Gm15 intervals, where there was higher transposon density, suggesting a correlation between structural changes and transposable elements. It is known that transposons can induce major genome rearrangements, including deletions, duplications, inversions, macrotransposition, and reciprocal translocations (Gray, 2000;Caceres et al, 2001;Lonnig and Saedler, 2002;Huang and Dooner, 2008;Lee et al, 2008;Zhang et al, 2009). We hypothesize that Gm15, with a higher transposon density, underwent more extensive structural changes (i.e., higher density of LTR retrotransposon, solo LTRs, and lower gene retention rate) and that transposable elements were likely an active force in this remodeling of a homoeologous chromosome in soybean (see Supplemental Figure 17 online).…”

Section: Ltr Retrotransposon Activity In Gm8 Gm15 and Pv5mentioning

confidence: 99%

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

et al. 2010

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Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ;1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ;13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in Gm8) and a nearly twofold increase in the deletion of long terminal repeat (LTR) retrotransposons via solo LTR formation. Functional analyses of Gm15 and Gm8 revealed decreases in gene expression and synonymous substitution rates for Gm15, for instance, a 38% increase in transcript levels from Gm8 relative to Gm15. Transcriptional divergence of homoeologs was found based on expression patterns among seven tissues and developmental stages. Our results indicate asymmetric evolution between homoeologous regions of soybean as evidenced by structural changes and expression variances of homoeologous genes.

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“…In eukaryotic organisms, much is known about the transposable element system, including the element structure, transposition mechanisms, copy number variance (CNV) and evolutionary history of transposable elements [ (Wicker et al, 2007) and (Langdon et al, 2003)]. In bacteria, insert sequences (IS) and miniature inverted-repeat transposable elements (MITEs) are two principal types of transposable elements, which can move from place to place via a DNA intermediate by a cut and paste mechanism (class II element) (Gray, 2000) or spread to other organisms by horizontal gene transfer [ (Kidwell, 1992) and (Leavis et al, 2007)]. Insertion sequences in prokaryotes were assumed to be an important driving force for novel genotypic and phenotypic variants.…”

Section: Introductionmentioning

confidence: 99%