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Scientific Reports Mar 2019Multiple sex chromosome systems have been described for several mammalian orders, with different species from the same genus sharing the same system (e.g., XXY or XYY)....
Multiple sex chromosome systems have been described for several mammalian orders, with different species from the same genus sharing the same system (e.g., XXY or XYY). This is important because the translocated autosome may be influenced by the evolution of the recipient sex chromosome, and this may be related to speciation. It is often thought that the translocation of an autosome to a sex chromosome may share a common origin among phylogenetically related species. However, the neo-X chromosomes of Proechimys goeldii (2n = 24♀, 25♂/NFa = 42) and Proechimys gr. goeldii (2n = 16♀, 17♂/NFa = 14) have distinct sizes and morphologies that have made it difficult to determine whether they have the same or different origins. This study investigates the origins of the XYY sex chromosome determination system in P. goeldii (PGO) and P. gr. goeldii (PGG) and elucidates the chromosomal rearrangements in this low-diploid-number group of Proechimys species. Toward this end, we produced whole-chromosome probes for P. roberti (PRO; 2n = 30♂/NFa = 54) and P. goeldii (2n = 25♂/NFa = 42) and used them in comparative chromosomal mapping. Our analysis reveals that multiple translocations and inversions are responsible for the karyotype diversity of these species, with only three whole-chromosomes conserved between PRO and PGO and eight between PGO and PGG. Our data indicate that multiple sex chromosome systems have originated twice in Proechimys. As small populations are prone to the fixation of chromosomal rearrangements, we speculate that biological features of Rodentia contribute to this fixation. We also highlight the potential of these rodents as a model for studying sex chromosome evolution.
Topics: Animals; Chromosome Inversion; Chromosomes, Mammalian; Evolution, Molecular; Female; Karyotype; Karyotyping; Male; Rodentia; Sex Chromosomes; Translocation, Genetic; X Chromosome
PubMed: 30858413
DOI: 10.1038/s41598-019-40593-8 -
Frontiers in Immunology 2020Ruminants are critical as prey in transferring solar energy fixed by plants into carnivorous species, yet the genetic signature of the driving forces leading to the...
Ruminants are critical as prey in transferring solar energy fixed by plants into carnivorous species, yet the genetic signature of the driving forces leading to the evolutionary success of the huge number of ruminant species remains largely unknown. Here we report a complete DNA map of the major histocompatibility complex (MHC) of the addax () genome by sequencing a total of 47 overlapping BAC clones previously mapped to cover the MHC region. The addax MHC is composed of 3,224,151 nucleotides, harboring a total of 150 coding genes, 50 tRNA genes, and 14 non-coding RNA genes. The organization of addax MHC was found to be highly conserved to those of sheep and cattle, highlighted by a large piece of chromosome inversion that divided the MHC class II into IIa and IIb subregions. It is now highly possible that all of the ruminant species in the family of Bovidae carry the same chromosome inversion in the MHC region, inherited from a common ancestor of ruminants. Phylogenetic analysis indicated that , a ruminant-specific gene located at the boundary of the inversion and highly expressed in dendritic cells, was possibly evolved from , with an estimated divergence time ~140 million years ago. Homology modeling showed that the overall predicted structure of addax DY was similar to that of HLA-DQ2. However, the pocket properties of P1, P4, P6, and P9, which were critical for antigen binding in the addax DY, showed certain distinctive features. Structural analysis suggested that the populations of peptide antigens presented by addax DY and HLA-DQ2 were quite diverse, which in theory could serve to promote microbial regulation in the rumen by ruminant species, contributing to enhanced grass utilization ability. In summary, the results of our study helped to enhance our understanding of the MHC evolution and provided additional supportive evidence to our previous hypothesis that an ancient chromosome inversion in the MHC region of the last common ancestor of ruminants may have contributed to the evolutionary success of current ruminants on our planet.
Topics: Amino Acids; Animals; Antelopes; Chromosome Inversion; Evolution, Molecular; Genome; Major Histocompatibility Complex; Mammals; Phylogeny; RNA, Untranslated; Repetitive Sequences, Nucleic Acid; Ruminants
PubMed: 32161588
DOI: 10.3389/fimmu.2020.00260 -
Molecular Ecology Sep 2022Chromosomal inversions are often thought to facilitate local adaptation and population divergence because they can link multiple adaptive alleles into non-recombining...
Chromosomal inversions are often thought to facilitate local adaptation and population divergence because they can link multiple adaptive alleles into non-recombining genomic blocks. Selection should thus be more efficient in driving inversion-linked adaptive alleles to high frequency in a population, particularly in the face of maladaptive gene flow. But what if ecological conditions and hence selection on inversion-linked alleles change? Reduced recombination within inversions could then constrain the formation of optimal combinations of pre-existing alleles under these new ecological conditions. Here, we outline this idea of inversions limiting adaptation and divergence when ecological conditions change across time or space. We reason and use simulations to illustrate that the benefit of inversions for local adaptation and divergence under one set of ecological conditions can come with a concomitant constraint for adaptation to novel sets of ecological conditions. This limitation of inversions to adaptation may contribute to the maintenance of polymorphism within species.
Topics: Acclimatization; Adaptation, Physiological; Alleles; Chromosome Inversion; Humans; Polymorphism, Genetic
PubMed: 35810344
DOI: 10.1111/mec.16609 -
International Journal of Molecular... Nov 2020Maternal uniparental disomy of chromosome 7 is present in 5-10% of patients with Silver-Russell syndrome (SRS), and duplication of 7p including (Growth Factor...
Maternal uniparental disomy of chromosome 7 is present in 5-10% of patients with Silver-Russell syndrome (SRS), and duplication of 7p including (Growth Factor Receptor-Bound Protein 10), an imprinted gene that affects pre-and postnatal growth retardation, has been associated with the SRS phenotype. Here, we report on a 17 year old girl referred to array-CGH analysis for short stature, psychomotor delay, and relative macrocephaly. Array-CGH analysis showed two copy number variants (CNVs): a ~12.7 Mb gain in 7p13-p11.2, involving and an ~9 Mb loss in 7q11.21-q11.23. FISH experiments performed on the proband's mother showed a chromosome 7 pericentric inversion that might have mediated the complex rearrangement harbored by the daughter. Indeed, we found that segmental duplications, of which chromosome 7 is highly enriched, mapped at the breakpoints of both the mother's inversion and the daughter's CNVs. We postulate that pairing of highly homologous sequences might have perturbed the correct meiotic chromosome segregation, leading to unbalanced outcomes and acting as the putative meiotic mechanism that was causative of the proband's rearrangement. Comparison of the girl's phenotype to those of patients with similar CNVs supports the presence of 7p in a locus associated with features of SRS syndrome.
Topics: Adolescent; Chromosome Inversion; Chromosomes, Human, Pair 7; DNA Copy Number Variations; Female; GRB10 Adaptor Protein; Humans; Meiosis; Mothers; Phenotype; Recombination, Genetic; Silver-Russell Syndrome
PubMed: 33187293
DOI: 10.3390/ijms21228487 -
Radiation Research Apr 2019It has now been over 60 years since U.S. nuclear testing was conducted in the Pacific islands and Nevada, exposing military personnel to varying levels of ionizing...
It has now been over 60 years since U.S. nuclear testing was conducted in the Pacific islands and Nevada, exposing military personnel to varying levels of ionizing radiation. Actual doses are not well-established, as film badges in the 1950s had many limitations. We sought a means of independently assessing dose for comparison with historical film badge records and dose reconstruction conducted in parallel. For the purpose of quantitative retrospective biodosimetry, peripheral blood samples from 12 exposed veterans and 12 age-matched (>80 years) veteran controls were collected and evaluated for radiation-induced chromosome damage utilizing directional genomic hybridization (dGH), a cytogenomics-based methodology that facilitates simultaneous detection of translocations and inversions. Standard calibration curves were constructed from six male volunteers in their mid-20s to reflect the age range of the veterans at time of exposure. Doses were estimated for each veteran using translocation and inversion rates independently; however, combining them by a weighted-average generally improved the accuracy of dose estimations. Various confounding factors were also evaluated for potential effects on chromosome aberration frequencies. Perhaps not surprisingly, smoking and age-associated increases in background frequencies of inversions were observed. Telomere length was also measured, and inverse relationships with both age and combined weighted dose estimates were observed. Interestingly, smokers in the non-exposed control veteran cohort displayed similar telomere lengths as those in the never-smoker exposed veteran group, suggesting that chronic smoking had as much effect on telomere length as a single exposure to radioactive fallout. Taken together, we find that our approach of combined chromosome aberration-based retrospective biodosimetry provided reliable dose estimation capability, particularly on a group average basis, for exposures above statistical detection limits.
Topics: Adult; Aged, 80 and over; Calibration; Chromosome Inversion; Humans; Male; Nuclear Weapons; Occupational Exposure; Radiometry; Retrospective Studies; Telomere; Translocation, Genetic; Veterans
PubMed: 30714852
DOI: 10.1667/RR15240.1 -
G3 (Bethesda, Md.) May 2020Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome...
Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.
Topics: Animals; Chromosome Inversion; Female; Genomics; Linkage Disequilibrium; Male; Oncorhynchus keta; Polymorphism, Single Nucleotide; Sex Chromosomes
PubMed: 32165371
DOI: 10.1534/g3.119.400972 -
Genome Biology and Evolution Jun 2021Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and...
Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and speciation. In particular, inversions are considered to be a major potential cause for chromosomal speciation. There are two closely related, partially sympatric lineages of ascidians in the genus Ciona, which we call type-A and type-B animals in the present study. Although these invertebrate chordates are largely isolated reproductively, hybrids can be found in wild populations, suggesting incomplete prezygotic barriers. Although the genome of type-A animals has been decoded and widely used, the genome for type-B animals has not been decoded at the chromosomal level. In the present study, we sequenced the genomes of two type-B individuals from different sides of the English Channel (in the zone of sympatry with type-A individuals) and compared them at the chromosomal level with the type-A genome. Although the overall structures were well conserved between type A and type B, chromosomal alignments revealed many inversions differentiating these two types of Ciona; it is probable that the frequent inversions have contributed to separation between these two lineages. In addition, comparisons of the genomes between the two type-B individuals revealed that type B had high rates of inversion polymorphisms and nucleotide polymorphisms, and thus type B might be in the process of differentiation into multiple new types or species. Our results suggest an important role of inversions in chromosomal speciation of these broadcasting spawners.
Topics: Animals; Chromosome Inversion; Ciona intestinalis; Genome Size; Polymorphism, Genetic; Sympatry
PubMed: 33822040
DOI: 10.1093/gbe/evab068 -
The Journal of International Medical... Sep 2020The pericentric inversion of chromosome 9 (inv9) is one of the most common structural balanced chromosomal variations, and it is considered to be a normal population...
OBJECTIVE
The pericentric inversion of chromosome 9 (inv9) is one of the most common structural balanced chromosomal variations, and it is considered to be a normal population variant. The aim of this study was to re-evaluate the clinical impact of patients with inv9.
METHODS
We studied the karyotypes from 4853 patients at a single center and retrospectively reviewed their clinical data.
RESULTS
There were 67 inv9 patients among 2988 adults, and 62 of them showed different clinical features, including male and female infertility, oligoasthenozoospermia, and azoospermia. Thirty-one cases of inv9 were found in 1865 fetuses, including two cases in chorionic villus (6.90%) and 29 in amniotic fluid (1.67%), but there were no cases in umbilical cord blood. The rates of fetal phenotype abnormal and adverse pregnancy outcome with inv9 in the chorionic villus were 100.00% (2/2), while only 17.24% (5/29) in the amniotic fluid showed abnormalities, among which 60.00% (3/5) had adverse pregnancy outcomes.
CONCLUSIONS
Although there is no clear evidence that inv9 is pathogenic, the genetic counseling on inv9 in early pregnancy and adults needs to be given more attention.
Topics: Adult; Chromosome Inversion; Chromosomes, Human, Pair 9; Female; Humans; Karyotyping; Male; Pregnancy; Pregnancy Outcome; Retrospective Studies
PubMed: 32957812
DOI: 10.1177/0300060520957820 -
Plant Biotechnology Journal Mar 2024Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates.... (Review)
Review
Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.
Topics: Plant Breeding; Gene Editing; Plants; Chromosome Inversion; Genome, Plant
PubMed: 37961986
DOI: 10.1111/pbi.14224 -
Nature Communications Jul 2023Earthquake focal mechanisms provide critical in-situ insights about the subsurface faulting geometry and stress state. For frequent small earthquakes (magnitude< 3.5),...
Earthquake focal mechanisms provide critical in-situ insights about the subsurface faulting geometry and stress state. For frequent small earthquakes (magnitude< 3.5), their focal mechanisms are routinely determined using first-arrival polarities picked on the vertical component of seismometers. Nevertheless, their quality is usually limited by the azimuthal coverage of the local seismic network. The emerging distributed acoustic sensing (DAS) technology, which can convert pre-existing telecommunication cables into arrays of strain/strain-rate meters, can potentially fill the azimuthal gap and enhance constraints on the nodal plane orientation through its long sensing range and dense spatial sampling. However, determining first-arrival polarities on DAS is challenging due to its single-component sensing and low signal-to-noise ratio for direct body waves. Here, we present a data-driven method that measures P-wave polarities on a DAS array based on cross-correlations between earthquake pairs. We validate the inferred polarities using the regional network catalog on two DAS arrays, deployed in California and each comprising ~ 5000 channels. We demonstrate that a joint focal mechanism inversion combining conventional and DAS polarity picks improves the accuracy and reduces the uncertainty in the focal plane orientation. Our results highlight the significant potential of integrating DAS with conventional networks for investigating high-resolution earthquake source mechanisms.
Topics: Humans; Earthquakes; Chromosome Inversion; Problem Solving; Signal-To-Noise Ratio; Acoustics
PubMed: 37443136
DOI: 10.1038/s41467-023-39639-3