Cloning and sequencing of the breakpoint regions of inversion 5g fixed in Drosophila buzzatii

Costa, Olivia Prazeres da; González, Josefa; Ruíz, Alfredo

doi:10.1007/s00412-008-0201-5

Cited by 9 publications

(7 citation statements)

References 67 publications

(74 reference statements)

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“…Although evolutionary CR breakpoints have been cloned in model organisms, including yeast (Fischer et al 2000), fruit flies (Prazeres da Costa et al 2009), malaria mosquitos (Sharakhov et al 2006), and primates (Goidts et al 2005), little is known about the breakpoint structure of fixed CRs in plants at the sequence level, in part due to the much more complex and dynamic nature of their genomes. Using a map-based comparative genomics approach, we identified the breakpoints of the 4AL/5AL translocation fixed in wheat at the sequence level, which are corroborated by four independent genome assemblies of diploid wheat T. monococcum and T. urartu and polyploid wheat T. aestivum , and validated by PCR assays in all wheat species.…”

Section: Discussionmentioning

confidence: 99%

Recurrence of Chromosome Rearrangements and Reuse of DNA Breakpoints in the Evolution of the Triticeae Genomes

Challa

Zhu

et al. 2016

G3 Genes|Genomes|Genetics

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Chromosomal rearrangements (CRs) play important roles in karyotype diversity and speciation. While many CR breakpoints have been characterized at the sequence level in yeast, insects, and primates, little is known about the structure of evolutionary CR breakpoints in plant genomes, which are much more dynamic in genome size and sequence organization. Here, we report identification of breakpoints of a translocation between chromosome arms 4L and 5L of Triticeae, which is fixed in several species, including diploid wheat and rye, by comparative mapping and analysis of the draft genome and chromosome survey sequences of the Triticeae species. The wheat translocation joined the ends of breakpoints downstream of a WD40 gene on 4AL and a gene of the PMEI family on 5AL. A basic helix-loop-helix transcription factor gene in 5AL junction was significantly restructured. Rye and wheat share the same position for the 4L breakpoint, but the 5L breakpoint positions are not identical, although very close in these two species, indicating the recurrence of 4L/5L translocations in the Triticeae. Although barley does not carry the translocation, collinearity across the breakpoints was violated by putative inversions and/or transpositions. Alignment with model grass genomes indicated that the translocation breakpoints coincided with ancient inversion junctions in the Triticeae ancestor. Our results show that the 4L/5L translocation breakpoints represent two CR hotspots reused during Triticeae evolution, and support breakpoint reuse as a widespread mechanism in all eukaryotes. The mechanisms of the recurrent translocation and its role in Triticeae evolution are also discussed.

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Section: Discussionmentioning

confidence: 99%

Recurrence of Chromosome Rearrangements and Reuse of DNA Breakpoints in the Evolution of the Triticeae Genomes

Challa

Zhu

et al. 2016

G3 Genes|Genomes|Genetics

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“…The relative contribution of the two mechanisms to the generation of natural Drosophila inversions is not yet clear. In Dipterans, clear-cut evidence for the implication of TEs in their generation has been found for a few polymorphic inversions [15,21-23] but has never been found for fixed inversions [6,11,24,25]. On the other hand, breakage and repair by NHEJ may be the prevalent mechanism in D. melanogaster and its close relatives [11].…”

Section: Introductionmentioning

confidence: 99%

Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution

Guillén

Ruíz

2012

BMC Genomics

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BackgroundChromosomal inversions have been pervasive during the evolution of the genus Drosophila, but there is significant variation between lineages in the rate of rearrangement fixation. D. mojavensis, an ecological specialist adapted to a cactophilic niche under extreme desert conditions, is a chromosomally derived species with ten fixed inversions, five of them not present in any other species.ResultsIn order to explore the causes of the rapid chromosomal evolution in D. mojavensis, we identified and characterized all breakpoints of seven inversions fixed in chromosome 2, the most dynamic one. One of the inversions presents unequivocal evidence for its generation by ectopic recombination between transposon copies and another two harbor inverted duplications of non-repetitive DNA at the two breakpoints and were likely generated by staggered single-strand breaks and repair by non-homologous end joining. Four out of 14 breakpoints lay in the intergenic region between preexisting duplicated genes, suggesting an adaptive advantage of separating previously tightly linked duplicates. Four out of 14 breakpoints are associated with transposed genes, suggesting these breakpoints are fragile regions. Finally two inversions contain novel genes at their breakpoints and another three show alterations of genes at breakpoints with potential adaptive significance.ConclusionsD. mojavensis chromosomal inversions were generated by multiple mechanisms, an observation that does not provide support for increased mutation rate as explanation for rapid chromosomal evolution. On the other hand, we have found a number of gene alterations at the breakpoints with putative adaptive consequences that directly point to natural selection as the cause of D. mojavensis rapid chromosomal evolution.

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“…In Drosophila, this process has been responsible for most of the inversions fixed between D. melanogaster and D. yakuba [43] as well as three D. melanogaster polymorphic inversions [44]–[46]. In addition, this mechanism likely generated several inversions fixed in other lineages where TEs were not detected at the breakpoints or when present were not involved in the origin of the inversion [47]–[50]. SDs represent a significant fraction of mammalian genomes and ectopic recombination between SDs seems to be a common mechanism inducing chromosomal inversions in these genomes.…”

Section: Introductionmentioning

confidence: 99%

The Transposon Galileo Generates Natural Chromosomal Inversions in Drosophila by Ectopic Recombination

et al. 2009

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BackgroundTransposable elements (TEs) are responsible for the generation of chromosomal inversions in several groups of organisms. However, in Drosophila and other Dipterans, where inversions are abundant both as intraspecific polymorphisms and interspecific fixed differences, the evidence for a role of TEs is scarce. Previous work revealed that the transposon Galileo was involved in the generation of two polymorphic inversions of Drosophila buzzatii.Methodology/Principal FindingsTo assess the impact of TEs in Drosophila chromosomal evolution and shed light on the mechanism involved, we isolated and sequenced the two breakpoints of another widespread polymorphic inversion from D. buzzatii, 2z 3. In the non inverted chromosome, the 2z 3 distal breakpoint was located between genes CG2046 and CG10326 whereas the proximal breakpoint lies between two novel genes that we have named Dlh and Mdp. In the inverted chromosome, the analysis of the breakpoint sequences revealed relatively large insertions (2,870-bp and 4,786-bp long) including two copies of the transposon Galileo (subfamily Newton), one at each breakpoint, plus several other TEs. The two Galileo copies: (i) are inserted in opposite orientation; (ii) present exchanged target site duplications; and (iii) are both chimeric.Conclusions/SignificanceOur observations provide the best evidence gathered so far for the role of TEs in the generation of Drosophila inversions. In addition, they show unequivocally that ectopic recombination is the causative mechanism. The fact that the three polymorphic D. buzzatii inversions investigated so far were generated by the same transposon family is remarkable and is conceivably due to Galileo's unusual structure and current (or recent) transpositional activity.

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Cloning and sequencing of the breakpoint regions of inversion 5g fixed in Drosophila buzzatii

Cited by 9 publications

References 67 publications

Recurrence of Chromosome Rearrangements and Reuse of DNA Breakpoints in the Evolution of the Triticeae Genomes

Recurrence of Chromosome Rearrangements and Reuse of DNA Breakpoints in the Evolution of the Triticeae Genomes

Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution

The Transposon Galileo Generates Natural Chromosomal Inversions in Drosophila by Ectopic Recombination

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