Pericentric Inversion Research Articles

Characterization of Dominant Cuticular Hydrocarbons in Inversion and Inversion-Free Strains of <i>Drosophila ananassae</i> (Doleschall)

Cuticular hydrocarbons (CHCs) of Drosophila ananassae (Doleschall) was characterized and identified using gas chromatography and mass spectrometry (GC-MS) analysis. A high % of methyl-branched alkanes were identified in all inversion (2LA, 3LA and 2LA+3LA) and inversion-free strains followed by linear alkanes and alkenes. The present work unfolds the significant patterns of variations in the isomeric forms of methylated alkanes between the inversion and inversion free strains (F-46.6; df-3, p 0.005), and non-significant between the sex (F-2.14; df-1, p 0.2394). But in linear alkanes shows significant variation between the inversion strains (F-30.49; df-3, p 0.009) and between the male and female (F-115.45; df-1, p 0.001) was observed. In particular there is a significant correlation between the chromosomal inversion and synthesis of CHCs in D. ananassae. Unique blend of CHCs in Drosophila performs dual role as desiccation resistance and act as chemical signalling molecule. Linear alkanes are majorly involved in desiccation resistance but in methyl- branched CHCs length variation is a key determinant of desiccation resistance. Presence of longer methyl- branched alkanes and higher desiccation resistance, shorter the carbon chain length act as a signalling molecules. The current study revealed the influence of chromosomal inversion on the cuticular hydrocarbon profile in D. ananassae.

Two large inversions seriously suppress recombination and are essential for key genotype fixation in cabbage (Brassica oleracea L. var. capitata)

Abstract Chromosomal inversion is an important structural variation that usually suppresses recombination and is critical for key genotype fixation. In a previous study, an 11.47 Mb recombination suppression region was identified in the yellow–green leaf locus BoYgl-1 on chromosome 1, but the cause of recombination suppression is still unclear. In this study, chlorophyll and carotenoid contents were found to be significantly decreased in the yellow–green leaf mutant YL-1. Genome assembly and comparative analysis revealed that two large inversions in YL-1 were responsible for the severe recombination suppression in the BoYgl-1 locus. Analyses with inversion-specific markers revealed that the inversions were present in 44 (including all wild cabbage; INV1 and INV2) of 195 cabbage inbred lines and 15 (INV1) ornamental kale inbred lines, indicating that these species with INV1 or INV2 may have evolved much earlier than other types of cabbage. Analyses with inversion-correlated markers revealed that the genotypes of CoINV1, CoINV2 and CoINV3 were highly correlated with INV1 and INV2, indicating that INVs could fix the key genotypes of the involved region. In addition, a 5.87 Mb assembly inversion was identified at the BoYgl-1 locus in the TO1000 genome by genome comparative analysis. This study provides new insight into the recombination suppression mechanism of chromosomal inversion and the application of genome fragment fixation in cabbage breeding.

Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse.

Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine-lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome-level genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked-read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo-overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation.

Preimplantation genetic testing in couples with balanced chromosome rearrangement: a four-year period real world retrospective cohort study

BackgroundCouples with balanced chromosome rearrangement (BCR) are at high risk of recurrent miscarriages or birth defects due to chromosomally abnormal embryos. This study aimed to provide real-world evidence of the euploidy rate of blastocysts from couples with BCR using preimplantation genetic testing (PGT) and to guide pretesting genetic counselling.MethodsA continuous four-year PGT data from couples with BCR were retrospectively analyzed. Biopsied trophectoderm cells were amplified using whole genome amplification, and next-generation sequencing was performed to detect the chromosomal numerical and segmental aberrations. Clinical data and molecular genetic testing results were analyzed and compared among the subgroups.ResultsA total of 1571 PGT cycles with 5942 blastocysts were performed chromosomal numerical and segmental aberrations detection during the four years. Of them, 1034 PGT cycles with 4129 blastocysts for BCR couples were included; 68.96% (713/1034) PGT cycles had transferable euploid embryos. The total euploidy rate of blastocysts in couples carrying the BCR was 35.29% (1457/4129). Couples with complex BCR had euploid blastocyst rates similar to those of couples with non-complex BCR (46.15% vs. 35.18%, P > 0.05). Chromosome inversion had the highest chance of obtaining a euploid blastocyst (57.27%), followed by Robertsonian translocation (RobT) (46.06%), and the lowest in reciprocal translocation (RecT) (30.11%) (P < 0.05). Couples with males carrying RobT had higher rates of euploid embryo both in each PGT cycles and total blastocysts than female RobT carriers did, despite the female age in male RobT is significant older than those with female RobT (P < 0.05). The proportions of non-carrier embryos were 52.78% (95/180) and 47.06% (40/85) in euploid blastocysts from couples with RecT and RobT, respectively (P > 0.05). RecT had the highest proportion of blastocysts with translocated chromosome-associated abnormalities (74.23%, 1527/2057), followed by RobT (54.60%, 273/500) and inversion (30.85%, 29/94) (P < 0.05).ConclusionsIn couples carrying BCR, the total euploidy rate of blastocysts was 35.29%, with the highest in inversion, followed by RobT and RecT. Even in couples carrying complex BCR, the probability of having a transferable blastocyst was 46.15%. Among the euploid blastocysts, the non-carrier ratios in RecT and RobT were 52.78% and 47.06%, respectively. RecT had the highest proportion of blastocysts with translocated chromosome-associated abnormalities.

First Cytogenetic Analysis of Hemidactylus mercatorius Gray, 1842 Provides Insights on Interspecific Chromosomal Diversification in the Genus Hemidactylus (Squamata: Gekkonidae).

This contribution provides the first karyotype description of Hemidactylus mercatorius and discusses the interspecific chromosome diversification in the genus. Chromosomal analysis was performed on samples from different Malagasy populations using standard karyotyping, Ag-NOR staining, and banding methods (sequential C-banding + Giemsa, + Chromomycin A3, +4',6-diamidino-2-phenylindole). Irrespective of sex or sampling locality, H. mercatorius shows a karyotype of 2n = 42 with metacentric (1, 18-21), submetacentric (4), subtelocentric (5, 11), and acrocentric pairs (all the remaining pairs). There was no heteromorphic chromosome pair and no clear distinction between macro- and microchromosomes. NORs were localised close to the centromeres of a medium acrocentric pair (14). Heterochromatic blocks were identified on the telomeric and centromeric regions of most chromosome pairs. A comparison with the karyotype of H. mabouia highlights that the different morphology of several chromosome pairs clearly distinguishes the two species, contrasting the previously proposed synonymy. The differences between the karyotypes of H. mercatorius and H. mabouia concern the number of biarmed and acrocentric elements, suggesting the occurrence of several chromosome inversions. Considering all the available karyotype data on Hemidactylus and its sister genus Cyrtodactylus, it is possible to advance an evolutionary hypothesis on their chromosomal evolution, starting from a common ancestor with 2n = 48 and all acrocentric elements. From this ancestral condition, the karyotype diversification in the two genera has been prevalently characterised by a progressive accumulation of fusions and inversions which have reduced the total chromosome count and increased the number of biarmed chromosomes.

Reproductive isolation in a three-way contact zone.

Contact zones between divergent forms within a species provide insight into the role of gene flow in adaptation and speciation. Previous work has focused on contact zones involving only two divergent forms, but in nature, many more than two populations may overlap simultaneously and experience gene flow. Patterns of introgression in wild populations are, therefore, likely much more complicated than is often assumed. We begin to address this gap in current knowledge by investigating patterns of divergence and introgression across a complex natural contact zone. We use phenotypic and genomic data to confirm the existence of a three-way contact zone among divergent freshwater resident, saltwater resident and saltwater migratory three-spined stickleback (Gasterosteus aculeatus) on the island of North Uist, Scottish Western Isles. We find evidence for hybridization, mostly between saltwater resident and saltwater migratory forms. Despite hybridization, genomic analyses reveal pairwise islands of divergence between all forms that are maintained across the contact zone. Genomic cline analyses also provide evidence for selection and/or hybrid incompatibilities in divergent regions. Divergent genomic regions occur across multiple chromosomes and involve many known adaptive loci and several chromosomal inversions. We also identify distinct immune gene expression profiles between forms, but no evidence for transgressive expression in hybrids. Our results suggest that reproductive isolation is maintained in this three-way contact zone, despite some hybridization, and that reduced recombination in chromosomal inversions may play an important role in maintaining this isolation.

Exploring the impact of pericentric inversion of chromosome 9 on fertility in sperm donors.

Pericentric inversion of chromosome 9 (inv[9]) is a common chromosomal structural variant, but its impact on clinical outcomes remains debated. The screening criteria of sperm banks are rarely mentioned to individuals with inv(9). In this study, we evaluated the fertility of sperm donors with inv(9) who met eligibility criteria for sperm banks (inv[9]-eligible donors). From March 2004 to May 2022, chromosomal analysis of 16 124 sperm donors at CITIC-Xiangya Human Sperm Bank in Hunan Province (Changsha, China) found that 251 (1.6%) had chromosome variations, with inv(9) being the most prevalent at 1.1%. All 169 inv(9)-eligible donors were contacted to collect fertility outcome data, along with 206 eligible donors without inv(9) as controls. In addition, semen samples from inv(9)-eligible donors and eligible donors underwent assessments of sperm fluorescence in situ hybridization (FISH), mitochondrial membrane potential, DNA fragmentation index, acrosome integrity, reactive oxygen species (ROS), and sperm morphology. Results showed that inv(9) did not significantly increase reproductive risks overall. Despite detecting ROS level differences, the clinical impact may be insignificant. This study provides new data on the inv(9) population that can serve as a valuable reference for decision-making by sperm banks as well as for genetic counseling and clinical guidance for individuals carrying inv(9) variant.

Optical Genome Mapping for Chromosomal Aberrations Detection-False-Negative Results and Contributing Factors.

Optical genome mapping (OGM) has been known as an all-in-one technology for chromosomal aberration detection. However, there are also aberrations beyond the detection range of OGM. This study aimed to report the aberrations missed by OGM and analyze the contributing factors. OGM was performed by taking both GRCh37 and GRCh38 as reference genomes. The OGM results were analyzed in blinded fashion and compared to standard assays. Quality control (QC) metrics, sample types, reference genome, effective coverage and classes and locations of aberrations were then analyzed. In total, 154 clinically reported variations from 123 samples were investigated. OGM failed to detect 10 (6.5%, 10/154) aberrations with GRCh37 assembly, including five copy number variations (CNVs), two submicroscopic balanced translocations, two pericentric inversion and one isochromosome (mosaicism). All the samples passed pre-analytical and analytical QC. With GRCh38 assembly, the false-negative rate of OGM fell to 4.5% (7/154). The breakpoints of the CNVs, balanced translocations and inversions undetected by OGM were located in segmental duplication (SD) regions or regions with no DLE-1 label. In conclusion, besides variations with centromeric breakpoints, structural variations (SVs) with breakpoints located in large repetitive sequences may also be missed by OGM. GRCh38 is recommended as the reference genome when OGM is performed. Our results highlight the necessity of fully understanding the detection range and limitation of OGM in clinical practice.

Chromosomal rearrangements played an important role in the speciation of rice rats of genus Cerradomys (Rodentia, Sigmodontinae, Oryzomyini)

Rodents of the genus Cerradomys belong to tribe Oryzomyini, one of the most diverse and speciose groups in Sigmodontinae (Rodentia, Cricetidae). The speciation process in Cerradomys is associated with chromosomal rearrangements and biogeographic dynamics in South America during the Pleistocene era. As the morphological, molecular and karyotypic aspects of Myomorpha rodents do not evolve at the same rate, we strategically employed karyotypic characters for the construction of chromosomal phylogeny to investigate whether phylogenetic relationships using chromosomal data corroborate the radiation of Cerradomys taxa recovered by molecular phylogeny. Comparative chromosome painting using Hylaeamys megacephalus (HME) whole chromosome probes in C. langguthi (CLA), Cerradomys scotii (CSC), C. subflavus (CSU) and C. vivoi (CVI) shows that karyotypic variability is due to 16 fusion events, 2 fission events, 10 pericentric inversions and 1 centromeric repositioning, plus amplification of constitutive heterochromatin in the short arms of the X chromosomes of CSC and CLA. The chromosomal phylogeny obtained by Maximum Parsimony analysis retrieved Cerradomys as a monophyletic group with 97% support (bootstrap), with CSC as the sister to the other species, followed by a ramification into two clades (69% of branch support), the first comprising CLA and the other branch including CVI and CSU. We integrated the chromosome painting analysis of Eumuroida rodents investigated by HME and Mus musculus (MMU) probes and identified several syntenic blocks shared among representatives of Cricetidae and Muridae. The Cerradomys genus underwent an extensive karyotypic evolutionary process, with multiple rearrangements that shaped extant karyotypes. The chromosomal phylogeny corroborates the phylogenetic relationships proposed by molecular analysis and indicates that karyotypic diversity is associated with species radiation. Three syntenic blocks were identified as part of the ancestral Eumuroida karyotype (AEK): MMU 7/19 (AEK 1), MMU 14 (AEK 10) and MMU 12 (AEK 11). Besides, MMU 5/10 (HME 18/2/24) and MMU 8/13 (HME 22/5/11) should be considered as signatures for Cricetidae, while MMU 5/9/14, 5/7/19, 5 and 8/17 for Sigmodontinae.

Translocations and inversions: major chromosomal rearrangements during Vigna (Leguminosae) evolution.

Inversions and translocations are the major chromosomal rearrangements involved in Vigna subgenera evolution, being Vigna vexillata the most divergent species. Centromeric repositioning seems to be frequent within the genus. Oligonucleotide-based fluorescence in situ hybridization (Oligo-FISH) provides a powerful chromosome identification system for inferring plant chromosomal evolution. Aiming to understand macrosynteny, chromosomal diversity, and the evolution of bean species from five Vigna subgenera, we constructed cytogenetic maps for eight taxa using oligo-FISH-based chromosome identification. We used oligopainting probes from chromosomes 2 and 3 of Phaseolus vulgaris L. and two barcode probes designed from V. unguiculata (L.) Walp. genome. Additionally, we analyzed genomic blocks among the Ancestral Phaseoleae Karyotype (APK), two V. unguiculata subspecies (V. subg. Vigna), and V. angularis (Willd.) Ohwi & Ohashi (V. subg. Ceratotropis). We observed macrosynteny for chromosomes 2, 3, 4, 6, 7, 8, 9, and 10 in all investigated taxa except for V. vexillata (L.) A. Rich (V. subg. Plectrotropis), in which only chromosomes 4, 7, and 9 were unambiguously identified. Collinearity breaks involved with chromosomes 2 and 3 were revealed. We identified minor differences in the painting pattern among the subgenera, in addition to multiple intra- and interblock inversions and intrachromosomal translocations. Other rearrangements included a pericentric inversion in chromosome 4 (V. subg. Vigna), a reciprocal translocation between chromosomes 1 and 5 (V. subg. Ceratotropis), a potential deletion in chromosome 11 of V. radiata (L.) Wilczek, as well as multiple intrablock inversions and centromere repositioning via genomic blocks. Our study allowed the visualization of karyotypic patterns in each subgenus, revealing important information for understanding intrageneric karyotypic evolution, and suggesting V. vexillata as the most karyotypically divergent species.

Citogenética comparativa em felídeos (Carnivora: Felidae): Leopardus wiedii, Panthera onca, Puma concolor e Felis catus

ABSTRACT This study aims to conduct a cytogenetic analysis on four South American feline species: the jaguar (Panthera onca), the puma (Puma concolor), the ocelot (Leopardus wiedii), and the domestic cat (Felis catus). We discovered that the jaguar and the puma mainly differ in their fundamental number of chromosomes. Furthermore, we observed a morphological difference in a pair of chromosomes between the jaguar and the domestic cat. This suggests that, over the course of evolution, there was a pericentric inversion in a pair of B4 group chromosomes, leading them to become part of the A group in the jaguar. When analyzing the puma, we noticed the presence of a fourth pair of chromosomes in the E group, along with a deletion in the F group. Additionally, we observed the presence of an additional pair of chromosomes in the C group in the ocelot. Another interesting aspect of the study was the location of nucleolar organizer regions (NORs) on the chromosomes. To elucidate the origin of other chromosome pairs, we employed chromosomal banding techniques, allowing us to better understand the evolution of the C3 pair in the Leopardus genus and the E4 pair in the Puma genus.

Cytogenetic profiles of two circumglobal snake mackerel species (Scombriformes: Gempylidae) from deep waters of the São Pedro and São Paulo Archipelago

Abstract Chromosomal patterns are valuable tools in evolutionary approaches. Despite the remarkable expansion of fish cytogenetic data, they are still highly deficient concerning deep oceanic species, including the Gempylidae snake mackerels. The snake mackerels are important commercial species composed by meso- and bento-pelagic predators with very limited information available about their lifestyle and genetics patterns. This study presents the first chromosomal data of two circumglobal species of this family, Ruvettus pretiosus and Promethichthys prometheus, from the São Pedro and São Paulo Archipelago. Conventional analyses, chromosomal staining with base-specific fluorochromes, and fluorescence in situ hybridization (FISH) for mapping of repetitive DNA classes were used. Both species have 2n = 48 chromosomes, but they highly differ regarding the karyotype formula (FN = 50 and FN = 84). The 18S rDNA/Ag-NOR and the 5S rDNA sites have a syntenic bi-telomeric array in R. pretiosus, but an independent distribution in P. prometheus. The transposable elements are dispersed, while the microsatellites are also clustered in the centromeric and terminal regions of some chromosomes. It is noteworthy that despite the 2n conservation, a marked macro and microstructural diversifications, mainly mediated by pericentric inversions, differentiates the karyotypes of the species, pointing to a particular chromosomal trajectory of the gempylids among marine fish.

Cas12a RNP-mediated co-transformation enables transgene-free multiplex genome editing, long deletions, and inversions in citrus chromosome.

Citrus canker, caused by Xanthomonas citri subsp. citri (Xcc), is a devastating disease worldwide. Previously, we successfully generated canker-resistant Citrus sinensis cv. Hamlin lines in the T0 generation. This was achieved through the transformation of embryogenic protoplasts using the ribonucleoprotein (RNP) containing Cas12a and one crRNA to edit the canker susceptibility gene, CsLOB1, which led to small indels. Here, we transformed embryogenic protoplasts of Hamlin with RNP containing Cas12a and three crRNAs. Among the 10 transgene-free genome-edited lines, long deletions were obtained in five lines. Additionally, inversions were observed in three of the five edited lines with long deletions, but not in any edited lines with short indel mutations, suggesting long deletions maybe required for inversions. Biallelic mutations were observed for each of the three target sites in four of the 10 edited lines when three crRNAs were used, demonstrating that transformation of embryogenic citrus protoplasts with Cas12a and three crRNAs RNP can be very efficient for multiplex editing. Our analysis revealed the absence of off-target mutations in the edited lines. These cslob1 mutant lines were canker- resistant and no canker symptoms were observed after inoculation with Xcc and Xcc growth was significantly reduced in the cslob1 mutant lines compared to the wild type plants. Taken together, RNP (Cas12a and three crRNAs) transformation of embryogenic protoplasts of citrus provides a promising solution for transgene-free multiplex genome editing with high efficiency and for deletion of long fragments.

Geographically variable mate preferences shed light on the processes maintaining inversion polymorphism

Abstract An important question in evolution is to understand the mechanisms that maintain phenotypic diversity, despite selection that should drive homogeneity. For example, selection by predators may promote the convergence of colour patterns among defended prey, resulting in the formation of mimetic communities. However, certain aposematic species, such as the Neotropical butterfly Heliconius numata, are polymorphic. In H. numata, wing pattern polymorphism, which is associated with chromosomal inversions, may be maintained via disassortative mating preferences, thought to favour the co-occurrence of individuals with different mimicry phenotypes in Peru. To test whether environmental variation due to geography influences mate choice, here we investigate the occurrence of disassortative mating among the two coexisting forms of H. numata in French Guiana, and its potential role in the maintenance of this polymorphism. Our experimental approach demonstrates that the two forms display weak and slightly asymmetrical disassortative mate preferences. Modelling and simulations suggest that this pattern of mate preference alone is not sufficient to maintain polymorphism, and predict the loss of the choosiest form, unless this form enjoys a survival advantage. In this aposematic species, such an advantage could arise from mimicry, but further studies into the benefits of mimicry and predator generalization are needed to test this hypothesis. More importantly, our results suggest that the balance between selective forces influencing polymorphism may vary across geographical and ecological contexts, and this warrants further study.

Impact of Z chromosome inversions on gene expression in testis and liver tissues in the zebra finch.

Chromosomal inversions have been identified in many natural populations and can be responsible for novel traits and rapid adaptation. In zebra finch, a large region on the Z chromosome has been subject to multiple inversions, which have pleiotropic effects on multiple traits but especially on sperm phenotypes, such as midpiece and flagellum length. To understand the effect, the Z inversion has on these traits, we examined testis and liver transcriptomes of young males at different maturation times. We compared gene expression differences among three inversion karyotypes: AA, B*B* and AB*, where B* denotes the inverted regions on Z with respect to A. In testis, 794 differentially expressed genes were found and most of them were located on chromosome Z. They were functionally enriched for sperm-related traits. We also identified clusters of co-expressed genes that matched with the inversion-related sperm phenotypes. In liver, there were some enriched functions and some overrepresentation on chromosome Z with similar location as in testis. In both tissues, the overrepresented genes were located near the distal end of Z but also in the middle of the chromosome. For the heterokaryotype, we observed several genes with one allele being dominantly expressed, similar to expression patterns in one or the other homokaryotype. This was confirmed with SNPs for three genes, and interestingly one gene, DMGDH, had allele-specific expression originating mainly from one inversion haplotype in the testis, yet both inversion haplotypes were expressed equally in the liver. This karyotype-specific difference in tissue-specific expression suggests a pleiotropic effect of the inversion and thus suggests a mechanism for divergent phenotypic effects resulting from an inversion.

Chromosome 9 aberrations diagnosed at a pediatric hospital in Tabasco, Mexico

Objective. To determine the frequency of patients diagnosed with chromosome 9 disorders in a pediatric hospital between the years 2012 and 2022. Materials and methods. A cross-sectional and descriptive study was performed in 2932 patients who attended the genetics consultation of a pediatric hospital in Tabasco, Mexico, from January 2012 to December 2022, based on the results of chromosomal diagnosis in peripheral blood. Results. Chromosomal alterations were present in 14.76% (433/2932). The most frequently involved chromosome was number 21 in 83.37% (361/433), followed by sex chromosome X with 5.31% (23/433) and chromosome 9 with 3.69% (16/433). Regarding chromosome 9, 50% (8/16) corresponded to morphological variants (9qh+), followed by pericentric inversion in 3 of the cases (18.75%), deletion in 2 (12.5%), insertion in 1 (6.6%), ring in 1 (6.6%), and a shunt (6.6%). Conclusion. The cytogenetic results found, according to the patients' reasons for referral, suggest the performance of peripheral blood karyotyping as a useful tool in the diagnosis of diseases with genetic suspicion. Key words: Chromosomal inversion; Karyotype; Infertility.

Genetic counseling for pre-implantation genetic testing of monogenic disorders (PGT-M).

Pre-implantation genetic testing (PGT) is a vital tool in preventing chromosomal aneuploidies and other genetic disorders including those that are monogenic in origin. It is performed on embryos created by intracytoplasmic sperm injection (ICSI). Genetic counseling in the area of assisted reproductive technology (ART) has also evolved along with PGT and is considered an essential and integral part of Reproductive Medicine. While PGT has the potential to prevent future progeny from being affected by genetic conditions, genetic counseling helps couples understand and adapt to the medical, psychological, familial and social implications of the genetic contribution to disease. Genetic counseling is particularly helpful for couples with recurrent miscarriages, advanced maternal age, a partner with a chromosome translocation or inversion, those in a consanguineous marriage, and those using donor gametes. Partners with a family history of genetic conditions including hereditary cancer, late onset neurological diseases and with a carrier status for monogenic disorders can benefit from genetic counseling when undergoing PGT for monogenic disorders (PGT-M). Genetic counseling for PGT is useful in cases of Mendelian disorders, autosomal dominant and recessive conditions and sex chromosome linked disorders and for the purposes of utilizing HLA matching technology for creating a savior sibling. It also helps in understanding the importance of PGT in cases of variants of uncertain significance (VUS) and variable penetrance. The possibilities and limitations are discussed in detail during the sessions of genetic counseling.

Drosophila melanogaster Transcriptome Response to Different Wolbachia Strains.

Wolbachia is a maternally inherited, intercellular bacterial symbiont of insects and some other invertebrates. Here, we investigated the effect of two different Wolbachia strains, differing in a large chromosomal inversion, on the differential expression of genes in D. melanogaster females. We revealed significant changes in the transcriptome of the infected flies compared to the uninfected ones, as well as in the transcriptome of flies infected with the Wolbachia strain, wMelPlus, compared to flies infected with the wMelCS112 strain. We linked differentially expressed genes (DEGs) from two pairwise comparisons, "uninfected-wMelPlus-infected" and "uninfected-wMelCS112-infected", into two gene networks, in which the following functional groups were designated: "Proteolysis", "Carbohydrate transport and metabolism", "Oxidation-reduction process", "Embryogenesis", "Transmembrane transport", "Response to stress" and "Alkaline phosphatases". Our data emphasized similarities and differences between infections by different strains under study: a wMelPlus infection results in more than double the number of upregulated DEGs and half the number of downregulated DEGs compared to a wMelCS112 infection. Thus, we demonstrated that Wolbachia made a significant contribution to differential expression of host genes and that the bacterial genotype plays a vital role in establishing the character of this contribution.

Impact of population structure in the estimation of recent historical effective population size by the software GONE

BackgroundEffective population size (Ne) is a crucial parameter in conservation genetics and animal breeding. A recent method, implemented by the software GONE, has been shown to be rather accurate in estimating recent historical changes in Ne from a single sample of individuals. However, GONE estimations assume that the population being studied has remained isolated for a period of time, that is, without migration or confluence of other populations. If this occurs, the estimates of Ne can be heavily biased. In this paper, we evaluate the impact of migration and admixture on the estimates of historical Ne provided by GONE through a series of computer simulations considering several scenarios: (a) the mixture of two or more ancestral populations; (b) subpopulations that continuously exchange individuals through migration; (c) populations receiving migrants from a large source; and (d) populations with balanced systems of chromosomal inversions, which also generate genetic structure.ResultsOur results indicate that the estimates of historical Ne provided by GONE may be substantially biased when there has been a recent mixture of populations that were previously separated for a long period of time. Similarly, biases may occur when the rate of continued migration between populations is low, or when chromosomal inversions are present at high frequencies. However, some biases due to population structuring can be eliminated by conducting population structure analyses and restricting the estimation to the differentiated groups. In addition, disregarding the genomic regions that are involved in inversions can also remove biases in the estimates of Ne.ConclusionsDifferent kinds of deviations from isolation and panmixia of the populations can generate biases in the recent historical estimates of Ne. Therefore, estimation of past demography could benefit from performing population structure analyses beforehand, by mitigating the impact of these biases on historical Ne estimates.

Examination of Large Chromosomal Inversions in the Genome of Erwinia amylovora Strains Reveals Worldwide Distribution and North America-Specific Types.

Erwinia amylovora is a relatively homogeneous species with low genetic diversity at the nucleotide level. However, phenotypic differences and genomic structural variations among E. amylovora strains have been documented. In this study, we identified 10 large chromosomal inversion (LCI) types in the Spiraeoideae-infecting (SI) E. amylovora strains by combining whole genome sequencing and PCR-based molecular markers. It was found that LCIs were mainly caused by homologous recombination events among seven rRNA operons (rrns) in SI E. amylovora strains. Although ribotyping results identified inter- and intra-variations in the internal transcribed spacer (ITS1 and ITS2) regions among rrns, LCIs tend to occur between rrns transcribed in the opposite directions and with the same tRNA content (tRNA-Glu or tRNA-Ile/Ala) in ITS1. Based on the LCI types, physical/estimated replichore imbalance (PRI/ERI) was examined and calculated. Among the 117 SI strains evaluated, the LCI types of Ea1189, CFBP1430, and Ea273 were the most common, with ERI values at 1.31, 7.87, and 4.47°, respectively. These three LCI types had worldwide distribution, whereas the remaining seven LCI types were restricted to North America (or certain regions of the United States). Our results indicated ongoing chromosomal recombination events in the SI E. amylovora population and showed that LCI events are mostly symmetrical, keeping the ERI less than 15°. These findings provide initial evidence about the prevalence of certain LCI types in E. amylovora strains, how LCI occurs, and its potential evolutionary advantage and history, which might help track the movement of the pathogen.