Pericentric Inversion Research Articles

Genome-wide association study reveals structural chromosome variations with phenotypic effects in wheat (Triticum aestivum L.).

Structural chromosome variations (SCVs) are large-scale genomic variations that can be detected by fluorescence insitu hybridization (FISH). SCVs have played important roles in the genome evolution of wheat (Triticum aestivum L.), but little is known about their genetic effects. In this study, a total of 543 wheat accessions from the Chinese wheat mini-core collection and the Shanxi Province wheat collection were used for chromosome analysis using oligonucleotide probe multiplex FISH. A total of 139 SCVs including translocations, pericentric inversions, presence/absence variations (PAVs), and copy number variations (CNVs) in heterochromatin were identified at 230 loci. The distribution frequency of SCVs varied between ecological regions and between landraces and modern cultivars. Structural analysis using SCVs as markers clearly divided the landraces and modern cultivars into different groups. There are very clear instances illustrating alien introgression and wide application of foreign germplasms improved the chromosome diversity of Chinese modern wheat cultivars. A genome-wide association study (GWAS) identified 29 SCVs associated with 12 phenotypic traits, and five (RT4AS•4AL-1DS/1DL•1DS-4AL, Mg2A-3, Mr3B-10, Mr7B-13, and Mr4A-7) of them were further validated using a doubled haploid population and advanced sib-lines, implying the potential value of these SCVs. Importantly, the number of favored SCVs that were associated with agronomic trait improvement was significantly higher in modern cultivars compared to landraces, indicating positive selection in wheat breeding. This study demonstrates the significant effects of SCVs during wheat breeding and provides an efficient method of mining favored SCVs in wheat and other crops.

Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley.

Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.

Novel Non-Coding, Coding and Structural Variants in Hairy Cell Leukemia from Whole Genome Transcriptome Sequencing

Background and Aims Hairy cell leukemia (HCL) is characterized by the BRAF V600E mutation in almost all cases. Other genomic abnormalities include co-mutations in KLF2 and CDKN1B in a proportion of patients (pts) as well as recurrent copy number (CN) abnormalities of 7q and chromosome 5. Targeted genomic approaches to date have not covered the full spectrum of genomic and transcriptomic abnormalities that may be present in HCL, therefore we aimed to comprehensively characterize HCL using whole genome transcriptome sequencing (WGTS) to detect novel genomic abnormalities. Methods WGTS was performed on 59 pts with HCL (peripheral blood [PB] n=36, bone marrow aspirates [BMA] n=23). WGTS libraries were sequenced on a NovaSeq and variant calling of sequence, CN and structural variants (SV) was performed using multiple tools including Strelka, Manta, STAR-Fusion, Arriba and FusionCatcher. ResultsBRAF V600E mutations were detected in all 59 pts. Co-mutations were detected in the known genes KLF2 (8%, 5/59), CDKN1B (8%, 5/59) KMT2C (5%, 3/59) and ARID1A (5%, 3/59). In addition we detected novel recurrently co-mutated genes including the JAK/STAT regulator PTPN6 (7%, 4/59), MAPK pathway regulator DUSP6 (5%, 3/59), SGK1 (5%, 3/59) and ACTB (5%, 3/59). CN abnormalities were detected in 32% (19/59) of pts. The most frequent CN change detected was loss of 7q (n=10) with a minimally deleted region (MDR) of approximately 6.2MB involving the telomere maintenance gene POT1. POT1 gene expression was significantly lower in patients harboring 7q deletion compared to those without (median log2CPM 2.41 vs 2.97, p<0.05). The MDR also involved the putative MAPK pathway inhibitor TMEM229A. Other recurrent CN changes included trisomy 5 (n=3) and monosomy 21 (n=3). Recurrent SVs were observed involving the TERT locus in 5/59 pts (8%) including two pts with chromosomal inversions and three with inter-chromosomal translocations. TERT SVs juxtaposed the TERT locus to known super-enhancers near genes overexpressed in HCL including MEF2C, PLEKHA2 and MTSS1. TERT expression was markedly elevated in pts with TERT SVs compared to those without (median log2CPM 2.2 vs -2.7, p<0.05). Non-coding TERT promoter mutations (TERTpmut) were identified in two patients (chr5:g.1295228G>A). Overall, 16/59 (27%) pts had genomic abnormalities affecting genes involved in telomere biology (including TERT promoter mutations, TERT SVs and deletions involving POT1). In order to exclude low variant allele frequency (VAF) TERTpmut we performed UMI-based error corrected sequencing (sensitivity 0.5% VAF) on an extension cohort of 19 pts with HCL and did not detect any low-level TERTpmut in this group. To understand the specificity of these findings in TERT for HCL, a focused evaluation of WGTS was performed on other patients with chronic B-cell neoplasms for both TERTpmut and TERT SVs resulting in locus transposition to regulatory elements. TERT SVs and/or TERTpmut were detected in 38% (24/64), 18% (7/40), 2% (6/349) and 24% (23/94) of patients with SBLPN (HCLv), SMZL, CLL and MCL respectively. TERT was over-expressed in patients with TERT SVs regardless of histological subtype. Finally, we assessed non-coding variants in pts with HCL by performing an enrichment analysis using bipartite graph models. Using this approach we detected a high frequency of activation-induced cytidine deaminase (AID) induced promoter/enhancer hypermutation of highly expressed genes including RHOH, MTSS1, ZFP36L1, TMSB4X and KLF2. Conclusion WGTS in this large cohort of pts with HCL has revealed a higher degree of genomic complexity than previously elucidated, with novel diverse coding and non-coding changes involving intracellular pathway regulators (DUSP6, PTPN6, TMEM229A), cytoskeletal proteins (ACTB, MTSS1) and recurrent genomic abnormalities affecting genes involved in telomere maintenance (TERT, POT1). Furthermore, our data reveals HCL has a high incidence of superenhancer juxtaposition and hypermutation associated with increased gene expression. These findings provide multiple future directions to investigate the unique biology of HCL and related neoplasms, in particular the specific consequences of regulatory element hypermutation and the avoidance of oncogene-induced senescence through aberrant telomere regulation.

Modeling Premalignant Transformation of Hematopoietic Stem Cells in a Nanobioreactor in Microgravity

Microgravity coupled with increased radiation exposure aboard the ISS provides a unique environment to simulate and study response to injury, inflammatory signaling, aging, and (pre-)malignant transformation of normal human hematopoietic stem cells (HSCs) in an accelerated timeframe. The NASA Twin study suggests that genomic, epigenomic, epitranscriptomic, and proteomic changes may detrimentally impact hematopoietic stem and immune cell fitness and induce stem cell exhaustion (Garrett-Bakelman et al., Science, 2019). Moreover, changes indicative of pre-cancer stem cell generation, such as increased chromosome translocations and inversions, occurred and persisted post-flight. Additionally, a recent publication entitled Multisystem Toxicity in Cancer: Lessons from NASA's Countermeasures Program found significant similarities between the multisystem physiological toxicities experienced in cancer patients as well as during spaceflight (Scott et al, Cell 2019). These reports highlight the benefits of studying injury response, changes in mutational profiles and cancer evolution in microgravity at the stem cell level. For this study, we designed a novel bioreactor system to support the culture of donor-derived human HSCs in low Earth orbit (LEO). A sponge matrix and stromal cells model the microenvironment HSCs reside in within the bone marrow niche. Testing on Earth confirmed our system's ability to maintain stem cell fitness over several weeks. To assess stem cell physiology in LEO over time, we lentivirally transduced a reporter into the HSCs pre-flight (Pineda et al., Scientific Reports 2016), which allows for cell cycle tracking via fluorescence imaging. This will provide data for assessment of stem cell health, maintenance and functionality. Furthermore, we are analyzing cytokine profiles and mutational status post-flight, with a focus on signatures we have previously connected to (pre-)malignant transformation via RNA sequencing analysis (Jiang, Cancer Cell 2019). The first batch of bioreactors launched with the SpX-24 mission in December 2021 and the second batch is currently on orbit as part of the SpX-25 mission. This investigation has the potential to provide valuable insights into the maintenance of hematopoietic stem cell health and functionality, HSC response to injury through accumulation of mutations and, eventually, the mechanisms fueling long-term (pre-)malignant transformation into leukemia stem cells.

CBFB-MYH11 Is Required for the Maintenance of Inv(16) AML

Acute myeloid leukemia (AML) is a heterogenous disease arising from the immature blood cells in the bone marrow. One of the most common chromosomal aberrations, inversion of chromosome 16 [inv(16)], generates the fusion gene Cbfb-MYH11 (CM) which is known to initiate leukemogenesis. Because the fusion protein is invariably found in patients at relapse, it is assumed that CM is also required after leukemic transformation. However, knockdown of CM in the inv(16) immortalized cell line ME-1, caused relatively subtle effects on differentiation but did not affect viability. This raises the possibility that CM may be dispensable after leukemic transformation. To address this possibility in primary leukemia cells, we generated a new knock-in mouse model with the CM fusion gene flanked by loxP sites (CbfbflMYH11). This allows for the fusion gene to be deleted by Cre Recombinase (Cre) after leukemia development. To test the effect of loss of CM in vitro, we transduced Cbfb+/flMYH11 leukemia cells from three independent CbfbflMYH11 mice with a lentivirus expressing Cre. We confirmed the deletion of CM by qPCR and western blot. In Cbfb+/flMYH11, Cre+ cells, we observed a statistically significant increase in Annexin V staining and a decrease in colony forming ability as compared to control Cbfb+/flMYH11 cells. To determine if the colonies that did grow from Cre-infected cells had successfully deleted CM, individual colonies were picked. We found that majority of the colonies retained the unexcised CM allele, but 5-20% of colonies had successfully deleted CM, indicating that a rare population of leukemia cells can survive without CMin vitro. To test the requirement for CM in vivo, we used an inducible shRNA against CM rather than Cre+CbfbflMYH11 leukemia cells, as the inducible knockdown model will allow us to avoid potential defects in engraftment. We transduced CM expressing leukemic cells with a lentiviral construct with a doxycycline (Dox) inducible shRNA against MYH11 (shMYH11) that also expresses GFP. To test the feasibility of this approach in vitro, the sorted shCM+ leukemia cells were incubated with Dox for 48 hours. We found that Cbfb-MYH11 mRNA and protein were decreased in Dox treated leukemia cells, as compared to control cells. In addition, Dox treated shCM+ cells showed increased apoptosis and decreased colony forming ability, similar to Cbfb+/flMYH11Cre+ cells. To test the effect of CM knockdown in vivo, shCM transduced leukemia cells were transplanted into sub-lethally irradiated mice and monitored for leukemic engraftment. Once significant leukemic burden in the peripheral blood was detected, mice were given Dox or vehicle in their drinking water. Starting on day 7, we observed a statistically significant decrease in leukemia burden in Dox treated mice in the peripheral blood and spleen, with the percent of leukemia cells below 5% starting on day 14. In the bone marrow, there was a statistically significant decrease in leukemic burden starting on day 14, but the leukemia cells remained at 30-40% through day 28. Our initial tests indicate that the remaining GFP+ leukemia cells in the bone marrow express reduced levels of CM, implying that these cells may not strictly require the fusion protein or may be able to survive with only low levels of Cbfb-MYH11 activity. In a separate, small cohort of shCM+ transplanted mice, we treated the mice with Dox or control water and monitored for leukemia development. All the control treated mice developed fatal leukemia by day 21, whereas the majority of the Dox treated mice survived until day 42 of treatment. Interestingly, among the 6 Dox treated mice, 2 showed re-emergence of GFP+ leukemia cells in the peripheral blood on day 21 and 28, respectively. We are currently testing whether these relapsed leukemia cells re-express CM. Taken together, our results indicate that Cbfb-MYH11 is largely required for leukemia maintenance, although a subset of cells may be able to survive without the fusion gene. These results imply that drugs targeting the Cbfb-MYH11 have the potential to be effective treatments for inv(16) AML, although substantial inhibition of the fusion protein will likely be needed for effective treatment of the disease.

MYCN Regulates Cell Survival Via EIF4G1 in Inv(16) Acute Myeloid Leukemia

Transcription factors are frequently deregulated in leukemia and are pivotal to its pathogenesis. The core-binding factor (CBF) transcription factor is a heterodimer of CBFβ and RUNX proteins, is critical to hematopoiesis, and dysregulated in AML. The fusion oncogene CBFβ-SMMHC expressed in AML with the chromosome inversion inv(16)(p13q22) acts as a driver oncogene in hematopoietic stem cells by sequestering RUNX1 by protein-protein interaction to induce AML. The CBFβ-SMMHC inhibitor, AI-10-49, specifically disrupts its binding to RUNX1 resulting in genome-wide RUNX1 binding, apoptosis induction, and enhanced survival in inv(16) mouse model [Illendula* and Pulikkan* et al, Science 2015]. While previous studies have demonstrated that AI-10-49 induced cell death is partly mediated by repression of MYC expression in inv(16) AML cells [Pulikkan et al, Cell 2018], the function of other MYC family members, in inv(16) cell survival, and overall in AML, remains poorly understood. By conducting Real Time RT-PCR in CD34+ bone marrow cells from human AML samples, we identified MYCN upregulation in inv(16) AML. Analysis of RNA-seq data from inv(16) AML cells treated with AI-10-49 revealed that MYCN expression is downregulated (7-fold). MYCN silencing via CRISPR/Cas9 induced apoptosis in inv(16) AML cells. Furthermore, MYCN genetic targeting by CRISPR/Cas9-RNP approach in human primary inv(16) AML cells transplanted in humanized NSGS xenograft mouse model displayed significant delay in leukemia development, underlining the role of MYCN in inv(16) AML maintenance. ChIP-seq analysis conducted in inv(16) AML cells treated with AI-10-49 demonstrated increased RUNX1 occupancy at MYCN distal genomic element located at +26 Kb (named 'MYCN-e26') downstream from MYCN TSS without any RUNX1 binding at MYCN TSS. ChIP-seq analysis for histone marks such as H3K27ac and H3K4Me1, and chromatin accessibility by ATAC-seq suggested MYCN-e26 acts as a transcriptionally active enhancer element. Analysis of DNase I hypersensitive sites (DHSs) representing accessible chromatin regions in primary AML samples revealed that MYCN-e26 is a bona fide AML enhancer. Finally, deletion of a genomic element in MYCN-e26 surrounding the RUNX1 binding site (200 bp) by CRISPR/Cas9 genome editing downregulated MYCN transcript levels and inhibited inv(16) AML cell survival. Taken together, MYCN-e26 is instrumental in MYCN transcription and cell survival in inv(16) AML cells as a RUNX1 target. To identify the mechanism(s) by which MYCN regulates inv(16) AML cell survival, we performed CUT&Tag sequencing for MYCN and H3K27ac histone mark in inv(16) AML cells. Gene ontology analysis for MYCN binding peaks in transcriptionally active regions revealed mRNA metabolism and stability as the major pathways orchestrated by MYCN in inv(16) AML cells. By comparing the mRNA metabolism/ stability signature genes with transcripts significantly deregulated in human primary inv(16) AML samples, we identified eukaryotic translation initiation factor 4 gamma 1 (EIF4G1) as one of the major genes regulated by MYCN in inv(16) AML cell survival. Our CUT&Tag sequencing analysis demonstrated MYCN binds to EIF4G1 promoter and enhances its transcription. MYCN silencing by CRISPR/Cas9 approach in inv(16) AML cells showed significant downregulation of EIF4G1, suggesting MYCN is required for EIF4G1 expression in inv(16) AML cells. EIF4G1 genetic silencing via CRISPR/Cas9 approach induced apoptosis in inv(16) AML cells in vitro, and significantly delayed leukemia development in NSGS xenograft mouse model, suggesting EIF4G1 is required for the survival of inv(16) leukemia-initiating cells. Our studies demonstrate that CBFβ-SMMHC modulates MYCN levels by inhibition of RUNX1 binding to MYCN distal enhancer in inv(16) AML cells. In addition, our studies bring novel function of MYCN in inv(16) leukemic cell survival by regulating EIF4G1. Future therapeutic approaches targeting MYCN/EIF4G1 axis in combination with AI-10-49 warrant better clinical outcome for the treatment of inv(16) AML.

Ribosomal RNA operons define a central functional compartment in the Streptomyces chromosome.

Streptomyces are prolific producers of specialized metabolites with applications in medicine and agriculture. These bacteria possess a large linear chromosome genetically compartmentalized: core genes are grouped in the central part, while terminal regions are populated by poorly conserved genes. In exponentially growing cells, chromosome conformation capture unveiled sharp boundaries formed by ribosomal RNA (rrn) operons that segment the chromosome into multiple domains. Here we further explore the link between the genetic distribution of rrn operons and Streptomyces genetic compartmentalization. A large panel of genomes of species representative of the genus diversity revealed that rrn operons and core genes form a central skeleton, the former being identifiable from their core gene environment. We implemented a new nomenclature for Streptomyces genomes and trace their rrn-based evolutionary history. Remarkably, rrn operons are close to pericentric inversions. Moreover, the central compartment delimited by rrn operons has a very dense, nearly invariant core gene content. Finally, this compartment harbors genes with the highest expression levels, regardless of gene persistence and distance to the origin of replication. Our results highlight that rrn operons are structural boundaries of a central functional compartment prone to transcription in Streptomyces.

Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Identification of Plasmodium-resistance genes in malaria vectors remains an elusive goal despite the recent availability of high-quality genomes of several mosquito vectors. Anopheles stephensi, with its three distinctly-identifiable forms at the egg stage, correlating with varying vector competence, offers an ideal species to discover functional mosquito genes implicated in Plasmodium resistance. Recently, the genomes of several strains of An. stephensi of the type-form, known to display high vectorial capacity, were reported. Here, we report a chromosomal-level assembly of an intermediate-form of An. stephensi strain (IndInt), shown to have reduced vectorial capacity relative to a strain of type-form (IndCh). The contig level assembly with a L50 of 4 was scaffolded into chromosomes by using the genome of IndCh as the reference. The final assembly shows a heterozygous paracentric inversion, 3Li, involving 8 Mbp, which is syntenic to the extensively-studied 2La inversion implicated in Plasmodium resistance in An. gambiae involving 21 Mbp. Deep annotation of genes within the 3Li region in the IndInt assembly using the state-of-the-art protein-fold prediction and other annotation tools reveals the presence of a tumor necrosis factor-alpha (TNF-alpha) like gene, which is the homolog of the Eiger gene in Drosophila. Subsequent chromosome-wide searches revealed homologs of Wengen (Wgn) and Grindelwald (Grnd) genes, which are known to be the receptors for Eiger in Drosophila. We have identified all the genes in IndInt required for Eiger-mediated signaling by analogy to the TNF-alpha system, suggesting the presence of a functionally-active Eiger signaling pathway in IndInt. Comparative genomics of the three type-forms with that of IndInt, reveals structurally disruptive mutations in Eiger gene in all three strains of the type-form, suggesting compromised innate immunity in the type-form as the likely cause of high vectorial capacity in these strains. This is the first report of the presence of a homolog of Eiger in malaria vectors, known to be involved in cell death in Drosophila, within an inversion region in IndInt syntenic to an inversion associated with Plasmodium resistance in An. gambiae.

The 8p11 myeloproliferative syndrome: Genotypic and phenotypic classification and targeted therapy

EMS(8p11 myeloproliferative syndrome, EMS) is an aggressive hematological neoplasm with/without eosinophilia caused by a rearrangement of the FGFR1 gene at 8p11-12. It was found that all cases carry chromosome abnormalities at the molecular level, not only the previously reported chromosome translocation and insertion but also a chromosome inversion. These abnormalities produced 17 FGFR1 fusion genes, of which the most common partner genes are ZNF198 on 13q11-12 and BCR of 22q11.2. The clinical manifestations can develop into AML (acute myeloid leukemia), T-LBL (T-cell lymphoblastic lymphoma), CML (chronic myeloid leukemia), CMML (chronic monomyelocytic leukemia), or mixed phenotype acute leukemia (MPAL). Most patients are resistant to traditional chemotherapy, and a minority of patients achieve long-term clinical remission after stem cell transplantation. Recently, the therapeutic effect of targeted tyrosine kinase inhibitors (such as pemigatinib and infigratinib) in 8p11 has been confirmed in vitro and clinical trials. The TKIs may become an 8p11 treatment option as an alternative to hematopoietic stem cell transplantation, which is worthy of further study.

Karyotype differentiation and male meiosis in European clades of the spider genus Pholcus (Araneae, Pholcidae).

Haplogyne araneomorphs are a diverse spider clade. Their karyotypes are usually predominated by biarmed (i.e., metacentric and submetacentric) chromosomes and have a specific sex chromosome system, X1X2Y. These features are probably ancestral for haplogynes. Nucleolus organizer regions (NORs) spread frequently from autosomes to sex chromosomes in these spiders. This study focuses on pholcids (Pholcidae), a highly diverse haplogyne family. Despite considerable recent progress in pholcid cytogenetics, knowledge on many clades remains insufficient including the most species-rich pholcid genus, Pholcus Walckenaer, 1805. To characterize the karyotype differentiation of Pholcus in Europe, we compared karyotypes, sex chromosomes, NORs, and male meiosis of seven species [P.alticeps Spassky, 1932; P.creticus Senglet, 1971; P.dentatus Wunderlich, 1995; P.fuerteventurensis Wunderlich, 1992; P.phalangioides (Fuesslin, 1775); P.opilionoides (Schrank, 1781); P.silvai Wunderlich, 1995] representing the dominant species groups in this region. The species studied show several features ancestral for Pholcus, namely the 2n♂ = 25, the X1X2Y system, and a karyotype predominated by biarmed chromosomes. Most taxa have a large acrocentric NOR-bearing pair, which evolved from a biarmed pair by a pericentric inversion. In some lineages, the acrocentric pair reverted to biarmed. Closely related species often differ in the morphology of some chromosome pairs, probably resulting from pericentric inversions and/or translocations. Such rearrangements have been implicated in the formation of reproductive barriers. While the X1 and Y chromosomes retain their ancestral metacentric morphology, the X2 chromosome shows a derived (acrocentric or subtelocentric) morphology. Pairing of this element is usually modified during male meiosis. NOR patterns are very diverse. The ancestral karyotype of Pholcus contained five or six terminal NORs including three X chromosome-linked loci. The number of NORs has been frequently reduced during evolution. In the Macaronesian clade, there is only a single NOR-bearing pair. Sex chromosome-linked NORs are lost in Madeiran species and in P.creticus. Our study revealed two cytotypes in the synanthropic species P.phalangioides (Madeiran and Czech), which differ by their NOR pattern and chromosome morphology. In the Czech cytotype, the large acrocentric pair was transformed into a biarmed pair by pericentric inversion.

Do chromosomal inversion carriers really need preimplantation genetic testing?

This study aimed to evaluate the rates of euploidy, aneuploidy, and mosaicism in preimplantation genetic testing for structural rearrangements (PGT-SR) cycles from chromosomal inversion carriers. In addition, this work also focused on assessing the impact of some contributors on the incidence of parental originating aneuploidy and mosaicism. This retrospective review enrolled chromosomal inversion carrier couples of whom the females were under 38years old undergoing PGT-SR at a single academic reproductive center. Subgroups were divided according to the gender of carriers, the inversion type, and the semen parameters of male carriers (male factor infertility (MF) or non-MF). Patient demographics, cycle characteristics, and PGT-SR outcomes were compared among subgroups. A total of 71 PGT-SR cycles from 57 inversion carrier couples were included for analysis. Among the 283 blastocysts, 48.4% were identified as euploidy, 27.9% as aneuploidy, and the remaining 23.7% as mosaicism. Only 32.9% of aneuploid embryos and 1.5% of mosaic embryos involved the parental inversion chromosomes. Notably, the female inversion carriers seemed to produce more parental originating aneuploid embryos than male inversion carriers (45.5% vs 23.9%, p = 0.044). The type of inversion and sperm parameters of male chromosomal inversion carriers did not affect the ploidy status of embryos. The incidence of parental originating aneuploidy in inversion carrier couples is lower than expected. For male chromosomal inversion carriers with normal sperm condition whose female partners are under 38years old, natural conception combined with prenatal diagnosis could be provided as an option during fertility counseling.

Constitutional pericentric inversion of chromosome 16, inv(16)(p13.1q22), mimicking acute myeloid leukemia.

An acquired abnormality, inv(16)(p13q22), is a hallmark of acute myeloid leukemia with eosinophilia (AML M4Eo), which leads to leukemogenesis by forming the CBFB::MYH11 fusion gene [1]. We experienced a case of inv(16)(p13.1q22) discovered incidentally during bone marrow examination without evidence of AML. A 64-year-old woman was referred to our hospital because of hypergammaglobulinemia. She was being treated for rheumatoid arthritis, but had no past and family history of AML. Laboratory examination showed polyclonal gammopathy but no significant abnormalities in complete blood count with differential. Bone marrow picture showed a normocellular marrow and mild increase in plasma cells to 3.8% (reference range, 0.2%–1.7%), but no evidence of hematological malignancy. Surprisingly, chromosome analysis of the bone marrow cells revealed that all 20 cells had inv(16)(p13.1q22) mimicking AML M4Eo (Figure 1A). We therefore performed fluorescence in situ hybridization (FISH) analysis of the bone marrow cells by using the Vysis CBFB Dual Color Break Apart Rearrangement Probe (Abbott Molecular Diagnostics, Des Plaines, IL, USA). The splitting of the red and green signals reflecting truncation of the CBFB locus on chromosome 16q22 was not observed (Figure 1B). In addition, a multiplex reverse transcriptase-polymerase chain reaction assay covering 28 leukemia-specific fusion transcripts including CBFB::MYH11 was performed by using the HemaVision-28Q kit (VERITAS, Tokyo, Japan), but none of them was detected. Therefore, it was suggested that the chromosome inversion of this patient did not disrupt the CBFB gene. High-resolution chromosome analysis of the phytohemagglutinin (PHA)-stimulated peripheral blood lymphocytes also revealed inv(16)(p13.1q22) in all 20 cells, indicating a constitutional abnormality of chromosome 16 (Figure 1C). Thus, this patient was not misdiagnosed as AML M4Eo and has been followed up without treatment. To the best of our knowledge, only a few cases with inv(16)(p13q22) unrelated to AML have been reported [2-5]. All of these were concluded to be constitutional abnormalities, and some cases have been confirmed as familial onset. In these reports, there was no misdiagnosis of AML M4Eo in individuals without hematological malignancy, and in the case of chronic myeloid leukemia with t(9;22)(q34;q11) and inv(16)(p13q22), FISH analysis showed no abnormality of the MYH11 gene and inv(16)(p13q22) was also found in her healthy father, which avoided misdiagnosis as an additional cytogenetic abnormality in chronic phase [4]. Therefore, although extremely rare, we should be aware of the presence of constitutional chromosome abnormalities mimicking hematological malignancies, and it is important to perform further tests such as FISH and genomic analysis for differential diagnosis. We thank Yoshiko Sato, MT (LSI Medience Corporation, Tokyo, Japan), for her technical support. The authors declare that there is no conflict of interest. All procedures in this study were performed in accordance with the principles of the Declaration of Helsinki and the institutional guidelines. Informed consent was obtained from the patient and her family. The data that support the findings of this study are available from the corresponding author upon reasonable request.

Replication-associated inversions are the dominant form of bacterial chromosome structural variation.

The structural arrangements of bacterial chromosomes vary widely between closely related species and can result in significant phenotypic outcomes. The appearance of large-scale chromosomal inversions that are symmetric relative to markers for the origin of replication (OriC) has been previously observed; however, the overall prevalence of replication-associated structural rearrangements (RASRs) in bacteria and their causal mechanisms are currently unknown. Here, we systematically identify the locations of RASRs in species with multiple complete-sequenced genomes and investigate potential mediating biological mechanisms. We found that 247 of 313 species contained sequences with at least one large (>50 Kb) inversion in their sequence comparisons, and the aggregated inversion distances away from symmetry were normally distributed with a mean of zero. Many inversions that were offset from dnaA were found to be centered on a different marker for the OriC Instances of flanking repeats provide evidence that breaks formed during the replication process could be repaired to opposing positions. We also found a strong relationship between the later stages of replication and the range in distance variation from symmetry.

The Effect of an Irradiation-Induced Recombination Suppressing Inversion on the Genetic Stability and Biological Quality of a White Eye-Based Aedes aegypti Genetic Sexing Strain.

Simple SummaryAedes aegypti is a vector of viruses transmitting diseases such as dengue, chikungunya, Zika, and yellow fever. Current vector population control methods, based mainly on insecticides, are ineffective and raise concerns due to their negative impact on the environment and human health. In this frame, the sterile insect technique (SIT), which relies on the mass production and release of sterile males to reduce fertile crosses in the natural population, has recently gained increased interest as an environment-friendly, species-specific method. Sterile males are the ‘active’ component of SIT, however, for SIT to be effectively applied in mosquitoes, the efficient elimination of females from the male release batch is a prerequisite, since they are blood-feeders and transmit pathogenic microorganisms. To this end, developing and utilizing genetic sexing strains (GSS) that facilitate sex separation are highly desirable. However, GSS must be stable during rearing and competitive in the field to be considered for operational release projects. Here, we present our findings regarding the genetic stability and biological quality of an Aedes aegypti GSS that is based on the white eye mutation. Moreover, we discuss the effects of the incorporation of a recombination-suppressing inversion on the strain’s biological quality and on important fitness parameters.Aedes aegypti is the primary vector of diseases such as dengue, chikungunya, Zika fever, and yellow fever. The sterile insect technique (SIT) has been proposed as a species-specific and environment-friendly tool for the suppression of mosquito vector populations as a major component of integrated vector management strategies. As female mosquitoes are blood-feeders and may transmit pathogenic microorganisms, mosquito SIT depends on the release of sterile males. Genetic sexing strains (GSS) can be used for the efficient and robust separation of males from females. Two Ae. aegypti GSS were recently developed by exploiting eye colour mutations, resulting in the Red-eye GSS (RGSS) and the White-eye GSS (WGSS). In this study, we compared two WGSS, with and without the chromosomal inversion 35 (Inv35), and evaluated their biological quality, including genetic stability. Our results suggest that the WGSS/Inv35 presents a low recombination rate and long-term genetic stability when recombinants are removed from the colony (filtering) and a slow accumulation of recombinants when they are not removed from the colony (non-filtering). The two strains were similar with respect to fecundity, pupal and adult recovery rates, pupation curve, and pupal weight. However, differences were detected in fertility, survival rate of females, and flight ability of males. The WGSS/Inv35 presented lower fertility, higher survival rate of females, and better flight ability of males compared to the WGSS.

Chromosomal inversion polymorphisms shape the genomic landscape of deer mice

Chromosomal inversions are an important form of structural variation that can affect recombination, chromosome structure and fitness. However, because inversions can be challenging to detect, the prevalence and hence the significance of inversions segregating within species remains largely unknown, especially in natural populations of mammals. Here, by combining population-genomic and long-read sequencing analyses in a single, widespread species of deer mouse (Peromyscus maniculatus), we identified 21 polymorphic inversions that are large (1.5–43.8 Mb) and cause near-complete suppression of recombination when heterozygous (0–0.03 cM Mb−1). We found that inversion breakpoints frequently occur in centromeric and telomeric regions and are often flanked by long inverted repeats (0.5–50 kb), suggesting that they probably arose via ectopic recombination. By genotyping inversions in populations across the species’ range, we found that the inversions are often widespread and do not harbour deleterious mutational loads, and many are likely to be maintained as polymorphisms by divergent selection. Comparisons of forest and prairie ecotypes of deer mice revealed 13 inversions that contribute to differentiation between populations, of which five exhibit significant associations with traits implicated in local adaptation. Taken together, these results show that inversion polymorphisms have a significant impact on recombination, genome structure and genetic diversity in deer mice and likely facilitate local adaptation across the widespread range of this species.

Allele-specific cis-regulatory methylation of the gene for vasoactive intestinal peptide in white-throated sparrows.

White-throated sparrows (Zonotrichia albicollis) offer a unique opportunity to connect genotype with behavioral phenotype. In this species, a rearrangement of the second chromosome is linked with territorial aggression; birds with a copy of this "supergene" rearrangement are more aggressive than those without it. The supergene has captured the gene VIP, which encodes vasoactive intestinal peptide, a neuromodulator that drives aggression in other songbirds. In white-throated sparrows, VIP expression is higher in the anterior hypothalamus of birds with the supergene than those without it, and expression of VIP in this region predicts the level of territorial aggression regardless of genotype. Here, we aimed to identify epigenetic mechanisms that could contribute to differential expression of VIP both in breeding adults, which exhibit morph differences in territorial aggression, and in nestlings, before territorial behavior develops. We extracted and bisulfite-converted DNA from samples of the hypothalamus in wild-caught adults and nestlings and used high-throughput sequencing to measure DNA methylation of a region upstream of the VIP start site. We found that the allele inside the supergene was less methylated than the alternative allele in both adults and nestlings. The differential methylation was attributed primarily to CpG sites that were shared between the alleles, not to polymorphic sites, which suggests that epigenetic regulation is occurring independently of the genetic differentiation within the supergene. This work represents an initial step toward understanding how epigenetic differentiation inside chromosomal inversions leads to the development of alternative behavioral phenotypes.

Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci.

Homomorphic sex chromosomes and their turnover are common in teleosts. We investigated the evolution of nascent sex chromosomes in several populations of two sister species of African annual killifishes, Nothobranchius furzeri and N. kadleci, focusing on their under-studied repetitive landscape. We combined bioinformatic analyses of the repeatome with molecular cytogenetic techniques, including comparative genomic hybridization, fluorescence in situ hybridization with satellite sequences, ribosomal RNA genes (rDNA) and bacterial artificial chromosomes (BACs), and immunostaining of SYCP3 and MLH1 proteins to mark lateral elements of synaptonemal complexes and recombination sites, respectively. Both species share the same heteromorphic XY sex chromosome system, which thus evolved prior to their divergence. This was corroborated by sequence analysis of a putative master sex determining (MSD) gene gdf6Y in both species. Based on their divergence, differentiation of the XY sex chromosome pair started approximately 2 million years ago. In all populations, the gdf6Y gene mapped within a region rich in satellite DNA on the Y chromosome long arms. Despite their heteromorphism, X and Y chromosomes mostly pair regularly in meiosis, implying synaptic adjustment. In N. kadleci, Y-linked paracentric inversions like those previously reported in N. furzeri were detected. An inversion involving the MSD gene may suppress occasional recombination in the region, which we otherwise evidenced in the N. furzeri population MZCS-121 of the Limpopo clade lacking this inversion. Y chromosome centromeric repeats were reduced compared with the X chromosome and autosomes, which points to a role of relaxed meiotic drive in shaping the Y chromosome repeat landscape. We speculate that the recombination rate between sex chromosomes was reduced due to heterochiasmy. The observed differences between the repeat accumulations on the X and Y chromosomes probably result from high repeat turnover and may not relate closely to the divergence inferred from earlier SNP analyses.

Identification and characterization of two DMD pedigrees with large inversion mutations based on a long-read sequencing pipeline.

Pathogenic large inversions are rarely reported on DMD gene due to the lack of effective detection methods. Here we report two DMD pedigrees and proposed a reliable pipeline to define large inversions in DMD patients. In the first pedigree, conventional approaches including multiplex ligation-dependent probe amplification, and whole-exome sequencing by next generation sequencing were failed to detect any pathologic variant. Then an advanced analysis pipeline which consists of RNA-seq, cDNA array capture sequencing, optical mapping, long-read sequencing was built. RNA-seq and cDNA capture sequencing showed a complete absence of transcripts of exons 3-55. Optical mapping identified a 55 Mb pericentric inversion between Xp21 and Xq21. Subsequently, long-read sequencing and Sanger sequencing determined the inversion breakpoints at 32,915,769 and 87,989,324 of the X chromosomes. In the second pedigree, long-read sequencing was directly conducted and Sanger sequencing was performed to verify the mutation. Long-read sequencing and Sanger sequencing found breakpoints at 32,581,576 and 127,797,236 on DMD gene directly. In conclusion, large inversion might be a rare but important mutation type in DMD gene. An effective pipeline was built in detecting large inversion mutations based on long-read sequencing platforms.

Evolution of physical linkage between loci controlling ecological traits and mating preferences.

Coupling of multiple barriers to gene-flow, such as divergent local adaptation and reproductive isolation, facilitates speciation. However, alleles at loci that contribute to barrier effects can be dissociated by recombination. Models of linkage between diverging alleles often consider elements that reduce recombination, such as chromosomal inversions and alleles that modify recombination rate between existing loci. In contrast, here, we consider the evolution of linkage due to the close proximity of loci on the same chromosome. Examples of such physical linkage exist in several species, but in other cases, strong associations are maintained without physical linkage. We use an individual-based model to study the conditions under which the physical linkage between loci controlling ecological traits and mating preferences might be expected to evolve. We modelled a single locus controlling an ecological trait that acts also as a mating cue. Mating preferences are controlled by multiple loci, formed by mutations that are randomly placed in the "genome", within varying distances from the ecological trait locus, allowing us to examine which genomic architectures spread across the population. Our model reveals that stronger physical linkage is favoured when mating preferences and selection are weaker. Under such conditions mating among divergent phenotypes is more frequent, and matching ecological trait and mating preference alleles are more likely to become dissociated by recombination, favouring the evolution of genetic linkage. While most theoretical studies on clustering of divergent loci focus on how physical linkage influences speciation, we show how physical linkage itself can arise, establishing conditions that can favour speciation.

Temperature-associated selection linked to putative chromosomal inversions in king scallop (Pecten maximus).

The genomic landscape of divergence—the distribution of differences among populations or species across the genome—is increasingly characterized to understand the role that microevolutionary forces such as natural selection and recombination play in causing and maintaining genetic divergence. This line of inquiry has also revealed chromosome structure variation to be an important factor shaping the landscape of adaptive genetic variation. Owing to a high prevalence of chromosome structure variation and the strong pressure for local adaptation necessitated by their sessile nature, bivalve molluscs are an ideal taxon for exploring the relationship between chromosome structure variation and local adaptation. Here, we report a population genomic survey of king scallop (Pecten maximus) across its natural range in the northeastern Atlantic Ocean, using a recent chromosome-level genome assembly. We report the presence of at least three large (12–22 Mb), putative chromosomal inversions associated with sea surface temperature and whose frequencies are in contrast to neutral population structure. These results highlight a potentially large role for recombination-suppressing chromosomal inversions in local adaptation and suggest a hypothesis to explain the maintenance of differences in reproductive timing found at relatively small spatial scales across king scallop populations.