Multiple and diverse structural changes affect the breakpoint regions of polymorphic inversions across the Drosophila genus

Puerma, Eva; Orengo, Dorcas J.; Aguadé, Montserrat

doi:10.1038/srep36248

Cited by 23 publications

(27 citation statements)

References 33 publications

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“…In turn, the same 309 bp sequence was present at both O 3 inversion breakpoints, indicating that at the origin of this inversion such region was duplicated, being present in 8 by the staggered double-strand break mechanism. This analysis also found that genes CG5225 and Prosβ2R2 are involved in multiple rearrangements (duplications and transpositions, in addition to inversions) occurring along the chromosomal evolution of the species of the genus Drosophila [87].…”

Section: Inversion Origin Via Staggered Breaks and Repair By Non-homomentioning

confidence: 68%

“…In addition, duplicate regions in these events range from a few hundred base pairs to about 8 Kbp (see Table 1), encompassing whole and partial genes in some of these duplications. However, no dose effect or generation of new transcripts was detected in the analyses [61,[84][85][86][87].…”

Section: Inversion Origin Via Staggered Breaks and Repair By Non-homomentioning

confidence: 84%

“…Inversions O 4 and O 8 Duplications in both breakpoints of the inversions; origin by staggered breaks [87]. recombination in males, mutation and structural chromosomal abnormalities [9].…”

Section: Subobscuramentioning

confidence: 99%

“…yakuba Burla, 1954 [59]; and the chromosomal polymorphism of the E and O chromosomes of D. subobuscura [61,[84][85][86][87]. The study of Ranz et al [59] analyzed the breakpoints of 29 interspecific inversions in these species through experimental and computational methods.…”

Section: Inversion Origin Via Staggered Breaks and Repair By Non-homomentioning

confidence: 99%

“…These inversions give rise to the complex arrangements E 1 + 2 , E 1 + 2 + 9 , E 1 + 2 + 9 + 3, and E 1 + 2 + 9 + 12 . These chromosome constitutions, besides providing a great system for the analysis of the mechanisms of origin of inversions, also provide a basis for studying the reuse of the inversion breakpoints at the molecular level [61,[85][86][87].…”

Section: Inversion Origin Via Staggered Breaks and Repair By Non-homomentioning

confidence: 99%

See 4 more Smart Citations

Drosophila Chromosomal Polymorphism: From Population Aspects to Origin Mechanisms of Inversions

Garcia¹,

Valente²

2018

Drosophila Melanogaster - Model for Recent Advances in Genetics and Therapeutics

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High rates of chromosomal rearrangements are remarkably abundant in Drosophila Fallén, 1832 (Insecta, Diptera) genus, highlighting the paracentric inversions. Since different species of this genus are paradigms for genetics, evolutionary, and population studies, polymorphism analyses for chromosomal inversions have provided basic knowledge for beautiful biological questions. Chromosomal inversions suppress meiotic recombination and thus, natural selection can act to preserve favorable gene complexes. Analyses of natural and laboratory populations show that these polymorphisms provide adaptive advantages to their carriers in relation to diverse factors, such as niche exploration and climatic factors. In addition, due to their monophyletic origin, they also serve as genetic markers for the construction of unrooted phylogenies. With the increasing domain of molecular techniques and genome sequencing, factors such as the reuse of breakpoints by different inversions and the mechanisms that give rise to these polymorphisms have been exploited with scientific refinement. These analyses show the presence of regions that are hot spots for breakpoints, fitting the fragile breakage chromosomal evolution model, as well as the involvement of transposition elements at the origin of chromosomal inversions.

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Section: Inversion Origin Via Staggered Breaks and Repair By Non-homomentioning

confidence: 68%

Section: Inversion Origin Via Staggered Breaks and Repair By Non-homomentioning

confidence: 84%

“…Inversions O 4 and O 8 Duplications in both breakpoints of the inversions; origin by staggered breaks [87]. recombination in males, mutation and structural chromosomal abnormalities [9].…”

Section: Subobscuramentioning

confidence: 99%

Section: Inversion Origin Via Staggered Breaks and Repair By Non-homomentioning

confidence: 99%

Section: Inversion Origin Via Staggered Breaks and Repair By Non-homomentioning

confidence: 99%

See 3 more Smart Citations

Drosophila Chromosomal Polymorphism: From Population Aspects to Origin Mechanisms of Inversions

Garcia¹,

Valente²

2018

Drosophila Melanogaster - Model for Recent Advances in Genetics and Therapeutics

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Population Genomics on the Fly: Recent Advances in Drosophila

Haudry

Laurent

Kapun

2020

Methods in Molecular Biology

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Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its world-wide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this bookchapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of non-coding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.

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Dense gene physical maps of the non-model species Drosophila subobscura

et al. 2017

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The comparative analysis of genetic and physical maps as well as of whole genome sequences had revealed that in the Drosophila genus, most structural rearrangements occurred within chromosomal elements as a result of paracentric inversions. Genome sequence comparison would seem the best method to estimate rates of chromosomal evolution, but the high-quality reference genomes required for this endeavor are still scanty. Here, we have obtained dense physical maps for Muller elements A, C, and E of Drosophila subobscura, a species with an extensively studied rich and adaptive chromosomal polymorphism. These maps are based on 462 markers: 115, 236, and 111 markers for elements A, C, and E, respectively. The availability of these dense maps will facilitate genome assembly and will thus greatly contribute to obtaining a good reference genome, which is a required step for D. subobscura to attain the model species status. The comparative analysis of these physical maps and those obtained from the D. pseudoobscura and D. melanogaster genomes allowed us to infer the number of fixed inversions and chromosomal evolutionary rates for each pairwise comparison. For all three elements, rates inferred from the more closely related species were higher than those inferred from the more distantly related species, which together with results of relative-rate tests point to an acceleration in the D. subobscura lineage at least for elements A and E.

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Multiple and diverse structural changes affect the breakpoint regions of polymorphic inversions across the Drosophila genus

Cited by 23 publications

References 33 publications

Drosophila Chromosomal Polymorphism: From Population Aspects to Origin Mechanisms of Inversions

Drosophila Chromosomal Polymorphism: From Population Aspects to Origin Mechanisms of Inversions

Population Genomics on the Fly: Recent Advances in Drosophila

Dense gene physical maps of the non-model species Drosophila subobscura

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