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PubMed2025

Genome-wide diversity of chromosomal inversions and their disease relationships.

Chromosomal inversions shape evolution and are implicated in human disease, yet their effects on genomic variation and health outcomes remain poorly understood. We analyze genome-wide human inversion polymorphisms, contrasting single-event and recurrent loci. Inversion recurrence is validated using structured-coalescent simulations. We show that single-event inversions evolve in near-complete isolation: inverted haplotypes show ~16-fold lower diversity and strong differentiation from direct haplotypes (median FST = 0.33). By contrast, recurrent inversions maintain gene flow, resulting in similar diversity across orientations and ~4-fold lower differentiation. We further find marked differences in coding sequence conservation between single-event and recurrent inversions. Using the NIH All of Us biobank, we impute inversions and identify four inversions with significant disease associations. Notably, the 17q21 inversion is associated with reduced risk of cognitive decline (OR=0.919) and breast cancer (OR=0.910) but with increased obesity risk (OR=1.097), consistent with pleiotropic selection. These findings establish inversions as major drivers of human genetic diversity and disease, with evolutionary outcomes critically dependent on recurrence.

Evolution↗
PubMed1983

Clinical implications of chromosomal inversions. A pericentric inversion in No. 18 segregating in a family ascertained through an abnormal proband.

Chromosomal inversions are being detected in humans with increasing frequency due to the application of chromosomal banding techniques. Inversions have occurred in all chromosomal groups. These structural aberrations may lead to infertility, reproductive loss, or abnormal offspring. To illustrate their clinical significance, we report a family in which an inversion in chromosome No. 18 is segregating. This family was ascertained through a proband whose anomalies were consistent with the deletion 18q syndrome. The chromosomal imbalance originated by recombination within the parental inversion during meiosis. Consideration of this family and 6 others with similar breakpoints (18p11 and 18q12 or q21) suggests that the risk of unbalanced (recombinant) livebirths may be higher for female inv(18) heterozygotes than for males. The paucity of male carriers detected could be due to prenatal selection or chance. Overall, there may be preferential segregation for the aberrant chromosomes (inversions plus recombinants). Amniocentesis and cytogenetic analysis of pregnancy losses is recommended for families in which inversions are detected.

Abnormalities, Multiple↗
PubMed1991

Correlated variation of chromosomal inversion (3R)C and extra bristles in Drosophila melanogaster.

Chromosomal inversion In(3R)C and extra dorsocentral and scutellar macrochaetae are correlated in Asturian natural populations of Drosophila melanogaster in that selection for extra bristles produced an increase in In(3R)C frequency. In the present work two populations with significantly different frequencies of the In(3R)C inversion were created and a significant positive correlation between In(3R)C frequency and frequency of individuals carrying extra bristles was found. This result confirms the correlation between bristles and In(3R)C. In addition, the correlation between the two characters is also demonstrated at the individual level.

Animals↗
PubMed2005

Chromosomal inversion discovered in C3H/HeJ mice.

Mice of the inbred mouse strain C3H/HeJ have been shown to be homozygous for a chromosomal inversion on Chromosome (Chr) 6. The inversion encompasses about 20% of the chromosome from approximately 73 Mb to approximately 116 Mb. The importance of this finding is that linkage crosses using C3H/HeJ will show no recombination in this region of Chr 6. The inversion has no apparent effect on the phenotype of C3H/HeJ mice and its presence should not affect biological studies; however, use of C3H/HeJ mice for genetic analysis of Chr 6 should be avoided or the results interpreted with the inversion in mind. The inversion has been named In(6)1J (inversion Chr 6, Jackson 1).

Animals↗
PubMed1997

Correlations among size-related traits affected by chromosome inversions in Drosophila buzzatii: the comparison within and across environments.

Genetic variation in correlations among size-related traits of head, thorax, and wings was examined in Drosophila buzzatii, by comparing the pattern of the Phenotypic Correlation Matrix (Rp) between inversion karyotypes of the second chromosome. No similarity in Rp was observed between some karyotypes in a natural population. The pattern of Rp in wild-reared heterokaryotypes, but not in homokaryotypes, was similar to the whole population represented by laboratory-reared flies. While phenotypic correlations in wild-reared flies were found to be larger than in laboratory-reared flies, similarity in the pattern of Rp was very high for one homokaryotype reared in both environments: the relatively homogeneous lab environment and the more variable field environment. While no such a similarity across environments was detected between different karyotypes, the pattern of Rp was similar for a same homokaryotype in different populations. Thus, the lack of karyotypic similarity in Rp is, at least partially, genetic. These results indicate that chromosomal inversions are factors affecting genetic correlations among traits known to be phenotypically correlated with adult fitness components in this species.

Animals↗
PubMed1993

Molecular variation of Adh and P6 genes in an African population of Drosophila melanogaster and its relation to chromosomal inversions.

Four-cutter molecular polymorphism of Adh and P6, and chromosome inversion polymorphism of chromosome II were investigated in 95 isogenic lines of an Ivory Coast population of Drosophila melanogaster, a species assumed to have recently spread throughout the world from a West African origin. The P6 gene showed little linkage disequilibrium with the In(2L)t inversion, although it is located within this inversion. This suggests that the inversion and the P6 locus have extensively exchanged genetic information through either double crossover or gene conversion. Allozymic variation in ADH was in linkage disequilibrium with In(2L)t and In(2R)NS inversions. Evidence suggests either that inversion linkage with the Fast allele is selectively maintained, or that this allele only recently appeared. Molecular polymorphism at the Adh locus in the Ivory Coast is not higher than in North American populations. New haplotypes specific to the African population were found, some of them connect the "WaS-like" haplotypes found at high frequencies in the United States to the other slow haplotypes. Their relation with In(2L)t supports the hypothesis that WaS recently recombined away from an In(2L)t chromosome which may be the cause of its divergence from the other haplotypes.

Africa, Western↗
PubMed2006

Localization and characterization of X chromosome inversion breakpoints separating Drosophila mojavensis and Drosophila arizonae.

Ectopic exchange between transposable elements or other repetitive sequences along a chromosome can produce chromosomal inversions. As a result, genome sequence studies typically find sequence similarity between corresponding inversion breakpoint regions. Here, we identify and investigate the breakpoint regions of the X chromosome inversion distinguishing Drosophila mojavensis and Drosophila arizonae. We localize one inversion breakpoint to 13.7 kb and localize the other to a 1-Mb interval. Using this localization and assuming microsynteny between Drosophila melanogaster and D. arizonae, we pinpoint likely positions of the inversion breakpoints to windows of less than 3000 bp. These breakpoints define the size of the inversion to approximately 11 Mb. However, in contrast to many other studies, we fail to find significant sequence similarity between the 2 breakpoint regions. The localization of these inversion breakpoints will facilitate future genetic and molecular evolutionary studies in this species group, an emerging model system for ecological genetics.

Animals↗
PubMed2006

Accommodating chromosome inversions in linkage analysis.

This work develops a population-genetics model for polymorphic chromosome inversions. The model precisely describes how an inversion changes the nature of and approach to linkage equilibrium. The work also describes algorithms and software for allele-frequency estimation and linkage analysis in the presence of an inversion. The linkage algorithms implemented in the software package Mendel estimate recombination parameters and calculate the posterior probability that each pedigree member carries the inversion. Application of Mendel to eight Centre d'Etude du Polymorphisme Humain pedigrees in a region containing a common inversion on 8p23 illustrates its potential for providing more-precise estimates of the location of an unmapped marker or trait gene. Our expanded cytogenetic analysis of these families further identifies inversion carriers and increases the evidence of linkage.

Algorithms↗
PubMed1987

Observations on the extent and temporal stability of latitudinal clines for alcohol dehydrogenase allozymes and four chromosome inversions in Drosophila melanogaster.

Previously we have presented evidence of large-scale latitudinal clines in the frequencies of four chromosome inversions and alleles at six enzyme loci in populations of D. melanogaster in Australasia, Asia and North America. Subsequent sampling by others in Japan and western U.S.A. has failed to repeat this observation for the steepest of the clines (alcohol dehydrogenase and the four chromosome inversions). We argue that this failure reflects the few populations and small latitudinal range sampled in these later studies. From extensive sampling over a long latitudinal transect in Australasia we here document Adh and inversion clines which are virtually identical to those originally obtained in different Australian populations four years earlier. We also repeat our observation that the Adh cline is largely independent of the cline in the linked inversion In(2L)t. We therefore retain our original conclusion that these polymorphisms are subject to natural selection. However the new Australasian data do not indicate an association between Adh and maximum rainfall which had been evident in the earlier data for Australasia, Asia and North America. We therefore retract our claim that the selective agent on Adh is related to rainfall.

Alcohol Dehydrogenase↗
PubMed1988

[Genetic counseling in balanced chromosomal inversions].

The genetic counseling given at carriers of equilibrated chromosomal inversions is in relation with the type of the inversion. The risk for carriers of pericentric inversions concerning euchromatic regions depends on many factors, i.e. the length of the inserted segment in relation with the total length of the chromosome involved, the sex of the carrier and the way of assortment. In contrast, the carriers of pericentric inversions concerning the heterochromatic regions, as well as of paracentric inversions, have not a particular risk for their descendance.

Aneuploidy↗
PubMed1991

Genetic and environmental factors in the resistance of Drosophila subobscura adults to high temperature shock. III. Chromosomal-inversion and enzymatic polymorphism variation in lines selected for heat shock resistance.

Two replicate selection experiments to increase and decrease heat shock resistance of Drosophila subobscura adults were carried out maintaining control lines. In the present paper, the chromosomal-inversion and enzymatic polymorphism variation with selection is analyzed. The results indicate an erratic variation of chromosomal arrangement frequencies for practically all the chromosomes in the selected lines, showing a loss of the less frequent arrangements especially in sensitive lines. Only the A chromosome and the O + 4 arrangement show a behaviour that may not be due to random effects, which points to the possible existence of heat shock factor(s) in these chromosomes. Similarly, an erratic variation of allele frequencies is observed for all the enzymes studied (Aph, Pept-1) except for the Hk-1 enzyme. We cannot establish the possible participation of this locus in heat shock resistance from the results obtained up to now. A significant decrease in heterozygosity is detected in sensitive lines from chromosomal-inversion polymorphism.

Animals↗
PubMed1998

Evidence of chromosomal inversion using fluorescence in situ hybridization to stretched DNA.

The resolution of fluorescence in situ hybridization techniques (FISH) can be improved using techniques of DNA stretching. The so-called DIRVISH technique has been used to demonstrate the existence of an inversion involving a small chromosomal segment of the long arm of chromosome 14. This inversion was suspected, but not proven, in patients with familial Alzheimer disease. Two-colour FISH using YAC and cosmid probes allowed us to limit the rearranged region around YAC 964e2, which encompasses the Presenilin 1 (PR1) gene. The existence of small-sized inversions within the genome becomes, thus, open to microscope analysis.

Age of Onset↗
PubMed2000

Evidence for symmetric chromosomal inversions around the replication origin in bacteria.

BACKGROUND: Whole-genome comparisons can provide great insight into many aspects of biology. Until recently, however, comparisons were mainly possible only between distantly related species. Complete genome sequences are now becoming available from multiple sets of closely related strains or species. RESULTS: By comparing the recently completed genome sequences of Vibrio cholerae, Streptococcus pneumoniae and Mycobacterium tuberculosis to those of closely related species - Escherichia coli, Streptococcus pyogenes and Mycobacterium leprae, respectively - we have identified an unusual and previously unobserved feature of bacterial genome structure. Scatterplots of the conserved sequences (both DNA and protein) between each pair of species produce a distinct X-shaped pattern, which we call an X-alignment. The key feature of these alignments is that they have symmetry around the replication origin and terminus; that is, the distance of a particular conserved feature (DNA or protein) from the replication origin (or terminus) is conserved between closely related pairs of species. Statistically significant X-alignments are also found within some genomes, indicating that there is symmetry about the replication origin for paralogous features as well. CONCLUSIONS: The most likely mechanism of generation of X-alignments involves large chromosomal inversions that reverse the genomic sequence symmetrically around the origin of replication. The finding of these X-alignments between many pairs of species suggests that chromosomal inversions around the origin are a common feature of bacterial genome evolution.

Bacteria↗
PubMed2003

Chromosomal inversions effect body size and shape in different breeding resources in Drosophila buzzatii.

The cactophilic Drosophila buzzatii provides an excellent model for the study of reaction norms across discrete environments because it breeds on rotting tissues (rots) of very different cactus species. Here we test the possible effects of second chromosome inversions on body size and shape (wing loading) across suitable natural breeding substrates. Using homokaryotypic stocks derived from several lines homozygous for four naturally occurring chromosomal inversions, we show that arrangements significantly affect size-related traits and wing loading. In addition, karyotypes show differing effects, across natural breeding resources, for wing loading. The 2st and 2jz(3) arrangements decrease and the 2j arrangement increases wing loading. For thorax length and wing loading, karyotypic correlations across host plants are slightly lower in females than in males. These results support the hypothesis that these traits have a genetic basis associated with the inversion polymorphism.

Animals↗
PubMed1995

Anopheles arabiensis and An. gambiae chromosomal inversion polymorphism, feeding and resting behaviour in relation to insecticide house-spraying in Tanzania.

Differential responses of the mosquitoes Anopheles arabiensis and An. gambiae sensu stricto to house-spraying with DDT or lambda-cyhalothrin were evaluated in relation to chromosomal inversion polymorphism, feeding and resting behaviour of these malaria vectors in Tanzania. Blood-fed mosquitoes from pit traps outdoors, exit traps on windows and indoor-resting catches were identified cytogenetically and the chromosomal inversion frequencies compared between samples and species. Their outdoor-resting behaviour was assessed by a mark-release-recapture experiment and by determining the proportion of freshly blood-fed individuals in exit traps. The source of bloodmeals was analysed by an ELISA method. Endophagic females of An. arabiensis were more likely than those of An.gambiae to exit from a house on the night of blood-feeding. Only in one out of three villages was there evidence that chromosomally distinct individuals within a species had different preferences for resting sites. There were indications, but not conclusive evidence, that mosquitoes caught indoors or outdoors had a tendency to return to the same type of resting site. In villages sprayed with either insecticide, the mean age of the vector populations was greatly reduced, compared with those in the unsprayed villages. An.arabiensis females exited from DDT sprayed houses after blood-feeding, whereas with lambda-cyhalothrin those exiting were mostly unfed and there was a decline in the human blood index. The excitorepellency of DDT was perceived as a disadvantage, whereas lambda-cyhalothrin apparently had more impact on malaria transmission by An.arabiensis.

Animals↗
PubMed2002

Analysis of the population structure of Anopheles funestus (Diptera: Culicidae) from western and coastal Kenya using paracentric chromosomal inversion frequencies.

In total, 324 Anopheles funestus Giles specimens collected from seven houses in western Kenya and seven in coastal Kenya were scored for their paracentric chromosomal inversions with the aim of determining the level of genetic differentiation based on these inversions. Houses in each area were within a 2-km radius. The two areas are approximately 700 km apart. Only inversions 2a, 3a, 3b, and 5a were found to be polymorphic. Levels of polymorphism varied greatly between inversions. There were no significant deviations from Hardy-Weinberg expectations for samples from individual houses at one site or when data for houses in each area were pooled. Overall, the level of differentiation between western and coastal Kenya was significant, suggesting that the two populations are genetically isolated. Results based on inversion 2a alone were, however, not consistent with this conclusion. Founder effects and selection against the 2a inversion are discussed as possible explanations for this discrepancy.

Animals↗
PubMed2006

Assaying chromosomal inversions by single-molecule haplotyping.

Inversions are an important form of structural variation, but they are difficult to characterize, as their breakpoints often fall within inverted repeats. We have developed a method called 'haplotype fusion' in which an inversion breakpoint is genotyped by performing fusion PCR on single molecules of human genomic DNA. Fusing single-copy sequences bracketing an inversion breakpoint generates orientation-specific PCR products, exemplified by a genotyping assay for the int22 hemophilia A inversion on Xq28. Furthermore, we demonstrated that inversion events with breakpoints embedded within long (>100 kb) inverted repeats can be genotyped by haplotype-fusion PCR followed by bead-based single-molecule haplotyping on repeat-specific markers bracketing the inversion breakpoint. We illustrate this method by genotyping a Yp paracentric inversion sponsored by >300-kb-long inverted repeats. The generality of our methods to survey for, and genotype chromosomal inversions should help our understanding of the contribution of inversions to genomic variation, inherited diseases and cancer.

Chromosome Inversion↗