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The article announces the winners of Development's Outstanding Paper Prize for papers published in 2023. The winning papers focus on developmental and stem cell biology. One paper demonstrates the potential of genome engineering techniques and pharmacological upregulation of the Wnt signaling pathway in treating frizzled 2-associated congenital malformations in mouse models. Another paper explores how Frizzled2 receives WntA signaling during butterfly wing pattern formation, providing insights into the complexity and evolution of signaling pathways. The article also mentions a study on the development of primordial germ cell-like cells using stem cell technologies. Additionally, the article discusses a study on the molecular functioning of WntA in butterfly wing color patterning, which involved collaboration between international teams and faced challenges in rearing and injecting butterflies in the lab. The researchers plan to further investigate butterfly color patterns. [Extracted from the article]

The sex chromosomes of skinks are usually poorly differentiated and hardly distinguished by cytogenetic methods. Therefore, identifying sex chromosomes in species lacking easily recognizable heteromorphic sex chromosomes is necessary to fully understand sex chromosome diversity. In this paper, we employed cytogenetics, sex quantification of genes, and transcriptomic approaches to characterize the sex chromosomes in Plestiodon elegans. Cytogenetic examination of metaphases revealed a diploid number of 2n = 26, consisting of 12 macrochromosomes and 14 microchromosomes, with no significant heteromorphic chromosome pairs, speculating that the sex chromosomes may be homomorphic or poorly differentiated. The results of the sex quantification of genes showed that Calumenin (calu), COPI coat complex subunit γ 2 (copg2), and Smoothened (smo) were at half the dose in males as in females, suggesting that they are on the X chromosome. Transcriptomic data analysis from the gonads yielded the excess expression male-specific genes (n = 16), in which five PCR molecular markers were developed. Restricting the observed heterozygosity to males suggests the presence of homomorphic sex chromosomes in P. elegans, XX/XY. This is the first breakthrough in the study of the sex chromosomes of Plestiodon. [ABSTRACT FROM AUTHOR]

In the diffusion approximation of the neutral Wright–Fisher model, the expected time until fixation or loss of a neutral allele is proportional to the initial entropy of the distribution of the allele in the population. No explanation is known for this coincidence. In this paper, we show that the rate of entropy dissipation is proportional to the number of segregating alleles. Since the final fixed state has zero entropy, the expected lifetime of segregating alleles is proportional to the initial entropy in the system. We show that classical formulae on the average time to loss of segregating alleles and the expected time to fixation of the last segregating allele stem from these properties of the diffusion process. We also extend our results to the case of population size changing in time. The dissipation of heterozygosity and entropy shows that superlinear population growth leads to infinite expected fixation times, i.e., neutral alleles in fast-growing populations could segregate forever without ever becoming fixed or disappearing by genetic drift. [ABSTRACT FROM AUTHOR]

In their paper, using zebrafish models, Gioacchino et al. have demonstrated the GATA2 haploinsufficiency, the genetic hallmark of GATA2 deficiency syndrome, promotes erythroid and myeloid cytopenia, and have discovered a self‐regulatory mechanism to compensate GATA2 levels and protein function. Commentary on: Gioacchino et al. GATA2 heterozygosity causes an epigenetic feedback mechanism resulting in myeloid and erythroid dysplasia. Br J Haematol 2024;205:580‐593. [ABSTRACT FROM AUTHOR]

Wisent Bison bonasus is an example of a species saved from extinction and reintroduced into nature after a few decades of captive breeding. There were only twelve founders of the Lowland–Caucasian line (LC) and even fewer (seven out of twelve) of Lowland (LB) animals. The genetic diversity in studies based on pedigree or markers is very low. In this paper, we present a summary of the long-term genetic monitoring conducted for the worldwide population of European bison. We summarized the long-term genetic monitoring studies conducted on the worldwide population of wisents to date. We genotyped 2227 wisents from two genetic lines (LC and LB) and different populations at ten microsatellite loci. We found low polymorphism, with only 2.7 alleles per locus, and much lower values of observed heterozygosity (0.380 and 0.348 in the LC and LB lines, respectively) than expected heterozygosity. The difference between the lines is only noticeable in allele proportions, so the number of markers is not enough to distinguish the two genetic lines. We also present the genetic distance among four free-roaming populations that are geographically close to each other. We found that the genetic distance of one of them is larger than that of the others, which could be the effect of genetic drift. [ABSTRACT FROM AUTHOR]

(1) Background: Germline variants in BRCA1/BRCA2 genes explain about 20% of hereditary breast/ovarian cancer (HBOC) cases. In the present paper, we aim to identify genetic determinants in BRCA-negative families from the South of Tunisia. (2) Methods: Exome Sequencing (ES) was performed on the lymphocyte DNA of patients negative for BRCA mutations from each Tunisian family with a high risk of HBOC. (3) Results: We focus on the canonical genes associated with HBOC and identified missense variants in DNA damage response genes, such as ATM, RAD52, and RAD54; however, no variants in PALB2, Chek2, and TP53 genes were found. To identify novel candidate genes, we selected variants harboring a loss of function and identified 17 stop-gain and 11 frameshift variants in genes not commonly known to be predisposed to HBOC. Then, we focus on rare and high-impact genes shared by at least 3 unrelated patients from each family and selected 16 gene variants. Through combined data analysis from MCODE with gene ontology and KEGG pathways, a short list of eight candidate genes (ATM, EP300, LAMA1, LAMC2, TNNI3, MYLK, COL11A2, and LAMB3) was created. The impact of the 24 selected genes on survival was analyzed using the TCGA data resulting in a selection of five candidate genes (EP300, KMT2C, RHPN2, HSPG2, and CCR3) that showed a significant association with survival. (4) Conclusions: We identify novel candidate genes predisposed to HBOC that need to be validated in larger cohorts and investigated by analyzing the co-segregation of selected variants in affected families and the locus-specific loss of heterozygosity to highlight their relevance for HBOC risk. [ABSTRACT FROM AUTHOR]

The use of genomic data makes it possible to examine genetic variability and calculate the genetic parameters of the population in an efficient and precise way. The aim of this research was to analyse linkage disequilibrium (LD), contemporary effective population size (Nec), haplotype block structure, minor allele frequency (MAF), observed (HO) and expected heterozygosity (HE), calculate the genomic relationship matrix and perform a principal component analysis (PCA) in the Serbian Holstein-Friesian cattle population using SNP data from the GGP Bovine 100K chip. After quality control (QC), 83 208 SNPs and 1 575 cows were retained for further analysis. LD on autosomes had an average value of ≥ 0.2 up to a distance of 50--60 kb (r² = 0.211), while on BTX r² ≥ 0.2 was represented at distances of 80--90 kb (r² = 0.211). LD differed between chromosomes. The average HO for autosomes and X chromosome SNPs was 0.412 and 0.422, respectively. 81.30% of SNPs that passed QC had MAF > 0.2. The total number of haplotype blocks in the studied population was 15 642. On average, blocks contained 2.932 SNPs. The average block length was 32.657 kb and ranged from a minimum of 0.019 kb (BTA21 and BTA26) to a maximum of 999.562 kb (BTX). The estimated value of Nec in the this cattle population was 142. The results of PCA showed a significant variability of genotypes in the population, but there was no clear stratification of the population. The obtained results will serve as a basis for future genomic analyses such as the detection of QTLs for important economic traits and the implementation of genomic selection. [ABSTRACT FROM AUTHOR]

Identifying mechanisms that drive population divergence under varying geographic and ecological scenarios can inform our understanding of evolution and speciation. In particular, analysis of genetic data from island populations with known colonisation timelines allows us to identify potential source populations of diverging island subspecies and current relationships among populations. Silvereyes (Zosterops lateralis) are a small passerine that have served as a valuable study system to investigate evolutionary patterns on both large and small geographic scales. We examined genetic relatedness and diversity of two silvereye subspecies, the mainland Z. l. cornwalli and island Z. l. chlorocephalus, and used 18 077 single nucleotide polymorphisms (SNPs), to compare locations across southeast Queensland, Australia. Although silvereyes are prolific island colonisers our findings revealed population divergence over relatively small spatial scales was strongly influenced by geographic isolation mediated by water barriers. Strong genetic connectivity was displayed between mainland sites, but minimal inter-island connectivity was shown despite comparable sampling distances. Genetic diversity analysis showed little difference in heterozygosity between island and mainland populations, but lower inbreeding scores among the island populations. Our study confirmed the range of the Z. l. chlorocephalus subspecies throughout the southern Great Barrier Reef. Our results show that water barriers and not geographic distance per se are important in driving incipient divergence in island populations. This helps to explain the relatively high number of phenotypically differentiated, but often geographically proximate, island silvereye subspecies compared to a lower number of phenotypically less well-defined Australian continental subspecies. [ABSTRACT FROM AUTHOR]

Cockayne syndrome (CS) is a rare autosomal recessive disorder caused by mutations in ERCC8 or ERCC6. Most pathogenic variants in ERCC8 are single nucleotide substitutions. Structural variants (SVs) have been reported in patients with ERCC8-related CS. However, comprehensive molecular detection, including SVs of ERCC8, in CS patients remains problematic. Herein, we present three Japanese patients with ERCC8-related CS in whom causative SVs were identified using whole-exome-based copy number variation (CNV) detection tools. One patient showed compound heterozygosity for a 259-kb deletion and a deletion of exon 4 which has previously been reported as an Asia-specific variant. The other two patients were homozygous for the same exon 4 deletion. The exon 4 deletion was detected only by the ExomeDepth software. Intrigued by the discrepancy in the detection capability of various tools for the SVs, we evaluated the analytic performance of four whole-exome-based CNV detection tools using an exome data set from 337 healthy individuals. A total of 1,278,141 exons were predicted as being affected by the 4 CNV tools. Interestingly 95.1% of these affected exons were detected by one tool alone. Thus, we expect that the use of multiple tools may improve the detection rate of SVs from aligned exome data. [ABSTRACT FROM AUTHOR]

Background: Recently, the substitution R1051Q in VEGFR2 has been described as a cancer-associated "gain of function" mutation. VEGFR2R1051Q phosphorylation is ligand-independent and enhances the activation of intracellular pathways and cell growth both in vitro and in vivo. In cancer, this mutation is found in heterozygosity, suggesting that an interaction between VEGFR2R1051Q and VEGFR2WT may occur and could explain, at least in part, how VEGFR2R1051Q acts to promote VEGFR2 signaling. Despite this, the biochemical/biophysical mechanism of the activation of VEGFR2R1051Q remains poorly understood. On these bases, the aim of our study is to address how VEGFR2R1051Q influences the biophysical behavior (dimerization and membrane dynamics) of the co-expressed VEGFR2WT. Methods: We employed quantitative FLIM/FRET and FRAP imaging techniques using CHO cells co-transfected with the two forms of VEGFR2 to mimic heterozygosity. Results: Membrane protein biotinylation reveals that VEGFR2WT is more exposed on the cell membrane with respect to VEGFR2R1051Q. The imaging analyses show the ability of VEGFR2WT to form heterodimers with VEGFR2R1051Q and this interaction alters its membrane dynamics. Indeed, when the co-expression of VEGFR2WT/VEGFR2R1051Q occurs, VEGFR2WT shows reduced lateral motility and a minor pool of mobile fraction. Conclusions: This study demonstrates that active VEGFR2R1051Q can affect the membrane behavior of the VEGFR2WT. [ABSTRACT FROM AUTHOR]

This study is the first report to characterize the Rhodus uyekii genome and study the development of microsatellite markers and their markers applied to the genetic structure of the wild population. Genome assembly was based on PacBio HiFi and Illumina HiSeq paired-end sequencing, resulting in a draft genome assembly of R. uyekii. The draft genome was assembled into 2652 contigs. The integrity assessment of the assemblies indicates that the quality of the draft assemblies is high, with 3259 complete BUSCOs (97.2%) in the database of Verbrata. A total of 31,166 predicted protein-coding genes were annotated in the protein database. The phylogenetic tree showed that R. uyekii is a close but distinct relative of Onychostoma macrolepis. Among the 10 fish genomes, there were significant gene family expansions (8–2387) and contractions (16–2886). The average number of alleles amplified by the 21 polymorphic markers ranged from 6 to 23, and the average PIC value was 0.753, which will be useful for evolutionary and genetic analysis. Using population genetic analysis, we analyzed genetic diversity and the genetic structures of 120 individuals from 6 populations. The average number of alleles per population ranged from 7.6 to 9.9, observed heterozygosity ranged from 0.496 to 0.642, and expected heterozygosity ranged from 0.587 to 0.783. Discriminant analysis of principal components According to the analysis method, the population was divided into three populations (BS vs. DC vs. GG, GC, MS, DC). In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of R. uyekii. [ABSTRACT FROM AUTHOR]

Patterns of genetic variation reflect interactions among microevolutionary forces that vary in strength with changing demography. Here, patterns of variation within and among samples of the mouthbrooding gafftopsail catfish (Bagre marinus, Family Ariidae) captured in the U.S. Atlantic and throughout the Gulf of Mexico were analyzed using genomics to generate neutral and non‐neutral SNP data sets. Because genomic resources are lacking for ariids, linkage disequilibrium network analysis was used to examine patterns of putatively adaptive variation. Finally, historical demographic parameters were estimated from site frequency spectra. The results show four differentiated groups, corresponding to the (1) U.S. Atlantic, and the (2) northeastern, (3) northwestern, and (4) southern Gulf of Mexico. The non‐neutral data presented two contrasting signals of structure, one due to increases in diversity moving west to east and north to south, and another to increased heterozygosity in the Atlantic. Demographic analysis suggested that recently reduced long‐term effective population size in the Atlantic is likely an important driver of patterns of genetic variation and is consistent with a known reduction in population size potentially due to an epizootic. Overall, patterns of genetic variation resemble that of other fishes that use the same estuarine habitats as nurseries, regardless of the presence/absence of a larval phase, supporting the idea that adult/juvenile behavior and habitat are important predictors of contemporary patterns of genetic structure. Gafftopsail catfish show high levels of genetic structuring across their distribution in the U.S., Atlantic and Gulf of Mexico. Non‐neutral data present two contrasting signals of structure and historical demography is likely an important driver of patterns of neutral and non‐neutral genetic variation. Results of this study are similar to what is seen in other fishes that use the same estuarine habitats as nurseries, but gafftopsail catfish lack a larval phase, supporting the idea that adult/juvenile behavior and habitat use are important predictors of contemporary patterns of genetic structure. [ABSTRACT FROM AUTHOR]

There are two primary measures of the amount of genetic variation in a population at a locus: heterozygosity and the number of alleles. Effective population size (Ne) provides both an expectation of the amount of heterozygosity in a population at drift‐mutation equilibrium and the rate of loss of heterozygosity because of genetic drift. In contrast, the number of alleles in a population at drift‐mutation equilibrium is a function of both Ne and census size (NC). In addition, populations with the same Ne can lose allelic variation at very different rates. Allelic variation is generally much more sensitive to bottlenecks than heterozygosity. Expressions used to adjust for the effects of violations of the ideal population on Ne do not provide good predictions of the loss of allelic variation. These effects are much greater for loci with many alleles, which are often important for adaptation. We show that there is a linear relationship between the reduction of NC and the corresponding reduction of the expected number of alleles at drift‐mutation equilibrium. This makes it possible to predict the expected effect of a bottleneck on allelic variation. Heterozygosity provides good estimates of the rate of adaptive change in the short‐term, but allelic variation provides important information about long‐term adaptive change. The guideline of long‐term Ne being greater than 500 is often used as a primary genetic metric for evaluating conservation status. We recommend that this guideline be expanded to take into account allelic variation as well as heterozygosity. [ABSTRACT FROM AUTHOR]

Background: The absence of heterozygosity (AOH) is a kind of genomic change characterized by a long contiguous region of homozygous alleles in a chromosome, which may cause human genetic disorders. However, no method of low-pass whole genome sequencing (LP-WGS) has been reported for the detection of AOH in a low-pass setting of less than onefold. We developed a method, termed CNVseq-AOH, for predicting the absence of heterozygosity using LP-WGS with ultra-low sequencing data, which overcomes the sparse nature of typical LP-WGS data by combing population-based haplotype information, adjustable sliding windows, and recurrent neural network (RNN). We tested the feasibility of CNVseq-AOH for the detection of AOH in 409 cases (11 AOH regions for model training and 863 AOH regions for validation) from the 1000 Genomes Project (1KGP). AOH detection using CNVseq-AOH was also performed on 6 clinical cases with previously ascertained AOHs by whole exome sequencing (WES). Results: Using SNP-based microarray results as reference (AOHs detected by CNVseq-AOH with at least a 50% overlap with the AOHs detected by chromosomal microarray analysis), 409 samples (863 AOH regions) in the 1KGP were used for concordant analysis. For 784 AOHs on autosomes and 79 AOHs on the X chromosome, CNVseq-AOH can predict AOHs with a concordant rate of 96.23% and 59.49% respectively based on the analysis of 0.1-fold LP-WGS data, which is far lower than the current standard in the field. Using 0.1-fold LP-WGS data, CNVseq-AOH revealed 5 additional AOHs (larger than 10 Mb in size) in the 409 samples. We further analyzed AOHs larger than 10 Mb, which is recommended for reporting the possibility of UPD. For the 291 AOH regions larger than 10 Mb, CNVseq-AOH can predict AOHs with a concordant rate of 99.66% with only 0.1-fold LP-WGS data. In the 6 clinical cases, CNVseq-AOH revealed all 15 known AOH regions. Conclusions: Here we reported a method for analyzing LP-WGS data to accurately identify regions of AOH, which possesses great potential to improve genetic testing of AOH. [ABSTRACT FROM AUTHOR]

Background: In prostate cancer (PCa), well-established biomarkers such as MSI status, TMB high, and PDL1 expression serve as reliable indicators for favorable responses to immunotherapy. Recent studies have suggested a potential association between CDK12 mutations and immunotherapy response; however, the precise mechanisms through which CDK12 mutation may influence immune response remain unclear. A plausible explanation for immune evasion in this subset of CDK12-mutated PCa may be reduced MHC expression. Results: Using genomic data of CDK12-mutated PCa from 48 primary and 10 metastatic public domain samples and a retrospective cohort of 53 low-intermediate risk primary PCa, we investigated how variation in the expression of the MHC genes affected associated downstream pathways. We classified the patients based on gene expression quartiles of MHC-related genes and categorized the tumors into "High" and "Low" expression levels. CDK12-mutated tumors with higher MHC-expressed pathways were associated with the immune system and elevated PD-L1, IDO1, and TIM3 expression. Consistent with an inflamed tumor microenvironment (TME) phenotype, digital cytometric analyses identified increased CD8 + T cells, B cells, γδ T cells, and M1 Macrophages in this group. In contrast, CDK12-mutated tumors with lower MHC expression exhibited features consistent with an immune cold TME phenotype and immunoediting. Significantly, low MHC expression was also associated with chromosome 6 loss of heterozygosity (LOH) affecting the entire HLA gene cluster. These LOH events were observed in both major clonal and minor subclonal populations of tumor cells. In our retrospective study of 53 primary PCa cases from this Institute, we found a 4% (2/53) prevalence of CDK12 mutations, with the confirmation of this defect in one tumor through Sanger sequencing. In keeping with our analysis of public domain data this tumor exhibited low MHC expression at the RNA level. More extensive studies will be required to determine whether reduced HLA expression is generally associated with primary tumors or is a specific feature of CDK12 mutated PCa. Conclusions: These data show that analysis of CDK12 alteration, in the context of MHC expression levels, and LOH status may offer improved predictive value for outcomes in this potentially actionable genomic subgroup of PCa. In addition, these findings highlight the need to explore novel therapeutic strategies to enhance MHC expression in CDK12-defective PCa to improve immunotherapy responses. [ABSTRACT FROM AUTHOR]

Background: Biallelic variants in EYS are the major cause of autosomal recessive retinitis pigmentosa (arRP) in certain populations, a clinically and genetically heterogeneous disease that may lead to legal blindness. EYS is one of the largest genes (~ 2 Mb) expressed in the retina, in which structural variants (SVs) represent a common cause of disease. However, their identification using short-read sequencing (SRS) is not always feasible. Here, we conducted targeted long-read sequencing (T-LRS) using adaptive sampling of EYS on the MinION sequencing platform (Oxford Nanopore Technologies) to definitively diagnose an arRP family, whose affected individuals (n = 3) carried the heterozygous pathogenic deletion of exons 32–33 in the EYS gene. As this was a recurrent variant identified in three additional families in our cohort, we also aimed to characterize the known deletion at the nucleotide level to assess a possible founder effect. Results: T-LRS in family A unveiled a heterozygous AluYa5 insertion in the coding exon 43 of EYS (chr6(GRCh37):g.64430524_64430525ins352), which segregated with the disease in compound heterozygosity with the previously identified deletion. Visual inspection of previous SRS alignments using IGV revealed several reads containing soft-clipped bases, accompanied by a slight drop in coverage at the Alu insertion site. This prompted us to develop a simplified program using grep command to investigate the recurrence of this variant in our cohort from SRS data. Moreover, LRS also allowed the characterization of the CNV as a ~ 56.4kb deletion spanning exons 32–33 of EYS (chr6(GRCh37):g.64764235_64820592del). The results of further characterization by Sanger sequencing and linkage analysis in the four families were consistent with a founder variant. Conclusions: To our knowledge, this is the first report of a mobile element insertion into the coding sequence of EYS, as a likely cause of arRP in a family. Our study highlights the value of LRS technology in characterizing and identifying hidden pathogenic SVs, such as retrotransposon insertions, whose contribution to the etiopathogenesis of rare diseases may be underestimated. [ABSTRACT FROM AUTHOR]

The present research aimed to characterize the genetic diversity and relationships among extant Arabian horse sire lines in Bulgaria, using 15 equine microsatellite markers. The evaluation included 537 Arabian horses representing nine sire lines (SAKLAWI I, LATIF, SEANDERICH, IBRAHIM, SHABAB, DJEBEL MOUSA, KUHAILAN AFAS, BAIRACTAR, and SARHAN). The obtained results indicated that within these lines, the mean number of alleles ranged from 4.15 in SARHAN to 5.54 in SAKLAWI I and LATIF. The mean expected heterozygosity (He) ranged from 0.54 in the SEANDERICH line to 0.67 in SAKLAWI I. The inbreeding coefficient for the entire Arabian populations was rather low: FIS = −0.109, fluctuating from −0.204 in SHABAB to −0.041 in SAKLAWI I. The mean genetic differentiation, FST, was 0.096, demonstrating that nearly 90% of the total genetic variation was due to genetic differentiation within each population. STRUCTURE analysis indicated a genetic similarity between SHABAB and LATIF, between IBRAHIM and KUHAILAN AFAS, as well as between SAKLAWI I, SEANDERICH, and BAIRACTAR. This study of the genetic diversity of Arabian sire lines in Bulgaria can assist in developing a national strategy for the exclusion of non-purebred animals from breeding programs in order to preserve the genetic profile of the original Arabian lines. [ABSTRACT FROM AUTHOR]

Background: Sheep is one of the important species of livestock in India contributing to meat production. India has 44 distinct breeds of sheep, out of which 10 are found in Tamil Nadu. The present study describes the characterization of recently registered breed-Katchaikatty sheep, genetic variability and genetic structure of the population by microsatellite marker analysis. Methods: The genomic DNA from 50 unrelated Katchaikatty sheep was amplified with 25 FAO recommended fluorescent tagged ovine-specific microsatellite markers and genotyped on an automated Genetic Analyzer. Microsatellite fragment sizing was performed by Gene Mapper software. In each locus, observed (no) and effective number of microsatellite alleles (ne), allele frequencies, observed (Ho) and expected (He) heterozygosity, heterozygosity deficit estimate (FIS) and Chi-square (X2) test for Hardy-Weinberg equilibrium (HWE) were assessed by POPGENE software and polymorphism information content (PIC) was calculated. Mode-shift analyses were performed for testing the genetic bottleneck by bottleneck software. Result: The study revealed a total of 144 alleles across all the loci. The number of alleles at each locus varied from one to 10 with a mean of 5.76 alleles. The PIC values in the microsatellite loci ranged from 0.34 (OarAE129) to 0.83 (OarFCB48) with an average of 0.59, which showed a high genetic polymorphism. Six out of 25 microsatellite loci studied were in Hardy-Weinberg equilibrium and 19 out of 25 loci showed positive FIS values. The overall mean observed and expected heterozygosity were 0.50 and 0.65 respectively and the estimates elucidated a substantial genetic variability in Katchaikatty sheep population. Mode shift analysis revealed a normal L-shaped curve, describing that the Katchaikatty population had not experienced any genetic bottleneck and remained in mutation-drift equilibrium. [ABSTRACT FROM AUTHOR]

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Background. Genome data have been used to find novel allergen from house dust mites. Here, we aim to construct a chromosome-level genome assembly of Dermatophagoides farinae, a common allergenic mite species. Methods. We achieved a chromosome-level assembly of D. farinae's genome by integrating PacBio single-molecule real-time sequencing, Illumina paired-end sequencing, and Hi-C technology, followed by annotating allergens and mapping them to specific chromosomes. Results. A 62.43 Mb genome was assembled with a 0.52% heterozygosity rate and a 36.11 Merqury-estimated quality value. The assembled genome represents 92.1% completeness benchmarking universal single-copy orthologs with a scaffold N50 value of 7.11 Mb. Hi-C scaffolding of the genome resulted in construction of 10 pseudochromosomes. The genome comprises 13.01% (7.66 Mb) repetitive sequences and predicts 10,709 protein-coding genes, 96.57% of which are functionally annotated. Moreover, we identified and located 36 allergen groups on specific chromosomes, including allergens Der f 1, Der f 2, Der f 23, Der f 4, Der f 5, Der f 7, and Der f 21 located on chromosomes 2, 1, 7, 3, 4, 6, and 4, respectively. Conclusion. This comprehensive genomic data provides valuable insights into mite biology and evolutionary adaptations, potentially advancing D. farinae allergy research and treatment strategies. [ABSTRACT FROM AUTHOR]

This study reports runs of homozygosity (ROH) and heterozygosity (ROHet) distributed in a large population of Holstein cattle on the basis of two microarrays of medium (50k; 2163 animals; 54 609 SNPs) and high single nucleotide polymorphism (SNP) density (HD; 600 animals; 777 692 SNPs). To assess the inbreeding values of Holstein cattle, the ROH-based genomic inbreeding coefficient (FROH) was calculated. The comparison of SNP panels suggested that FROH values above 4 Mb should be considered for panels of medium densities as a relatively reliable measure of inbreeding. Moreover, ROH hotspots and coldspots were identified and compared between the HD and 50k SNP panels and were carefully examined for association with production and functional traits. The obtained results pinpointed genomic regions presumably under selection pressure in Holstein cattle. The regions overlapped with a large number of genes, including GHR, GBF1, SUMF1, CCL28, NIM1K, U6, BTRC and FABP1, many of which are involved in important Holstein cattle characteristics. We also found that some ROH hotspots and coldspots identified with the HD panel were not detected with the 50k panel, mainly because of insufficient SNP density in certain genomic regions. This suggests that using medium-density panels might not be the best choice when precise identification of ROH patterns is the main goal. In summary, in this work, we confirmed that a high-density SNP panel compared to a medium-density SNP panel allows for more precise identification of ROH patterns, especially in the case of short ROH that could be associated with ancestral inbreeding. [ABSTRACT FROM AUTHOR]

K+ channel Kir7.1 expressed at the apical membrane of the retinal pigment epithelium (RPE) plays an essential role in retinal function. An isoleucine-to-threonine mutation at position 120 of the protein is responsible for blindness-causing vitreo-retinal dystrophy. We have studied the molecular mechanism of action of Kir7.1-I120T in vitro by heterologous expression and in vivo in CRISPR-generated knockin mice. Full-size Kir7.1-I120T reaches the plasma membrane but lacks any activity. Analysis of Kir7.1 and the I120T mutant in mixed transfection experiments, and that of tandem tetrameric constructs made by combining wild type (WT) and mutant protomers, leads us to conclude that they do not form heterotetramers in vitro. Homozygous I120T/I120T mice show cleft palate and tracheomalacia and do not survive beyond P0, whereas heterozygous WT/I120T develop normally. Membrane conductance of RPE cells isolated from WT/WT and heterozygous WT/I120T mice is dominated by Kir7.1 current. Using Rb+ as a charge carrier, we demonstrate that the Kir7.1 current of WT/I120T RPE cells corresponds to approximately 50% of that in cells from WT/WT animals, in direct proportion to WT gene dosage. This suggests a lack of compensatory effects or interference from the mutated allele product, an interpretation consistent with results obtained using WT/– hemizygous mouse. Electroretinography and behavioral tests also show normal vision in WT/I120T animals. The hypomorphic ion channel phenotype of heterozygous Kir7.1-I120T mutants is therefore compatible with normal development and retinal function. The lack of detrimental effect of this degree of functional deficit might explain the recessive nature of Kir7.1 mutations causing human eye disease. NEW & NOTEWORTHY: Human retinal pigment epithelium K+ channel Kir7.1 is affected by generally recessive mutations leading to blindness. We investigate one such mutation, isoleucine-to-threonine at position 120, both in vitro and in vivo in knockin mice. The mutated channel is inactive and in heterozygosis gives a hypomorphic phenotype with normal retinal function. Mutant channels do not interfere with wild-type Kir7.1 channels which are expressed concomitantly without hindrance, providing an explanation for the recessive nature of the disease. [ABSTRACT FROM AUTHOR]

Okra [Abelmoschus esculentus (L.) Moench] also known as bhindi or lady's finger is an important vegetable crop in India, West Africa, South Africa, Brazil, USA and Turkey. It belongs to the family Malvaceae. Okra is mainly grown in tropics and subtropics of the world. The studies regarding the molecular marker development are very limited; still there is no SSR marker development from comprehensive transcriptome data in this crop. This study presents the first comprehensive transcriptome data, using RNA from different parts of okra such as root, stem, leaf, bud, flower, different stages of developing pod and from twenty days old plantlets of heat, drought and salt stressed. A total of 10,492 SSRs were identified in this study. Among these tri repeats (2112) were found to be predominant followed by di (1285), tetra (149), penta (24) and hexa repeats. Thirty-four SSRs were standardized for PCR and screened in 36 okra genotypes and accessions. Among these, 18 SSR primers were found to be highly polymorphic with the PIC values more than 0.5. And the overall results of analysis showed that expected heterozygosity ranged from 0.125 to 0.971 with a mean of 0.593; the values for observed heterozygosity ranged from 0.000 to 0.839 with the mean of 0.203; the number of allele per locus ranged from 1 to 30 and the polymorphic information content (PIC) ranged from 0.119 to 0.955 with the mean value of 0.554. The genic SSR markers developed will help in germplasm characterization mapping, genetic diversity studies, molecular assisted breeding and also in gene discovery. [ABSTRACT FROM AUTHOR]

[Objective] The purpose of this paper was to explore the genetic diversity of the tea variety ’Zijuan’ and its mutagenesis progeny.[Method] The selected ’Zijuan’ and ’Zijuan’ mutated progeny were investigated from several aspects of botanical characters, biochemical components and EST-SSR markers. [Result] It was found that the color of buds and leaves of 15 materials were similar to that of ’Zijuan’,only two materials in the leaf shape of mature leaves that were the same as ’Zijuan’,which was lanceolate, and the others were elliptic or long elliptic. There were 9 materials with the same leaf color as ’Zijuan’,all of which are purple green, while 7 materials were yellow-green. Among the variation coefficients of biochemical components in spring and summer, the highest variation coefficient was anthocyanin, which reached 72.16% in spring and 77.86% in summer. The content of anthocyanin changed more in summer than in spring. A total of 165 alleles were detected by microsatellite markers, the average number of alleles was 7.5,the effective number of alleles was 2.562,Shannon information index was 0.997,polymorphic information content was 0.492,observed heterozygosity was 0.629,and expected heterozygosity was 0.565. [Conclusion] The above analysis results of traits, physiological and biochemical characteristics and microsatellite markers showed that the mutant progeny of ’Zijuan’ had a relatively rich genetic diversity. [ABSTRACT FROM AUTHOR]

As one of the most abundant groups in marine fish families, Gobiidae fish are important fishery resources in China, and some are also invasive species in certain regions worldwide. However, the phylogenetic relationships of Gobiidae fish remain ambiguous, and the study of their invasion-related genes is still scarce. This study used high-throughput sequencing technology to conduct a whole-genome survey of five Gobiidae fish species: Acanthogobius flavimanus, Acanthogobius stigmothonus, Favonigobius gymnauchen, Ctenotrypauchen microcephalus, and Tridentiger barbatus. De novo assembly of five fish genomes was performed, and genomic traits were compared through K-mer analysis. Among the five Gobiidae fish genomes, F. gymnauchen had the largest genome size (1601.98 Mb) and the highest heterozygosity (1.56%) and repeat rates (59.83%). Phylogenetic studies showed that A. flavimanus was most closely linked to A. stigmothonus, while Apogonidae and Gobiidae were closely related families. PSMC analysis revealed that C. microcephalus experienced a notable population expansion than the other four fish species in the Early Holocene. By using the KOG, GO, and KEGG databases to annotate single-copy genes, the annotated genes of the five fish were mainly classified as "signal transduction mechanisms", "cellular process", "cellular anatomical entity", and "translation". Acanthogobius flavimanus, A. stigmothonus, and T. barbatus had more genes classified as "response to stimulus" and "localization", which may have played an important role in their invasive processes. Our study also provides valuable material about Gobiidae fish genomics and genetic evolution. [ABSTRACT FROM AUTHOR]

Background: Lagerstroemia indica is a widely cultivated ornamental woody shrub/tree of the family Lythraceae that is used as a traditional medicinal plant in East Asia and Egypt. However, unlike other ornamental woody plants, its genome is not well-investigated, which hindered the discovery of the key genes that regulate important traits and the synthesis of bioactive compounds. Results: In this study, the genomic sequences of L. indica were determined using several next-generation sequencing technologies. Altogether, 324.01 Mb sequences were assembled and 98.21% (318.21 Mb) of them were placed in 24 pseudo-chromosomes. The heterozygosity, repeated sequences, and GC residues occupied 1.65%, 29.17%, and 38.64% of the genome, respectively. In addition, 28,811 protein-coding gene models, 327 miRNAs, 552 tRNAs, 214 rRNAs, and 607 snRNAs were identified. The intra- and interspecies synteny and Ks analysis revealed that L. indica exhibits a hexaploidy. The co-expression profiles of the genes involved in the phenylpropanoid (PA) and flavonoid/anthocyanin (ABGs) pathways with the R2R3 MYB genes (137 members) showed that ten R2R3 MYB genes positively regulate flavonoid/anthocyanin biosynthesis. The colors of flowers with white, purple (PB), and deep purplish pink (DPB) petals were found to be determined by the levels of delphinidin-based (Dp) derivatives. However, the substrate specificities of LiDFR and LiOMT probably resulted in the different compositions of flavonoid/anthocyanin. In L. indica, two LiTTG1s (LiTTG1-1 and LiTTG1-2) were found to be the homologs of AtTTG1 (WD40). LiTTG1-1 was found to repress anthocyanin biosynthesis using the tobacco transient transfection assay. Conclusions: This study showed that the ancestor L. indica experienced genome triplication approximately 38.5 million years ago and that LiTTG1-1 represses anthocyanin biosynthesis. Furthermore, several genes such as LiDFR, LiOMTs, and R2R3 LiMYBs are related to anthocyanin biosynthesis. Further studies are required to clarify the mechanisms and alleles responsible for flower color development. [ABSTRACT FROM AUTHOR]

The blue whale, Balaenoptera musculus , is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research. [ABSTRACT FROM AUTHOR]

Siphonophores (Cnidaria: Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k -mer spectra in six specimens, ranging from 0.7 to 2.3 Gb, with heterozygosity estimates between 0.69% and 2.32%. Incremental k -mer counting indicates k -mer peaks can be absent with nearly 20× read coverage, suggesting minimum genome sizes range from 1.4 to 5.6 Gb in the 25 samples without peaks in the k -mer spectra. This work confirms most siphonophore nuclear genomes are large relative to the genomes of other cnidarians, but also identifies several with reduced size that are tractable targets for future siphonophore nuclear genome assembly projects. We also assembled complete mitochondrial genomes for 33 specimens from these new data, indicating a conserved gene order shared among nonsiphonophore hydrozoans, Cystonectae, and some Physonectae, revealing the ancestral mitochondrial gene order of siphonophores. Our results also suggest extensive rearrangement of mitochondrial genomes within other Physonectae and in Calycophorae. Though siphonophores comprise a small fraction of cnidarian species, this survey greatly expands our understanding of cnidarian genome diversity. This study further illustrates both the importance of deep phylogenetic sampling and the utility of k -mer–based genome skimming in understanding the genomic diversity of a clade. [ABSTRACT FROM AUTHOR]

High-quality genomes obtained using long-read data allow not only for a better understanding of heterozygosity levels, repeat content, and more accurate gene annotation and prediction when compared to those obtained with short-read technologies, but also allow to understand haplotype divergence. Advances in long-read sequencing technologies in the last years have made it possible to produce such high-quality assemblies for non-model organisms. This allows us to revisit genomes, which have been problematic to scaffold to chromosomescale with previous generations of data and assembly software. Nematoda, one of the most diverse and speciose animal phyla within metazoans, remains poorly studied, and many previously assembled genomes are fragmented. Using long reads obtained with Nanopore R10.4.1 and PacBio HiFi, we generated highly contiguous assemblies of a diploid nematode of the Mermithidae family, for which no closely related genomes are available to date, as well as a collapsed assembly and a phased assembly for a triploid nematode from the Panagrolaimidae family. Both genomes had been analysed before, but the fragmented assemblies had scaffold sizes comparable to the length of long reads prior to assembly. Our new assemblies illustrate how long-read technologies allow for a much better representation of species genomes. We are now able to conduct more accurate downstream assays based on more complete gene and transposable element predictions. [ABSTRACT FROM AUTHOR]

Habitat loss and population fragmentation pose severe threats to biodiversity and the survival of many species. Population isolation and the decline in effective population size lead to increased genetic drift and inbreeding. In turn, this reduces neutral diversity, and it also affects the genetic load of deleterious mutations. Here, we analyse the effect of such genomic erosion by designing a spatially explicit, individual based model in SLiM, simulating the effects of the recorded habitat loss in Mauritius over the past ~ 250 years. We show that the loss of neutral diversity (genome-wide heterozygosity) was barely noticeable during the first 100 years of habitat loss. Changes to the genetic load took even more time to register, and they only became apparent circa 200 years after the start of habitat decline. Although a considerable number of deleterious mutations were lost by drift, others increased in frequency. The masked load was thus converted into a realised load, which compromised individual fitness and population viability after much of the native habitat had been lost. Importantly, genomic erosion continued after the metapopulation had stabilised at low numbers. Our study shows that historic habitat loss can pose a sustained threat to populations also in future generations, even without further habitat loss. The UN's Decade on Ecosystem Restoration needs to lead to transformative change to save species from future extinction, and this requires the urgent restoration of natural habitats. [ABSTRACT FROM AUTHOR]

The ancestral recombination graph (ARG) is a structure that represents the history of coalescent and recombination events connecting a set of sequences (Hudson RR. In: Futuyma D, Antonovics J, editors. Gene genealogies and the coalescent process. In: Oxford Surveys in Evolutionary Biology; 1991. p. 1 to 44.). The full ARG can be represented as a set of genealogical trees at every locus in the genome, annotated with recombination events that change the topology of the trees between adjacent loci and the mutations that occurred along the branches of those trees (Griffiths RC, Marjoram P. An ancestral recombination graph. In: Donnelly P, Tavare S, editors. Progress in population genetics and human evolution. Springer; 1997. p. 257 to 270.). Valuable insights can be gained into past evolutionary processes, such as demographic events or the influence of natural selection, by studying the ARG. It is regarded as the "holy grail" of population genetics (Hubisz M, Siepel A. Inference of ancestral recombination graphs using ARGweaver. In: Dutheil JY, editors. Statistical population genomics. New York, NY: Springer US; 2020. p. 231–266.) since it encodes the processes that generate all patterns of allelic and haplotypic variation from which all commonly used summary statistics in population genetic research (e.g. heterozygosity and linkage disequilibrium) can be derived. Many previous evolutionary inferences relied on summary statistics extracted from the genotype matrix. Evolutionary inferences using the ARG represent a significant advancement as the ARG is a representation of the evolutionary history of a sample that shows the past history of recombination, coalescence, and mutation events across a particular sequence. This representation in theory contains as much information, if not more, than the combination of all independent summary statistics that could be derived from the genotype matrix. Consistent with this idea, some of the first ARG-based analyses have proven to be more powerful than summary statistic-based analyses (Speidel L, Forest M, Shi S, Myers SR. A method for genome-wide genealogy estimation for thousands of samples. Nat Genet. 2019:51(9):1321 to 1329.; Stern AJ, Wilton PR, Nielsen R. An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data. PLoS Genet. 2019:15(9):e1008384.; Hubisz MJ, Williams AL, Siepel A. Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet. 2020:16(8):e1008895.; Fan C, Mancuso N, Chiang CWK. A genealogical estimate of genetic relationships. Am J Hum Genet. 2022:109(5):812–824.; Fan C, Cahoon JL, Dinh BL, Ortega-Del Vecchyo D, Huber C, Edge MD, Mancuso N, Chiang CWK. A likelihood-based framework for demographic inference from genealogical trees. bioRxiv. 2023.10.10.561787. 2023.; Hejase HA, Mo Z, Campagna L, Siepel A. A deep-learning approach for inference of selective sweeps from the ancestral recombination graph. Mol Biol Evol. 2022:39(1):msab332.; Link V, Schraiber JG, Fan C, Dinh B, Mancuso N, Chiang CWK, Edge MD. Tree-based QTL mapping with expected local genetic relatedness matrices. bioRxiv. 2023.04.07.536093. 2023.; Zhang BC, Biddanda A, Gunnarsson ÁF, Cooper F, Palamara PF. Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits. Nat Genet. 2023:55(5):768–776.). As such, there has been significant interest in the field to investigate 2 main problems related to the ARG: (i) How can we estimate the ARG based on genomic data, and (ii) how can we extract information of past evolutionary processes from the ARG? In this perspective, we highlight 3 topics that pertain to these main issues: The development of computational innovations that enable the estimation of the ARG; remaining challenges in estimating the ARG; and methodological advances for deducing evolutionary forces and mechanisms using the ARG. This perspective serves to introduce the readers to the types of questions that can be explored using the ARG and to highlight some of the most pressing issues that must be addressed in order to make ARG-based inference an indispensable tool for evolutionary research. [ABSTRACT FROM AUTHOR]

Coat color and pattern are a distinguished feature in mammalian carnivores, shaped by climatic cycles and habitat type. It can be expressed in various ways, such as gradients, polymorphisms, and rare color variants. Although natural selection explains much of the phenotypic variation found in the wild, genetic drift and heterozygote deficiency, as prominent in small and fragmented populations, may also affect phenotypic variability through the fixation of recessive alleles. The aim of this study was to test whether rare color variants in the wild could relate to a deficiency of heterozygotes, resulting from habitat fragmentation and small population size. We present an overview of all rare color variants in the order Carnivora, and compiled demographic and genetic data of the populations where they did and did not occur, to test for significant correlations. We also tested how phylogeny and body weight influenced the presence of color variants with phylogenetic generalized linear mixed models (PGLMMs). We found 40 color‐variable species and 59 rare color variants. In 17 variable phenotypic populations for which genetic diversity was available, the average AR was 4.18, HO = 0.59, and HE = 0.66, and FIS = 0.086. We found that variable populations displayed a significant reduction in heterozygosity and allelic richness compared to non‐variable populations across species. We also found a significant negative correlation between population size and inbreeding coefficients. Therefore, it is possible that small effective size had phenotypic consequences on the extant populations. The high frequency of the rare color variants (averaging 20%) also implies that genetic drift is locally overruling natural selection in small effective populations. As such, rare color variants could be added to the list of phenotypic consequences of inbreeding in the wild. [ABSTRACT FROM AUTHOR]

Objective: Adenylosuccinate lyase (ADSL) deficiency is a rare inherited metabolic disorder with a wide phenotypic presentation, classically grouped into three types (neonatal, type I, and type II). We aim to better delineate the pathological spectrum, focusing on the electroclinical characteristics and phenotypic differences of patients with ADSL deficiency. Patients and Methods: Seven patients, from four different families, underwent serial electroencephalogram (EEG), clinical assessment, and neuroimaging. We also performed a systematic review of the cases published in the literature, summarizing the available clinical, neurophysiological, and genetic data. Results: We report seven previously unreported ADSL deficiency patients with long‐term follow‐up (10–34 years). From the literature review, we collected 81 previously reported cases. Of the included patient population, 58 % (51/88) were classified as having ADSL deficiency type I, 28% (25/88) as having type II, and 14% (12/88) as having neonatal. The most frequently reported pathogenic variants are p.R426H homozygous (19 patients), p.Y114H in compound heterozygosity (13 patients), and p.D430N homozygous (6 patients). In the majority (89.2%), disease onset was within the first year of life. Epilepsy is present in 81.8% of the patients, with polymorphic and often intractable seizures. EEG features seem to display common patterns and developmental trajectories: (i) poor general background organization with theta‐delta activity; (ii) hypsarrhythmia with spasms, usually adrenocorticotropic hormone‐responsive; (iii) generalized epileptic discharges with frontal or frontal temporal predominance; and (iv) epileptic discharge activation in sleep with an altered sleep structure. Imaging features present consistent findings of cerebral atrophy with frontal predominance, cerebellar atrophy, and white matter abnormalities among the three types. Significance: ADSL deficiency presents variable phenotypic expression, whose severity could be partially attributed to residual activity of the mutant protein. Although a precise phenotype‐genotype correlation was not yet feasible, we delineated a common pattern of clinical, neuroradiological, and neurophysiological features. [ABSTRACT FROM AUTHOR]

Chagas is an endemic disease in tropical regions of Latin America, caused by the parasite Trypanosoma cruzi. High intraspecies variability and genome complexity have been challenges to assemble high quality genomes needed for studies in evolution, population genomics, diagnosis and drug development. Here we present a chromosome-level phased assembly of a TcI T. cruzi strain (Dm25). While 29 chromosomes show a large collinearity with the assembly of the Brazil A4 strain, three chromosomes show both large heterozygosity and large divergence, compared to previous assemblies of TcI T. cruzi strains. Nucleotide and protein evolution statistics indicate that T. cruzi Marinkellei separated before the diversification of T. cruzi in the known DTUs. Interchromosomal paralogs of dispersed gene families and histones appeared before but at the same time have a more strict purifying selection, compared to other repeat families. Previously unreported large tandem arrays of protein kinases and histones were identified in this assembly. Over one million variants obtained from Illumina reads aligned to the primary assembly clearly separate the main DTUs. We expect that this new assembly will be a valuable resource for further studies on evolution and functional genomics of Trypanosomatids. [ABSTRACT FROM AUTHOR]

Caveolae constitute membrane microdomains where receptors and ion channels functionally interact. Caveolin-3 (cav-3) is the key structural component of muscular caveolae. Mutations in CAV3 lead to caveolinopathies, which result in both muscular dystrophies and cardiac diseases. In cardiomyocytes, cav-1 participates with cav-3 to form caveolae; skeletal myotubes and adult skeletal fibers do not express cav-1. In the heart, the absence of cardiac alterations in the majority of cases may depend on a conserved organization of caveolae thanks to the expression of cav-1. We decided to focus on three specific cav-3 mutations (Δ62-64YTT; T78K and W101C) found in heterozygosis in patients suffering from skeletal muscle disorders. We overexpressed both the WT and mutated cav-3 together with ion channels interacting with and modulated by cav-3. Patch-clamp analysis conducted in caveolin-free cells (MEF-KO), revealed that the T78K mutant is dominant negative, causing its intracellular retention together with cav-3 WT, and inducing a significant reduction in current densities of all three ion channels tested. The other cav-3 mutations did not cause significant alterations. Mathematical modelling of the effects of cav-3 T78K would impair repolarization to levels incompatible with life. For this reason, we decided to compare the effects of this mutation in other cell lines that endogenously express cav-1 (MEF-STO and CHO cells) and to modulate cav-1 expression with an shRNA approach. In these systems, the membrane localization of cav-3 T78K was rescued in the presence of cav-1, and the current densities of hHCN4, hKv1.5 and hKir2.1 were also rescued. These results constitute the first evidence of a compensatory role of cav-1 in the heart, justifying the reduced susceptibility of this organ to caveolinopathies. [ABSTRACT FROM AUTHOR]

Although various methods have been developed to detect structural variations (SVs) in genomic sequences, few are used to validate these results. Several commonly used SV callers produce many false positive SVs, and existing validation methods are not accurate enough. Therefore, a highly efficient and accurate validation method is essential. In response, we propose SVvalidation—a new method that uses long-read sequencing data for validating SVs with higher accuracy and efficiency. Compared to existing methods, SVvalidation performs better in validating SVs in repeat regions and can determine the homozygosity or heterozygosity of an SV. Additionally, SVvalidation offers the highest recall, precision, and F1-score (improving by 7-16%) across all datasets. Moreover, SVvalidation is suitable for different types of SVs. The program is available at https://github.com/nwpuzhengyan/SVvalidation. [ABSTRACT FROM AUTHOR]

In species that primarily reproduce asexually, occasional sex can have important evolutionary consequences. Many plant species in the genus Oenothera have a genetic system called permanent translocation heterozygosity (PTH), which renders plants functionally asexual when they self-fertilize. PTH results from reciprocal translocations of chromosomes that suppress recombination and a balanced lethal mortality of homozygous gametes that prevents independent assortment of alleles. When PTH plants self-fertilize, the offspring are genetically identical to the parents, but when they outcross they can create new genotypes. Here, we sought to determine the outcrossing rate of natural populations of PTH Oenothera biennis L. (Onagraceae). We genotyped 46 parents from 14 populations in Tompkins County, NY, USA, and 754 of their offspring at highly polymorphic microsatellite loci. 99.5% of offspring were genetically identical to their seed parents, whereas 4 offspring out of 754 exhibited allelic mismatches with their seed parent. The estimated outcrossing rate ranged from 0.1% to 0.4%. Our study design also permitted us to estimate mutation rate of microsatellite loci, which ranged from 1.33 × 10−3 to 3.98 × 10−3. These results show that O. biennis typically exhibits a functionally asexual genetic system, but rare outcrossing events can generate novel genotypes that may have important evolutionary consequences. [ABSTRACT FROM AUTHOR]

Pistacia lentiscus L., the mastic tree, is an evergreen shrub distributed across the entire Mediterranean Basin. This species, known for millennia for its medicinal, food and cosmetic value is currently threatened by overexploitation and climate change. To help prioritize conservation actions, we studied its genetic diversity using seventy four Mediterranean accessions and seven microsatellite loci. Genomic DNA was extracted from mastic tree leaves. Allelic frequency and population structure estimates were calculated as well as the relationship between studied populations. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.493 to 0.788 and 0.518 to 0.781 respectively. Shannon’s Information Index (I) ranged from 0.858 to 1.819 with a mean value of 1.420. The mean fixation index (Fst) value was estimated to 0.124. AMOVA analysis showed that only 7% of the variance existed among populations. In addition, the STRUCTURE analysis showed a clear distinction between the eastern and the western Mediterranean populations when the number of clusters (K) was set at 2. The study of genetic diversity of the Mediterranean P. lentiscus is of interest for conservation of genetic resources and it contributed to the understanding of the evolutionary history of this species. [ABSTRACT FROM AUTHOR]

Citrus polyploidy is associated with a wide range of morphological, genetic, and physiological changes that are often advantageous for breeding. Citrus triploid hybrids are very interesting as new seedless varieties. However, tetraploid rootstocks promote adaptation to different abiotic stresses and promote resilience. Triploid and tetraploid hybrids can be obtained through sexual hybridizations using tetraploid parents (2x × 4x, 4x × 2x, or 4x × 4x), but more knowledge is needed about the inheritance pattern of tetraploid parents to optimize the efficiency of triploid varieties and tetraploid rootstock breeding strategies. In this work, we have analyzed the inheritance pattern of three tetraploid genotypes: ‘Chandler’ pummelo (Citrus maxima) and ‘Cleopatra’ mandarin (Citrus reticulata), which represent two clear examples of autotetraploid plants constituted by the genome of a single species, and the ‘Sevillano’ sour orange, which is an allotetraploid interspecific hybrid between C. maxima and C. reticulata. Polymorphic simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers were used to estimate parental heterozygosity restitution, and allele frequencies for centromeric loci were used to calculate the preferential pairing rate related to the proportion of disomic and tetrasomic segregation. The tetraploid pummelo and mandarin displayed tetrasomic segregation. Sour orange evidenced a clear intermediate inheritance for five of the nine chromosomes (1, 2, 5, 7, and 8), a slight tendency toward tetrasomic inheritance on chromosome 3, and intermediate inheritance with a tendency toward disomy for chromosomes 4, 6, and 9. These results indicate that the interspecific versus intraspecific phylogenomic origin affects preferential pairing and, therefore, the inheritance patterns. Despite its high level of heterozygosity, the important preferential chromosome pairing observed in sour orange results in a limited diversity of the genotypic variability of its diploid gametes, and consequently, a large part of the genetic value of the original diploid sour orange is transferred to the tetraploid progenies. [ABSTRACT FROM AUTHOR]

Developing synchronous bilateral Wilms tumor suggests an underlying (epi)genetic predisposition. Here, we evaluate this predisposition in 68 patients using whole exome or genome sequencing (n = 85 tumors from 61 patients with matched germline blood DNA), RNA-seq (n = 99 tumors), and DNA methylation analysis (n = 61 peripheral blood, n = 29 non-diseased kidney, n = 99 tumors). We determine the predominant events for bilateral Wilms tumor predisposition: 1)pre-zygotic germline genetic variants readily detectable in blood DNA [WT1 (14.8%), NYNRIN (6.6%), TRIM28 (5%), and BRCA-related genes (5%)] or 2)post-zygotic epigenetic hypermethylation at 11p15.5 H19/ICR1 that may require analysis of multiple tissue types for diagnosis. Of 99 total tumor specimens, 16 (16.1%) have 11p15.5 normal retention of imprinting, 25 (25.2%) have 11p15.5 copy neutral loss of heterozygosity, and 58 (58.6%) have 11p15.5 H19/ICR1 epigenetic hypermethylation (loss of imprinting). Here, we ascertain the epigenetic and genetic modes of bilateral Wilms tumor predisposition. The genetic and epigenetic predisposition of bilateral Wilms tumour remains to be investigated. Here, the authors perform multiomics analysis and identify the predominant genetic and epigenetic events associated with bilateral Wilms tumour predisposition. [ABSTRACT FROM AUTHOR]

Background: The use of primaquine for mass drug administration (MDA) is being considered as a key strategy for malaria elimination. In addition to being the only drug active against the dormant and relapsing forms of Plasmodium vivax, primaquine is the sole potent drug against mature/infectious Plasmodium falciparum gametocytes. It may prevent onward transmission and help contain the spread of artemisinin resistance. However, higher dose of primaquine is associated with the risk of acute haemolytic anaemia in individuals with a deficiency in glucose-6-phosphate dehydrogenase. In many P. falciparum endemic areas there is paucity of information about the distribution of individuals at risk of primaquine-induced haemolysis at higher dose 45 mg of primaquine. Methods: A retrospective cross-sectional study was carried out using archived samples to establish the prevalence of G6PD deficiency in a malaria hotspot area in Misungwi district, located in Mwanza region, Tanzania. Blood samples collected from individuals recruited between August and November 2010 were genotyped for G6PD deficiency and submicroscopic parasites carriage using polymerase chain reaction. Results: A total of 263 individuals aged between 0 and 87 were recruited. The overall prevalence of the X-linked G6PD A− mutation was 83.7% (220/263) wild type, 8% (21/263) heterozygous and 8.4% (22/263) homozygous or hemizygous. Although, assessment of the enzymatic activity to assign the phenotypes according to severity and clinical manifestation as per WHO was not carried out, the overall genotype and allele frequency for the G6PD deficiency was 16.4% and 13. 2%, respectively. There was no statistically significant difference in among the different G6PD genotypes (p > 0.05). Out of 248 samples analysed for submicroscopic parasites carriage, 58.1% (144/248) were P. falciparum positive by PCR. G6PD heterozygous deficiency were associated with carriage of submicroscopic P. falciparum (p = 0.029). Conclusions: This study showed that 16.4% of the population in this part of North-western Tanzania carry the G6PD A− mutation, within the range of 15–32% seen in other parts of Africa. G6PD gene mutation is widespread and heterogeneous across the study area where primaquine would be valuable for malaria control and elimination. The maps and population estimates presented here reflect potential risk of higher dose of primaquine being associated with the risk of acute haemolytic anaemia (AHA) in individuals with a deficiency in glucose-6-phosphate dehydrogenase and call further research on mapping of G6PD deficiency in Tanzania. Therefore, screening and education programmes for G6PD deficiency is warranted in a programme of malaria elimination using a higher primaquine dose. [ABSTRACT FROM AUTHOR]

In order to study the genetics of local adaptation in all main deserts of northwest China, whole genomes of 169 individuals were resequenced, which covers 20 populations of Zygophyllum loczyi (Zygophyllales: Zygophylaceae). We describe more than 15 million single nucleotide polymorphisms and numerous InDels. The expected heterozygosity and PIC values associated with local adaptation varied significantly across biogeographic regions. Variation in environmental factors contributes largely to the population genetic structure of Z. loczyi. Bayesian analysis performed with STRUCTURE defined four genetic clusters, while the results of principle component analysis were similar. Our results shows that the Qaidam Desert group appears to be diverging into two branches characterized by significant geographic separation and gene flow with two neighboring deserts. Geological data assume that it is possible that the Taklamakan Desert was the original distribution site, and Z. loczyi could have migrated later on and expanded within other desert areas. The above findings provide insights into the processes involved in biogeography, phylogeny, and differentiation within the northwest deserts of China. [ABSTRACT FROM AUTHOR]

Background: Richter transformation (RT) is the development of aggressive lymphoma in patients with chronic lymphocytic leukemia (CLL) or small lymphocytic lymphoma (SLL). This rare disease is characterised by dismal prognosis. In recent years, there has been a deeper understanding of RT molecular pathogenesis, and disruptions of apoptosis (TP53) and proliferation (CDKN2A, MYC, NOTCH1) has been described as typical aberrations in RT. Results: A single-institution cohort of 33 RT patients were investigated by karyotyping, fluorescence in situ hybridization and single nucleotide polymorphism/copy number (CN) arrays. Most of RTs were typically manifested by diffuse large B-cell lymphoma, not otherwise specified, among the remaining cases one was classified as high-grade B-cell lymphoma with 11q aberrations. The most frequent alterations (40–60% of cases) were represented by MYC rearrangement/gain, deletions of TP53 and CDKN2A, IGH rearrangement and 13q14 deletion. Several other frequent lesions included losses of 14q24.1-q32.33, 7q31.33-q36.3, and gain of 5q35.2. Analysis of 13 CLL/SLL-RT pairs showed that RT arised from the CLL/SLL by acquiring of 10 ~ 12 cytogenetic or CN lesions/case, but without acquisition of loss of heterozygosity regions. Our result affirmed the higher genetic complexity in RT than CLL/SLL and confirmed the linear features of RT clonal evolution as predominant. Conclusions: Cytogenomic profile was concordant with the literature data, however the role of IGH rearrangement, 14q deletion and 5q35.2 gain need to be explored. We anticipate that further characterization of RT lesions will probably facilitate better understanding of the RT clonal evolution. [ABSTRACT FROM AUTHOR]

Cerebral Cavernous Malformations (CCMs) are vascular malformations of the central nervous system which can lead to moderate to severe neurological phenotypes in patients. A majority of CCM lesions are driven by a cancer-like three-hit mutational mechanism, including a somatic, activating mutation in the oncogene PIK3CA, as well as biallelic loss-of-function mutations in a CCM gene. However, standard sequencing approaches often fail to yield a full complement of pathogenic mutations in many CCMs. We suggest this reality reflects the limited sensitivity to identify low-frequency variants and the presence of mutations undetectable with bulk short-read sequencing. Here we report a single-nucleus DNA-sequencing approach that leverages the underlying biology of CCMs to identify lesions with somatic loss-of-heterozygosity, a class of such hidden mutations. We identify an alternative genetic mechanism for CCM pathogenesis and establish a method that can be repurposed to investigate the genetic underpinning of other disorders with multiple somatic mutations. Here the authors establish somatic loss-of-heterozygosity as a genetic underpinning of Cerebral Cavernous Malformations (CCMs): using single-nucleus DNA sequencing, they show homozygosity of chromosomes 7p and/or 7q leads to biallelic inactivation of CCM genes in resected lesions. [ABSTRACT FROM AUTHOR]

Meiotic crossovers can be formed through the interfering pathway, in which one crossover prevents another from forming nearby, or by an independent non-interfering pathway. In Arabidopsis, local sequence polymorphism between homologs can stimulate interfering crossovers in a MSH2-dependent manner. To understand how MSH2 regulates crossovers formed by the two pathways, we combined Arabidopsis mutants that elevate non-interfering crossovers with msh2 mutants. We demonstrate that MSH2 blocks non-interfering crossovers at polymorphic loci, which is the opposite effect to interfering crossovers. We also observe MSH2-independent crossover inhibition at highly polymorphic sites. We measure recombination along the chromosome arms in lines differing in patterns of heterozygosity and observe a MSH2-dependent crossover increase at the boundaries between heterozygous and homozygous regions. Here, we show that MSH2 is a master regulator of meiotic DSB repair in Arabidopsis, with antagonistic effects on interfering and non-interfering crossovers, which shapes the crossover landscape in relation to interhomolog polymorphism. Interhomolog polymorphism, which is detected by MSH2-containing heterodimers, may affect crossover outcomes during meiosis. Here, the authors revealed antagonistic effects of MSH2 on interfering and non-interfering crossover pathways in Arabidopsis. [ABSTRACT FROM AUTHOR]