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Background: Triploid bananas are almost sterile. However, we succeeded in harvesting seeds from two edible triploid banana individuals (Genotype: ABB) in our conservation repository where various wild diploid bananas were also grown. The resulting rare offspring survived to seedling stages. DNA content analyses reveal that they are tetraploid. Since bananas contain maternally inherited plastids and paternally inherited mitochondria, we sequenced and assembled plastomes and mitogenomes of these seedlings to trace their hybridization history. Results: The coding sequences of both organellar genomic scaffolds were extracted, aligned, and concatenated for constructing phylogenetic trees. Our results suggest that these tetraploid seedlings be derived from hybridization between edible triploid bananas and wild diploid Musa balbisiana (BB) individuals. We propose that generating female triploid gametes via apomeiosis may allow the triploid maternal bananas to produce viable seeds. Conclusions: Our study suggests a practical avenue towards expanding genetic recombination and increasing genetic diversity of banana breeding programs. Further cellular studies are needed to understand the fusion and developmental processes that lead to formation of hybrid embryos in banana reproduction, polyploidization, and evolution. [ABSTRACT FROM AUTHOR]

Background: Inflammatory breast cancer (IBC) is a rare disease characterized by rapid progression, early metastasis, and a high mortality rate. Methods: Genome-wide DNA methylation analysis (EPIC BeadChip platform, Illumina) and somatic gene variants (105 cancer-related genes) were performed in 24 IBCs selected from a cohort of 140 cases. Results: We identified 46,908 DMPs (differentially methylated positions) (66% hypomethylated); CpG islands were predominantly hypermethylated (39.9%). Unsupervised clustering analysis revealed three clusters of DMPs characterized by an enrichment of specific gene mutations and hormone receptor status. The comparison among DNA methylation findings and external datasets (TCGA-BRCA stages III-IV) resulted in 385 shared DMPs mapped in 333 genes (264 hypermethylated). 151 DMPs were associated with 110 genes previously detected as differentially expressed in IBC (GSE45581), and 68 DMPs were negatively correlated with gene expression. We also identified 4369 DMRs (differentially methylated regions) mapped on known genes (2392 hypomethylated). BCAT1, CXCL12, and TBX15 loci were selected and evaluated by bisulfite pyrosequencing in 31 IBC samples. BCAT1 and TBX15 had higher methylation levels in triple-negative compared to non-triple-negative, while CXCL12 had lower methylation levels in triple-negative than non-triple-negative IBC cases. TBX15 methylation level was associated with obesity. Conclusions: Our findings revealed a heterogeneous DNA methylation profile with potentially functional DMPs and DMRs. The DNA methylation data provided valuable insights for prognostic stratification and therapy selection to improve patient outcomes. [ABSTRACT FROM AUTHOR]

Research studies on the conservation genetics of endangered plants play a crucial role in establishing management plans for biodiversity conservation. Phoebe chekiangensis is a precious and scarce tree species resource in the East China region. To comprehend the origin, evolutionary history, geographical, and historical factors that has contributed to the current distribution pattern of Phoebe chekiangensis in the East China region, we conducted a phylogeographic analysis that utilized intergenic spacers of chloroplast DNA (cpDNA). We amplified and sequenced three spacer regions of cpDNA (psbC-trnS, trnL-Intro, and Ycf3) intergenic spacer regions of 306 individuals from 11 populations, encompassing the majority of its geographical range in China. Our analysis revealed a total of 11 haplotypes. The research findings show that the spacer regions of the cpDNA genetic diversity of Phoebe chekiangensis was Hd = 0.423, and the nucleotide diversity was Pi × 10−3 = 0.400. At the species level, the population differentiation index Fst = 0.25610 (p < 0.05), and the gene flow Nm = 0.73. The genetic variation between populations was 29.14%, while within populations, it was 70.86%, with the inter-population genetic variation much lower than the within-population variation. The divergence time between the genera Phoebe and Machilus was estimated to be approximately 37.87 mya (PP = 1; 95%HPD: 25.63–44.54 mya), and the crown group time of the genus Phoebe was estimated to be 21.30 mya (PP = 1; 95%HPD: 9.76–34.94 mya). The common ancestor of the 11 Phoebe chekiangensis haplotypes was 7.85 mya, while the H7, H8, and H10 haplotypes of Phoebe chekiangensis (northern region) differentiated relatively late, with a divergence time of 1.90 mya. Neutrality tests (NTs) and mismatch distribution analysis (MDA) suggest that the time frame for Phoebe chekiangensis to expand southwestward along Wuyishan was relatively short and its adaptability to the environment was low, thereby limiting the formation of new haplotypes. These results suggest that Phoebe chekiangensis exhibited greater adaptation to the northern subtropics than to the central subtropics, offering valuable insights for the conservation and utilization of germplasm resources. [ABSTRACT FROM AUTHOR]

The aquatic perennial herb Sagittaria trifolia L. commonly known as arrowhead, has been utilized in China both as a culinary vegetable and in traditional medicines. Characterizing the phylogenetic relationships and genetic diversity of arrowheads is crucial for improved management, conservation, and efficient utilization of the germplasm resources associated with this species. Herein, we presented the phenotypic traits and genome-wide DNA marker-based analyses of 111 arrowhead accessions, most of which were from China. Cluster analysis revealed that arrowhead could be categorized into two clusters based on 11 phenotypic traits, with Cluster 1 comprising two subclusters. All accessions were clustered into three sub-clusters based primarily on leaf shape and tuber weight. A set of 759,237 high-quality single-nucleotide polymorphisms was identified and used to assess the phylogenetic relationships. Population structure and phylogenetic tree analyses suggested that the accessions could be classified into two major groups, Group I was further subdivided into two subgroups, aligning with the clusters identified through morphological classification. By employing Sagittaria lichuanensis as an outgroup, the rooted tree revealed that the evolutionary relationships within the three groups followed a progression from Group I-1 to Group I-2 and finally to Group II. The landraces were clustered into one group along with the remaining wild accessions. The level of genetic diversity for Group I (π = 0.26) was slightly lower than that which was estimated for Group II (π = 0.29). The lowest pairwise differentiation levels (Fst, 0.008) were obtained from the comparison between groups I-2 and II, indicating that the two groups were the most closely related. This study provides novel insights into germplasm classification, evolutionary relationships, genomics and arrowhead breeding. [ABSTRACT FROM AUTHOR]

Background: The techniques for detecting single nucleotide polymorphisms (SNP) require lengthy and complex experimental procedures and expensive instruments that may only be available in some laboratories. Thus, a deoxyribonucleic acid (DNA)-based lateral flow assay (LFA) was developed as a point-of-care test (POCT) diagnostic tool for genotyping. In this study, single nucleotide variation (E101K) in the low-density lipoprotein receptor (LDLR) gene leading to familial hypercholesterolemia (FH) was chosen as a model. Methods: Hypercholesterolemic individuals (n = 103) were selected from the Malaysian Cohort project (UKM Medical Molecular Biology Institute) while the control samples were selected from the Biobank (UKM Medical Molecular Biology Institute). The DNA samples were isolated from whole blood. Polymerase chain reaction (PCR) amplification process was performed using bifunctional labelled primers specifically designed to correspond to the variant that differentiates wild-type and mutant DNA for visual detection on LFA. The variant was confirmed using Sanger sequencing, and the sensitivity and specificity of the LFA detection method were validated using the Agena MassARRAY® technique. Results: Out of 103 hypercholesterolemic individuals, 5 individuals (4.8%) tested positive for E101K, LDLR mutation and the rest, including healthy control individuals, tested negative. This result was concordant with Sanger sequencing and Agena MassARRAY®. These five individuals could be classified as Definite FH, as the DNA diagnosis was confirmed. The sensitivity and specificity of the variant detection by LFA is 100% compared to results using the genotyping method using Agena MassARRAY®. Conclusion: The developed LFA can potentially be used in the POC setting for detecting the E101K variant in the LDLR gene. This LFA can also be used to screen family members with E101K variant in the LDLR gene and is applicable for other SNP's detection. [ABSTRACT FROM AUTHOR]

Octopus cyanea (Gray, 1849), abundant in the South‐West Indian Ocean (SWIO), constitutes a vital resource for both subsistence and commercial fisheries. However, despite this socioeconomic importance, and recent indications of overfishing, little is known about the population structure of O. cyanea in the region. To inform sustainable management strategies, this study assessed the spatio‐temporal population structure and genetic variability of O. cyanea at 20 sites in the SWIO (Kenya, Tanzania, Mozambique, Madagascar, Mauritius, Rodrigues, and the Seychelle Islands) by complementary analysis of mitochondrial DNA (mtDNA) noncoding region (NCR) sequences and microsatellite markers. MtDNA analysis revealed a shallow phylogeny across the region, with demographic tests suggesting historic population fluctuations that could be linked to glacial cycles. Contrary to expectations, NCR variation was comparable to other mtDNA regions, indicating that the NCR is not a hypervariable region. Both nuclear and mtDNA marker types revealed a lack of genetic structure compatible with high gene flow throughout the region. As adults are sedentary, this gene flow likely reflects connectivity by paralarval dispersal. All samples reported heterozygote deficits, which, given the overall absence of structure, likely reflect ephemeral larval recruitment variability. Levels of mtDNA and nuclear variability were similar at all locations and congruent with those previously reported for harvested Octopodidae, implying resilience to genetic erosion by drift, providing current stock sizes are maintained. However, as O. cyanea stocks in the SWIO represent a single, highly connected population, fisheries may benefit from additional management measures, such as rotational closures aligned with paralarval ecology and spanning geopolitical boundaries. [ABSTRACT FROM AUTHOR]

Undiagnosed monogenic diseases represent a challenging group of human conditions highly suspicious to have a genetic origin, but without conclusive evidences about it. We identified two brothers born prematurely from a nonconsanguineous healthy couple, with a neonatal-onset, chronic disease characterized by severe skin and bone inflammatory manifestations and a fatal outcome in infancy. We conducted DNA and mRNA analyses in the patients' healthy relatives to identify the genetic cause of the patients' disease. DNA analyses were performed by both Sanger and next-generation sequencing, which identified two novel heterozygous IL1RN variants: the intronic c.318 + 2T>G variant in the father and a -2,600-bp intragenic deletion in the mother. IL1RN mRNA production was markedly decreased in both progenitors when compared with healthy subjects. The mRNA sequencing performed in each parent identified two novel, truncated IL1RN transcripts. Additional experiments revealed a perfect intrafamilial phenotype-genotype segregation following an autosomal recessive inheritance pattern. The evidences shown here supported for the presence of two novel loss-of-function (LoF) IL1RN pathogenic variants in the analyzed family. Biallelic LoF variants at the IL1RN gene cause the deficiency of interleukin-1 receptor antagonist (DIRA), a monogenic autoinflammatory disease with marked similarities with the patients described here. Despite the non-availability of the patients' samples representing the main limitation of this study, the collected evidences strongly suggest that the patients described here suffered from a lethal form of DIRA likely due to a compound heterozygous genotype at IL1RN, thus providing a reliable genetic diagnosis based on the integration of old medical information with currently obtained genetic data. [ABSTRACT FROM AUTHOR]

Background: The sustainable supply of medicinal plants is important, and cultivating and domesticating them has been suggested as an optimal strategy. However, this can lead to a loss of genetic diversity. Tripterygium wilfordii Hook. f. is a medicinal plant commonly used in traditional Chinese medicine, but its wild populations are dwindling due to excessive harvesting. To protect the species and meet the increasing demand, it is urgent to cultivate it on a large scale. However, distinguishing between T. wilfordii and T. hypoglaucum, two similar species with different medicinal properties, is challenging. Therefore, it is crucial to understand the genetic diversity and population structure of these species for their sustainable utilization. Results: In this study, we investigated the genetic diversity and population structure of the two traditional medicinal semiwoody vines plant species, Tripterygium wilfordii and T. hypoglaucum, including wild and cultivated populations using chloroplast DNA (cpDNA) sequences and microsatellite loci. Our results indicated that the two species maintain a high level of genetic divergence, indicating possible genetic bases for the different contents of bioactive compounds of the two species. T. wilfordii showed lower genetic diversity and less subdivided population structures of both markers than T. hypoglaucum. The potential factors in shaping these interesting differences might be differentiated pollen-to-seed migration rates, interbreeding, and history of population divergence. Analyses of cpDNA and microsatellite loci supported that the two species are genetically distinct entities. In addition, a significant reduction of genetic diversity was observed for cultivated populations of the two species, which mainly resulted from the small initial population size and propagated vegetative practice during their cultivation. Conclusion: Our findings indicate significant genetic divergence between T. wilfordii and T. hypoglaucum. The genetic diversity and population structure analyses provide important insights into the sustainable cultivation and utilization of these medicinal plants. Accurate identification and conservation efforts are necessary for both species to ensure the safety and effectiveness of crude drug use. Our study also highlighted the importance of combined analyses of different DNA markers in addressing population genetics of medicinal plants because of the contrasts of inheritance and rates of gene flow. Large-scale cultivation programs should consider preserving genetic diversity to enhance the long-term sustainability of T. wilfordii and T. hypoglaucum. Our study proposed that some populations showed higher genetic diversity and distinctness, which can be considered with priority for conservation and as the sources for future breeding and genetic improvement. [ABSTRACT FROM AUTHOR]

Simple Summary: Cleidocranial dysplasia is a rare disease, manifested by anomalies in the skull, face, teeth, thorax, clavicle, extremities, and short stature. The disease is caused by mutations in the RUNX2 gene, which is involved in the differentiation of cells that give rise and formation of bones. In this study, the genetic material of four patients and their families was analyzed, with the purpose of identifying changes in the sequence of the RUNX2 gene, finding three new changes and one change already reported in the literature. One patient presented cataract and damage to the retina of the eye, and data were not reported in other patients. A bioinformatic analysis of the RUNX2 protein was carried out with the aim of predicting mechanisms, such as the function, stability, and conformation of the protein, and of trying to understand its relationship with the variable presentation of signs and symptoms in this condition. These results can be useful in the genetic counselling of patients. Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal dysplasia characterized by persistent open skull sutures with bulging calvaria, hypoplasia, or aplasia of clavicles permitting abnormal opposition of the shoulders; wide public symphysis; short middle phalanx of the fifth fingers; and vertebral, craniofacial, and dental anomalies. It is a rare disease, with a prevalence of 1–9/1,000,000, high penetrance, and variable expression. The gene responsible for CCD is the Runt-related transcription factor 2 (RUNX2) gene. We characterize the clinical, genetic, and bioinformatic results of four CCD cases: two cases within Mexican families with six affected members, nine asymptomatic individuals, and two sporadic cases with CCD, with one hundred healthy controls. Genomic DNA analyses of the RUNX2 gene were performed for Sanger sequencing. Bioinformatics tools were used to predict the function, stability, and structural changes of the mutated RUNX2 proteins. Three novel heterozygous mutations (c.651_652delTA; c.538_539delinsCA; c.662T>A) and a previously reported mutation (c.674G>A) were detected. In silico analysis showed that all mutations had functional, stability-related, and structural alterations in the RUNX2 protein. Our results show novel mutations that enrich the pool of RUNX2 gene mutations with CCD. Moreover, the proband 1 presented clinical data not previously reported that could represent an expanded phenotype of severe expression. [ABSTRACT FROM AUTHOR]

PRDM9-mediated reproductive isolation was first described in the progeny of Mus musculus musculus (MUS) PWD/Ph and Mus musculus domesticus (DOM) C57BL/6J inbred strains. These male F1 hybrids fail to complete chromosome synapsis and arrest meiosis at prophase I, due to incompatibilities between the Prdm9 gene and hybrid sterility locus Hstx2. We identified 14 alleles of Prdm9 in exon 12, encoding the DNA-binding domain of the PRDM9 protein in outcrossed wild mouse populations from Europe, Asia, and the Middle East, 8 of which are novel. The same allele was found in all mice bearing introgressed t -haplotypes encompassing Prdm9. We asked whether 7 novel Prdm9 alleles in MUS populations and the t -haplotype allele in 1 MUS and 3 DOM populations induce Prdm9 -mediated reproductive isolation. The results show that only combinations of the dom2 allele of DOM origin and the MUS msc1 allele ensure complete infertility of intersubspecific hybrids in outcrossed wild populations and inbred mouse strains examined so far. The results further indicate that MUS mice may share the erasure of PRDM9msc1 binding motifs in populations with different Prdm9 alleles, which implies that erased PRDM9 binding motifs may be uncoupled from their corresponding Prdm9 alleles at the population level. Our data corroborate the model of Prdm9-mediated hybrid sterility beyond inbred strains of mice and suggest that sterility alleles of Prdm9 may be rare. [ABSTRACT FROM AUTHOR]

Simple Summary: As a tumor grows, DNA fragments from cancer cells shed into the bloodstream. Known as circulating tumor DNA (ctDNA), these fragments can be used to inform on cancer diagnosis, treatment, and prognosis. However, despite the potential for these uninavasive liquid biopsies to revolutionize cancer monitoring and treatment, ctDNA can show poor genetic concordance between blood and the main tumor tissue, hampering its general clinical utility. For liquid biopsy technologies and ctDNA analyses to transform cancer care, from early screening and diagnosis through treatment and long-term follow-up, we need to better understand how to interpret the genetic diversity measured in the blood and how it can be used to describe the true composition of the tumor tissue. In this work we study the evolutionary processes that can lead to genetic discordance between a blood sample and the main tumor tissue and specifically, how tumor spatial heterogeneity shapes these genetic differences. We find that spatial heterogeneity in apoptosis and cellular shedding across different regions of a tumor can significantly bias the mutational composition of ctDNA and emphasize important directions for further theoretical and clinical investigation into the effect of the microenvironment on ctDNA origin and quantification. Circulating tumor DNA (ctDNA) monitoring, while sufficiently advanced to reflect tumor evolution in real time and inform cancer diagnosis, treatment, and prognosis, mainly relies on DNA that originates from cell death via apoptosis or necrosis. In solid tumors, chemotherapy and immune infiltration can induce spatially variable rates of cell death, with the potential to bias and distort the clonal composition of ctDNA. Using a stochastic evolutionary model of boundary-driven growth, we study how elevated cell death on the edge of a tumor can simultaneously impact driver mutation accumulation and the representation of tumor clones and mutation detectability in ctDNA. We describe conditions in which invasive clones are over-represented in ctDNA, clonal diversity can appear elevated in the blood, and spatial bias in shedding can inflate subclonal variant allele frequencies (VAFs). Additionally, we find that tumors that are mostly quiescent can display similar biases but are far less detectable, and the extent of perceptible spatial bias strongly depends on sequence detection limits. Overall, we show that spatially structured shedding might cause liquid biopsies to provide highly biased profiles of tumor state. While this may enable more sensitive detection of expanding clones, it could also increase the risk of targeting a subclonal variant for treatment. Our results indicate that the effects and clinical consequences of spatially variable cell death on ctDNA composition present an important area for future work. [ABSTRACT FROM AUTHOR]

Characterization of genetic resources is a prerequisite for plant breeding and germplasm management. In this context, the use of molecular markers for validation of genetic passports based on DNA analyses is crucial for identification of cultivars and traceability in coffee breeding programs. A total of 96 Coffea canephora genotypes cultivated in the Western Amazonia were evaluated, including plants of the botanical varieties Conilon, Robusta, and hybrids from the germplasm bank of the Brazilian Agricultural Research Corporation (Embrapa), as well as clones in the public domain coming from growers in the state. The germplasm was evaluated with 12 simple sequence repeat (SSR) marker to quantify the genetic diversity also considering the discrimination power of these markers. Were identified 96 unique fingerprint profiles and a set of primers of higher efficiency for discrimination C. canephora genotypes. The genetic relationships illustrated by hierarchical clusterings and discriminant analyses showed distinction between the botanical varieties Conilon and Robusta and higher diversity in the Robusta variety. The set of molecular markers allowed to identify hybrid genotypes that were misclassified in populations of Conilon and Robusta botanical varieties as well as genealogy mistakes. Unique genetic profiles were detected for each clone in the public domain of the state. Previously unknown, these genotypes were classified according to their phenotypic similarities with each other and with the Conilon, Robusta, and hybrid accessions. These results are valuable for future management of the Amazonian coffee and useful to assist and accelerate the selection and crosses in the genetic breeding program. [ABSTRACT FROM AUTHOR]

Autism spectrum disorder (ASD) is a common condition with lifelong implications. The last decade has seen dramatic improvements in DNA sequencing and related bioinformatics and databases. We analyzed the raw DNA sequencing files on the Variantyx® bioinformatics platform for the last 50 ASD patients evaluated with trio whole-genome sequencing (trio-WGS). "Qualified" variants were defined as coding, rare, and evolutionarily conserved. Primary Diagnostic Variants (PDV), additionally, were present in genes directly linked to ASD and matched clinical correlation. A PDV was identified in 34/50 (68%) of cases, including 25 (50%) cases with heterozygous de novo and 10 (20%) with inherited variants. De novo variants in genes directly associated with ASD were far more likely to be Qualifying than non-Qualifying versus a control group of genes (p = 0.0002), validating that most are indeed disease related. Sequence reanalysis increased diagnostic yield from 28% to 68%, mostly through inclusion of de novo PDVs in genes not yet reported as ASD associated. Thirty-three subjects (66%) had treatment recommendation(s) based on DNA analyses. Our results demonstrate a high yield of trio-WGS for revealing molecular diagnoses in ASD, which is greatly enhanced by reanalyzing DNA sequencing files. In contrast to previous reports, de novo variants dominate the findings, mostly representing novel conditions. This has implications to the cause and rising prevalence of autism. [ABSTRACT FROM AUTHOR]

Background: Cornelia de Lange Syndrome (CdLS) is a rare genetic disorder characterized by a range of physical, cognitive, and behavioral abnormalities. This study aimed to perform a comprehensive review of the literature on CdLS and investigate two cases of CdLS with distinct phenotypes that underwent WES to aid in their diagnosis. Methods: We conducted a comprehensive review of the literature on CdLS along with performing whole-exome sequencing on two CdLS patients with distinct phenotypes, followed by Sanger sequencing validation and in-silico analysis. Results: The first case exhibited a classic CdLS phenotype, but the initial WES analysis of blood-derived DNA failed to identify any mutations in CdLS-related genes. However, a subsequent WES analysis of skin-derived DNA revealed a novel heterozygous mutation in the NIPBL gene (NM_133433.4:c.6534_6535del, p.Met2178Ilefs*8). The second case was presented with a non-classic CdLS phenotype, and WES analysis of blood-derived DNA identified a heterozygous missense variant in the SMC1A gene (NM_006306.4:c.2320G>A, p.Asp774Asn). Conclusions: The study shows the importance of considering mosaicism in classic CdLS cases and the value of WES for identifying genetic defects. These findings contribute to our understanding of CdLS genetics and underscore the need for comprehensive genetic testing to enhance the diagnosis and management of CdLS patients. [ABSTRACT FROM AUTHOR]

DNA metabarcoding requires reference libraries that link DNA sequences to species. Mitochondrial gene regions cytochrome c oxidase I (COI), 12S ribosomal RNA (12S rRNA), 16S ribosomal RNA (16S rRNA), cytochrome b (cyt b) and the hypervariable control region (D-loop) are routinely used in studies that measure genetic diversity in animal species. This study aimed to review the state of DNA reference libraries for small South African mammals as small mammals constitute a large portion of small and medium carnivore diet. Analyses of DNA records revealed that of 193 small mammal species in South Africa, only 141 have DNA sequences available for one or more of the mitochondrial genes examined. Cyt b had the highest species coverage, with 59.1% of South African species represented in the reference libraries. COI only has 33.7%, 12S rRNA has 23.8%, D-loop has 17.6%, and 16S rRNA has the lowest species coverage of 15%. This study supports the use of multiple gene regions when performing scat metabarcoding, particularly when wanting to determine the small mammal component of the diet. Additionally, it emphasises the need to build comprehensive DNA reference libraries linking sequences to taxonomically identified species. [ABSTRACT FROM AUTHOR]

A Barred rainbowfish (Chilatherina fasciata) is one of the native fish species found in Western New Guinea of Indonesia. This study aimed to observe the levels of haplotype diversity in the partial Cytochrome-c oxidase subunit I (COI) gene of Barred rainbowfish. For the DNA analysis, thirty (30) Barred rainbowfishes were caught from the Mamberamo River. Three (3) molecular packages of BioEdit, MEGA, and DNAsp were used to analyze twenty (30) forward sequences of the COI gene (502 bp). The research showed four (4) haplotypes for the examined population, a total of seven (7) mutations, and low genetic diversity detected in the partial COI gene with the haplotype diversity (Hd) = 0.405 and nucleotide diversity (pi) = 0.003. Meanwhile, the Fu's and Tajima's tests were 1.21 and -0.69, respectively. The UPGMA tree with 1,000 × bootstrap replications revealed that Barred rainbowfishes are grouped into similar clusters with Melanotaenia vanheurni, Chilatherina alleni, and Chilatherina bleheri. In conclusion, haplotype 3 (77%) was detected as the common haplotype for Barred rainbowfishes at the Mamberamo River of Western New Guinea. [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]

Introduction: The common bottlenose dolphin (Tursiops truncatus) is one of the most studied cetaceans worldwide; however, information about the genetic structure of wild populations is scarce in some regions like Central America and the Caribbean. There are two known genetic forms identified in the Caribbean based on mitochondrial DNA Control Region (mtDNA-CR) data: the 'inshore (or coastal) form' and the 'Worldwide distributed form'. In general, the inshore form refers to coastal and highly philopatric populations that show low genetic diversity. Worldwide distributed form refers to highly mobile populations with coastal and oceanic individuals that do not show philopatry and usually display high genetic diversity. Objective: To determine the preliminary genetic status of common bottlenose dolphins in La Guajira, Colombian Caribbean, using a hypervariable portion of mtDNA-CR. The obtained haplotypes were compared with samples collected in Panama (likely 'inshore form') and with haplotypes previously found in other areas of the Caribbean. Methods: In 2016, a total of 26 skin samples were obtained by remote biopsy system (PAXARMS) in two locations, La Guajira (Colombia, N=7) and Bocas del Toro (Panama, N=19). DNA was extracted, samples sexed, and a segment of mtDNA-CR (~550-750 bp) was amplified by PCR. The successfully amplified DNA sequences were manually reviewed and cleaned, and subsequently compared with 44 haplotypes previously reported for the Caribbean. Results: The mtDNA-CR sequences from Bocas del Toro shared the same unique inshore haplotype previously reported for this population, while the samples from La Guajira represented six novel haplotypes, five belonging to the Worldwide distributed form and one to the 'inshore form.' Population structure analysis revealed two phylogroups for the Caribbean (FST=0.1353, ΦST=0.3330) with high haplotype diversity: Panama(Bocas del Toro)- Bahamas-Cuba-Mexico (h=0.8489, p=4.2536 %) and Colombia-Costa Rica-Honduras-Puerto Rico (h=0.8837, π=4.2423 %). Conclusions: These findings support the results previously reported for common bottlenose dolphins in Bocas del Toro-Panama and reinforce the need to protect this vulnerable 'inshore' population by treating it as a unique population management unit. Mitochondrial DNA analysis of samples collected from La Guajira dolphins provide the first insight into the genetic diversity of common bottlenose dolphins in this region, indicating the presence of both inshore and Worldwide distributed genetic forms. The potential connectivity of this last form among La Guajira-Colombia, Costa Rica, and Honduras in Central America highlights the need for more genetic and ecological studies to determine the appropriate management units for this species in Central America and the Caribbean. [ABSTRACT FROM AUTHOR]

Upon DNA replication stress, cells utilize the postreplication repair pathway to repair single-stranded DNA and maintain genome integrity. Postreplication repair is divided into 2 branches: error-prone translesion synthesis, signaled by proliferating cell nuclear antigen (PCNA) monoubiquitination, and error-free template switching, signaled by PCNA polyubiquitination. In Saccharomyces cerevisiae, Rad5 is involved in both branches of repair during DNA replication stress. When the PCNA polyubiquitination function of Rad5 s disrupted, Rad5 recruits translesion synthesis polymerases to stalled replication forks, resulting in mutagenic repair. Details of how mutagenic repair is carried out, as well as the relationship between Rad5-mediated mutagenic repair and the canonical PCNA-mediated mutagenic repair, remain to be understood. We find that Rad5-mediated mutagenic repair requires the translesion synthesis polymerase ζ but does not require other yeast translesion polymerase activities. Furthermore, we show that Rad5-mediated mutagenic repair is independent of PCNA binding by Rev1 and so is separable from canonical mutagenic repair. In the absence of error-free template switching, both modes of mutagenic repair contribute additively to replication stress response in a replication timing-independent manner. Cellular contexts where error-free template switching is compromised are not simply laboratory phenomena, as we find that a natural variant in RAD5 is defective in PCNA polyubiquitination and therefore defective in error-free repair, resulting in Rad5- and PCNAmediated mutagenic repair. Our results highlight the importance of Rad5 in regulating spontaneous mutagenesis and genetic diversity in S. cerevisiae through different modes of postreplication repair. [ABSTRACT FROM AUTHOR]

Philippine native pigs (PhNP) are small black pigs domesticated in rural communities in the Philippines. They are valued locally for their various sociocultural roles. Recently, considerable literature has accumulated in the field of native pig production and marketing. However, there is limited research on the genetic diversity of PhNP. No previous study has investigated the evolutionary relatedness among native pigs from various islands and provinces in Luzon and the Visayas, Philippines. In addition, a much debated question is whether the PhNP were interbreeding with or even domesticated from endemic wild pigs. This study aims to clarify some of the uncertainties surrounding the identity and classification of PhNP based on mitochondrial DNA (mtDNA) signatures. Native pig samples (n = 157) were collected from 10 provinces in Luzon and the Visayas. Approximately 650 base pairs of the mtDNA D-loop region were sequenced and analyzed together with publicly available sequences. Pairwise-distance analysis showed genetic separation of North and South Luzon (SL) and the clustering of SL with Visayan pigs. Phylogenetic analysis showed that the PhNP clustered within 3 recognized Asian pig domestication centers: D2 (East Asia), D7 (Southeast Asia) and the Cordillera clade (sister to the Lanyu). We identified 19 haplotypes (1–38 samples each), forming 4 haplogroups, i.e., North Luzon, South Luzon and Visayas, Asian mix and the Cordillera cluster. No endemic wild pig mtDNA was detected in the native pig population, but evidence of interspecific hybridization was observed. This study showed that the Philippine native pigs have originated from at least 3 Sus scrofa lineage and that they were not domesticated from the endemic wild pigs of the Philippines. [ABSTRACT FROM AUTHOR]

In recent decades, the use of genetic polymorphisms related to specific phenotypes, such as eye color, has greatly contributed to the development of the research field called forensic DNA phenotyping (FDP), enabling the investigators of crime cases to reduce the number of suspects, making their work faster and more precise. Eye color is a polygenic phenotype, and many genetic variants have been highlighted, with the major contributor being the HERC2-OCA2 locus, where many single nucleotide variations (SNPs) were identified. Interestingly, the HERC2-OCA2 locus, containing the intronic SNP rs12913832, the major eye color determinant, shows a high level of evolutionary conservation across many species of vertebrates. Currently, there are some genetic panels to predict eye color by genomic DNA analysis, even if the exact role of the SNP variants in the formation of eye color is still poorly understood, with a low level of predictivity in the so-called intermediate eye color. Many variants in OCA2, HERC2, and other genes lie in introns or correspond to synonymous variants, highlighting greater complexity in the mechanism of action of such genes than a simple missense variation. Here, we show the main genes involved in oculocutaneous pigmentation and their structural and functional features, as well as which genetic variants show the highest level of eye color predictivity in currently used FDP assays. Despite the great recent advances and impact of FDP in criminal cases, it is necessary to enhance scientific research to better understand the mechanism of action behind each genetic variant involved in eye color, with the goal of obtaining higher levels of prediction. [ABSTRACT FROM AUTHOR]

The spotted sleeper, Odontobutis interrupta, is a fish species endemic to Korea and shows potential as an aquaculture species. Nevertheless, the population size of this species has declined significantly in recent years. To characterize the population structure and genetic diversity of O. interrupta in Korea, we analyzed four microsatellite loci in twelve populations from four major river systems. The provenance of the population was investigated to discern the origin of the translocated populations. The genetic diversity of the microsatellite ranged from 0.440 to 0.756, showing a high level of diversity similar to that of other freshwater fishes. However, mitochondrial DNA analysis exhibited low genetic diversity (Hd: 0.000–0.674, π: 0.00000–0.00159). The FST values of microsatellites and mitochondrial DNA ranged from 0.096 to 0.498 and −0.046 to 0.951, suggesting genetic admixture among populations. All populations exhibited an effective population size of <100; therefore, preservation efforts to prevent inbreeding depression would be required. The genetic structure could be divided into unique genotypes from the Seomjingang and Geumgang Rivers. However, genetic admixture was observed in all populations, rendering it impossible to distinguish them. Our findings provide fundamental but significant genetic insights pursuant to devising conservation strategies for O. interrupta. [ABSTRACT FROM AUTHOR]

Individuals with specific language impairment (SLI) struggle with language acquisition despite average non-verbal intelligence and otherwise typical development. One SLI account focuses on grammar acquisition delay. The current study aimed to detect novel rare genetic variants associated with performance on a grammar assessment, the Test of Early Grammatical Impairment (TEGI), in English-speaking children. The TEGI was selected due to its sensitivity and specificity, consistently high heritability estimates, and its absence from all but one molecular genetic study. We performed whole exome sequencing (WES) in eight families with SLI (n = 74 total) and follow-up Sanger sequencing in additional unrelated probands (n = 146). We prioritized rare exonic variants shared by individuals with low TEGI performance (n = 34) from at least two families under two filtering workflows: (1) novel and (2) previously reported candidate genes. Candidate variants were observed on six new genes (PDHA2, PCDHB3, FURIN, NOL6, IQGAP3, and BAHCC1), and two genes previously reported for overall language ability (GLI3 and FLNB). We specifically suggest PCDHB3, a protocadherin gene, and NOL6 are critical for ribosome synthesis, as they are important targets of SLI investigation. The proposed SLI candidate genes associated with TEGI performance emphasize the utility of precise phenotyping and family-based genetic study. [ABSTRACT FROM AUTHOR]

Simple Summary: The Arabian horse is probably one of the most historic horse breeds worldwide. It has been selectively bred by the Bedouin tribes in the steppes of Arabia for over 2000 years. Bedouin tribes have created their own classification of strains based on maternal lines. The aim of our study was to investigate genetic differentiation at the level of (i) the current populations (Desert-Bred, Straight Egyptian and Polish Arabians) and (ii) the traditional Bedouin strains. Two hundred and eleven Arabian individuals, representing 12 strains, were sampled. Mitochondrial DNA D-loop analysis showed higher genetic diversity in the Egyptian and Polish Arabian populations than in the Desert-Bred. No genetic markers distinguishing the traditional strains were highlighted in this study, a fact probably due to the lack of interest in this component in modern breeding programs. Some Polish Arabian individuals, who could not be traced back to the Bedouin tribes, appeared to be genetically distinct from the other studied horses, requiring more in-depth study. This research, complemented by future SNP and Y-chromosome analyses, may provide a more accurate evaluation of the relationships between Arabian horse populations′ genetic and traditional classification. Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a subset of the Kingdom of Saudi Arabia (KSA), United Arab Emirates (UAE) and Bahrain (BAH), the Straight Egyptian (EG) and the Polish bloodline (PL), and (ii) to assess the accuracy of the traditional strain classification system based on maternal lines, as stated by the Bedouin culture. To that end, we collected 211 hair samples from stud farms renowned for breeding Arabian show horses from Nejd KSA, Bahrain, Egypt, Qatar, Morocco, UAE, and Poland. The phylogenetic and network analyses of the whole mitochondrial DNA D-loop sequence highlighted a great genetic diversity among the Arabian horse populations, in which about 75% of variance was assigned to populations and 25% to strains. The discriminant analysis of principal components illustrated a relative distinction between those populations. A clear subdivision between traditional strains was found in PL, in contrast to the situation of DB and EG populations. However, several Polish horse individuals could not be traced back to the Bedouin tribes by historical documentation and were shown to differ genetically from other studied Bedouin strains, hence motivating extended investigations. [ABSTRACT FROM AUTHOR]

The implementation of NGS methods into clinical practice allowed researchers effectively to establish the molecular cause of a disorder in cases of a genetically heterogeneous pathology. In cases of several potentially causative variants, we need additional analysis that can help in choosing a proper causative variant. In the current study, we described a family case of hereditary motor and sensory neuropathy (HMSN) type 1 (Charcot–Marie–Tooth disease). DNA analysis revealed two variants in the SH3TC2 gene (c.279G>A and c.1177+5G>A), as well as a previously described variant c.449−9C>T in the MPZ gene, in a heterozygous state. This family segregation study was incomplete because of the proband's father's unavailability. To evaluate the variants' pathogenicity, minigene splicing assay was carried out. This study showed no effect of the MPZ variant on splicing, but the c.1177+5G>A variant in the SH3TC2 gene leads to the retention of 122 nucleotides from intron 10 in the RNA sequence, causing a frameshift and an occurrence of a premature stop codon (NP_078853.2:p.Ala393GlyfsTer2). [ABSTRACT FROM AUTHOR]

Frankliniella Karny is the third most speciose genus within Thysanoptera, with 236 valid species. Despite its high economic relevance and remarkable diversity, the Linnean and Wallacean deficits, as well as the paucity of biological and ecological data are evident, especially due to the confusing taxonomy of the group. In this sense, we carried out a molecular analysis based on the Cytochrome C Oxidase subunit I (COI) gene and an extensive data set towards understanding the molecular delimitation, as well as establishing genetic diversity thresholds among Frankliniella species. Our study included 348 specimens (20 from the present study) referring to 43 BINs (Barcode Index Numbers) available in BOLD. For that, the traditional analysis of DNA barcode (Neighbor-Joining and genetic distances) and the determination of the diversity threshold were carried out, together with two types of phylogenetic analyses (Maximum Likelihood and Bayesian Inference) and five species delimitation algorithms (ABGD, PTP, GMYC, PhyloMap, BIN). Our analyses identified with high confidence 42 putative species in Frankliniella, suggesting cases of taxonomic misidentification, and a threshold of 2.35%, which allowed us to recognize a cryptic diversity and/or species complexes in five species of the genus: F. insularis (Franklin), F. intonsa (Trybom), F. occidentalis (Pergande), F. schultzei (Trybom) and F. tritici (Fitch). The present data demonstrate the efficiency of molecular markers for the identification of independent evolutionary units in Frankliniella, reinforcing the need to carry out an extensive taxonomic review in this important group of thrips since different studies already pointed to incongruity in the diagnosis of species through traditional taxonomy. [ABSTRACT FROM AUTHOR]

In this work, we report a rare allele 29 at locus D2S1338, established during routine forensic practice in a case of first-degree kinship (parenthood). This rare allele variant 29 at locus D2S1338, to the best of our knowledge, is reported for the first time in the Bulgarian population. So far it has not been registered in studies of allele frequencies in the same locus for 20 population groups in Europe and Asia. The presentation of similar genotyping findings relating to rare/unexpected population genetic variation is very important for the examination and documentation of such anomalies. The analysis has been performed for 16 STR loci: D2S1338, SE33, D16S539, D18S51, TH01, D12S391, D3S1358, FGA, vWA, D21S11, D1S1656, D2S441, D8S1179, D19S433, D22S1045, D10S1248 and 2 sex determination systems - Amelogenin and Y indel, set in NGM DetectTM PCR Amplification Kit (Applied Biosystems). The use of allelic witnesses in the diagnostic practice is mandatory in the standard fragment DNA analysis. The allelic witness contains well-known preset alleles for the examined locus. Establishing alleles that are outside the factory preset is important for broadening the scope of the witness and heightening the accuracy of the analysis. Rare allelic variants significantly increase the strength of discrimination when DNA profiles are compared. In this regard, it is important to report any new information about the emergence of rare allele variants detected in a particular population group. [ABSTRACT FROM AUTHOR]

Background: Toxoplasmosis is a parasitic disease caused by compilation protozoan agent Toxoplasma gondii, leading to significant financial and quality-adjusted life-year losses. Overcooked or raw meat consumption has been a considerable transmission route. The present study was conducted to determine the seropositivity rate of T. gondii in sheep and goats by serological and molecular tests and genotyping of obtained isolates in northeast Iran. Methods: Blood and tissue samples (diaphragm, heart) of 296 animals (including 168 sheep and 128 goats) were collected from the slaughterhouse in Quchan Country from august 2016 to April 2017. Modified agglutination test (MAT) and the PCR method performed to detect parasite DNA on tissues.PCR-RFLP method of GRA6 gene was used to determine the genotype of T. gondii. In addition, sequencing analysis was performed to evaluate the Toxoplasma type strains. Results: Serum positive for MAT results were found in 27.4% of sheep and 23.4% of goats. Positive PCR of B1 gene results in diaphragm and heart tissues of sheep and goats was 47.8% and 26.1%, 40% and 23.3%, respectively. PCR of GRA6 gene results were positive in 10 samples that RFLP technique results using MseI enzyme revealed genotype I. Sequencing and phylogenetic analysis revealed DNA of all samples was closely related to Toxoplasma type I. Conclusion: Concerning the high seropositivity rate of toxoplasmosis, undertaking an appropriate preventive program for reducing the prevalence of T. gondii infection by raw or undercooked meat consumption of livestock is recommended. Our study supports the notion that these animals' consumption of raw and undercooked meat can be a probable source of human toxoplasmosis. [ABSTRACT FROM AUTHOR]

Simple Summary: Head and Neck Squamous Cell Carcinomas (HNSCCs) are cancers that originate from cells of the head and neck region, including the mouth, nose, and throat. The diversity of these cell types is also mirrored by the high number of different mutations that promote cancer development and progression. For the clinical management of this disease, it is important to identify biomarkers that allow early detection or predict relapse and resistance to therapy. A non-invasive way to monitor these markers over time are so called liquid biopsies, which mostly refers to the detection and analysis of tumor cells or cell-free DNA (cfDNA) in the blood of patients. This review summarizes our current understanding of HNSCC genetics and discusses how the detection of genetic variation in the cfDNA of HNSCC patients can be used to monitor disease and guide therapy. Tumors shed cell-free DNA (cfDNA) into the plasma. "Liquid biopsies" are a diagnostic test to analyze cfDNA in order to detect minimal residual cancer, profile the genomic tumor landscape, and monitor cancers non-invasively over time. This technique may be useful in patients with head and neck squamous cell carcinoma (HNSCC) due to genetic tumor heterogeneity and limitations in imaging sensitivity. However, there are technical challenges that need to be overcome for the widespread use of liquid biopsy in the clinical management of these patients. In this review, we discuss our current understanding of HNSCC genetics and the role of cfDNA genomic analyses as an emerging precision diagnostic tool. [ABSTRACT FROM AUTHOR]

Background: Fetal Alcohol Spectrum Disorders (FASD) are the most common cause of neurocognitive impairment and social inadaptation, affecting 1 birth in 100. Despite the existence of precise diagnostic criteria, the diagnosis remains difficult, often confounded with other genetic syndromes or neurodevelopmental disorders. Since 2016, Reunion Island has been a pilot region for the identification, diagnosis, and care of FASD in France. Objective: To evaluate the prevalence and the types of Copy Number Variations (CNV) in FASD patients. Methods: A retrospective chart review of 101 patients diagnosed with FASD in the Reference Center for developmental anomalies and in the FASD Diagnostic Center of the University Hospital was performed. Records of all patients were reviewed to obtain their medical history, family history, clinical phenotype, and investigations, including genetic testing (CGH- or SNP-array). Results: A rate of 20.8% (n = 21) of CNVs was found including 57% (12/21) of pathogenic variants and 29% (6/21) of variants of uncertain signification (VUS). Conclusion: A particularly high number of CNVs was found in children and adolescents with FASD. It reinforces the plea for a multidisciplinary approach for developmental disorders to explore both environmental factors, such as avoidable teratogens and intrinsic vulnerabilities, especially genetic determinants. [ABSTRACT FROM AUTHOR]

Simple Summary: The characterisation of normal-karyotype acute myeloid leukaemia (AML-NK) requires further refinement based on genetic variations. In this study, we ascertained genomic biomarkers via DNA and RNA sequencing in eight AML-NK patients during diagnosis and after achieving complete remission. We discovered putative variants affecting gene regulation and functional enrichments dysregulating transcription and DNA-binding transcription activator activity RNA polymerase II-specific in our cohort. Characterising genomic variants is paramount in understanding the pathogenesis and heterogeneity of normal-karyotype acute myeloid leukaemia (AML-NK). In this study, clinically significant genomic biomarkers were ascertained using targeted DNA sequencing and RNA sequencing on eight AML-NK patients' samples collected at disease presentation and after complete remission. In silico and Sanger sequencing validations were performed to validate variants of interest, and they were followed by the performance of functional and pathway enrichment analyses for overrepresentation analysis of genes with somatic variants. Somatic variants involving 26 genes were identified and classified as follows: 18/42 (42.9%) as pathogenic, 4/42 (9.5%) as likely pathogenic, 4/42 (9.5%) as variants of unknown significance, 7/42 (16.7%) as likely benign and 9/42 (21.4%) as benign. Nine novel somatic variants were discovered, of which three were likely pathogenic, in the CEBPA gene with significant association with its upregulation. Transcription misregulation in cancer tops the affected pathways involving upstream genes (CEBPA and RUNX1) that were deregulated in most patients during disease presentation and were closely related to the most enriched molecular function gene ontology category, DNA-binding transcription activator activity RNA polymerase II-specific (GO:0001228). In summary, this study elucidated putative variants and their gene expression profiles along with functional and pathway enrichment in AML-NK patients. [ABSTRACT FROM AUTHOR]

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Knowledge of the spatial distribution of European chestnut (Castanea sativa Mill.) cultivar diversity is essential for managing and conserving the genetic resources of this fruit tree species in Southern Italy. To this goal, the present work investigated the feasibility of mapping, through spatial representation, the distribution of genetic diversity of traditional chestnut varieties in the area of the Roccamonfina Regional Park in the Campania Region. After Principal Coordinates Analysis (PCoA) of molecular-genetic data, chestnuts formed varietal groups in a leopard spot on PCoA plots with a relatively high degree of genetic diversity. Successively, a Geographic Information System (GIS) tool utilized these molecular-genetic data to create a genetic divergence surface by geospatial interpolation on the geographic map of the Regional Park corresponding to each chestnut variety. The regions containing more biodiversity richness resulted in differentially colored from those containing cultivars less genetically distant from each other; thus, the area in study was consistently colored according to the allelic richness as evaluated by molecular-genetic markers. The combined use of tools for molecular and spatial analysis allowed for drafting genetic landscapes with the aim of extracting useful information for the safeguarding of the chestnut biodiversity at risk. [ABSTRACT FROM AUTHOR]

Melon is an important horticultural crop with a pleasant aromatic flavor and abundance of health-promoting substances. Numerous melon varieties have been cultivated worldwide in recent years, but the high number of varieties and the high similarity between them poses a major challenge for variety evaluation, discrimination, as well as innovation in breeding. Recently, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), two robust molecular markers, have been utilized as a rapid and reliable method for variety identification. To elucidate the genetic structure and diversity of melon varieties, we screened out 136 perfect SSRs and 164 perfect SNPs from the resequencing data of 149 accessions, including the most representative lines worldwide. This study established the DNA fingerprint of 259 widely-cultivated melon varieties in China using Target-seq technology. All melon varieties were classified into five subgruops, including ssp. agrestis, ssp. melo, muskmelon and two subgroups of foreign individuals. Compared with ssp. melo, the ssp. agrestis varieties might be exposed to a high risk of genetic erosion due to their extremely narrow genetic background. Increasing the gene exchange between ssp. melo and ssp. agrestis is therefore necessary in the breeding procedure. In addition, analysis of the DNA fingerprints of the 259 melon varieties showed a good linear correlation (R2 = 0.9722) between the SSR genotyping and SNP genotyping methods in variety identification. The pedigree analysis based on the DNA fingerprint of 'Jingyu' and 'Jingmi' series melon varieties was consistent with their breeding history. Based on the SNP index analysis, ssp. agrestis had low gene exchange with ssp. melo in chromosome 4, 7, 10, 11and 12, two specific SNP loci were verified to distinguish ssp. agrestis and ssp. melon varieties. Finally, 23 SSRs and 40 SNPs were selected as the core sets of markers for application in variety identification, which could be efficiently applied to variety authentication, variety monitoring, as well as the protection of intellectual property rights in melon. [ABSTRACT FROM AUTHOR]

Cerebral adrenoleukodystrophy (CALD) is a fatal genetic disease characterized by rapid, devastating neurological decline, with a narrow curative treatment window in the early stage. Non-canonical splice-site (NCSS) variants can easily be missed during genomic DNA analyses, and only a few of them in ABCD1 have been explored. Here, we studied a Chinese patient with clinical features similar to those of early-stage CALD but with a negative molecular diagnosis and a sibling who had presumably died of CALD. Trio-based whole-exome sequencing (trio-WES) and RNA sequencing (RNA-Seq) revealed a novel hemizygote NCSS variant c.901-25_901-9 del in ABCD1 intron 1, resulting in a complex splicing pattern. The in vitro minigene assay revealed that the c.901-25_901-9 del construct contained two aberrant transcripts that caused skipping of exon 2 and a small 48-bp deletion on left of the same exon. We identified a novel NCSS variant, that extends the spectrum of the known ABCD1 variants, and demonstrated the pathogenicity of this gene variant. Our findings highlight the importance of combining RNA-Seq and WES techniques for prompt diagnosis of leukodystrophy with NCSS variants. [ABSTRACT FROM AUTHOR]

Local adaptation and phenotypic plasticity can lead to environment-related morphological and genetic variations in freshwater fish. Studying the responses of fish to environmental changes is crucial to understand their vulnerability to human-induced changes. Here, we used a latitudinal gradient as a proxy for past and present environmental factors and tested its influences on both genetic and morphological patterns. We selected as a suitable biogeographic model, the barbels, which inhabit 17 Adriatic basins of the central-southern Italian Peninsula, and explored association among attributes from genetic, morphological, and environmental analyses. The analysis of the mitochondrial DNA control region evidenced a southward significant increase in the number of private haplotypes, supporting the isolation of the southernmost populations related to the Mio-Pleistocene events. In contrast, morphology was mainly affected by changes in the present environmental conditions. Particularly, the number of scales and fish coloration were clearly associated to latitude, and thus thermal and hydrological conditions. Other morphometric and functional traits varied under the selective pressure of other environmental factors like elevation and distance from headwater. These results highlight the sensitivity of barbels to climate changes, which can serve as a basis for future eco-evolutionary and conservation studies. [ABSTRACT FROM AUTHOR]

The incapacity to synthesize certain components of pulmonary surfactant causes a heterogeneous group of rare respiratory diseases called genetic disorders of surfactant dysfunction. We report a female full-term infant with neonatal respiratory distress of early onset due to inherited SP-B deficiency. The infant failed oxygen weaning at multiple trials. Chest computed tomography was performed on the 29th day of life revealing groundglass opacities, regular interlobular septal thickening and fine interlobular reticulations. Analysis of genomic DNA showed homozygosity for an extremely rare SFTPB gene variant (c.620A>G, p. Tyr207Cys). Both parents were heterozygotes for the mutation. The diagnosis of congenital SP-B deficiency should be suspected whenever an early and acute respiratory failure in a term or near-term infant does not resolve after five days of age: diagnostic confirmation can be easily and rapidly obtained with the analysis of genomic DNA. [ABSTRACT FROM AUTHOR]

A few months after its publication, my friend Naoyuki Takahata presented me with a copy of the book he had written with Jan Klein. The cover of the book was most unusual. It was the reproduction of a portion of the painting of Paul Gauguin's masterpiece, now in the Museum of Fine Arts in Boston, "D'oú Venons-Nous? Que Sommes-Nous? Où Allons-Nous?" ("Where Do We Come From? What Are We? Where Are We Going?"), painted in Tahiti in 1897, six years before his tragic death. Gauguin's painting (which, interestingly, has to be viewed from right to left) depicts the spectrum of human activity from birth to death. Klein and Takahata titled their book Where Do We Come From? The Molecular Evidence for Human Descent, which I reviewed in Current Science (10 September 2002). [ABSTRACT FROM AUTHOR]

Background: Coronary heart disease has become the leading cause of death in developed countries, and dyslipidemia is closely associated with the risk of cardiovascular disease. Dyslipidemia is caused by the abnormal regulation of several genes and signaling pathways, and dyslipidemia is influenced mainly by genetic variation. AMFR, FBXW7, INSIG1, INSIG2, and MBTPS1 genes are associated with lipid metabolism. In a recent GWAS study, the GRINA gene has been reported to be associated with dyslipidemia, but its molecular mechanism has not been thoroughly investigated. The correlation between the DNA methylation of these genes and lipid metabolism has not been studied. This study aimed to examine the relationship between the DNA methylation of these genes and the risk of dyslipidemia by comparing the methylation levels of dyslipidemia and control samples. Methods: A case-control research method was used in this study. The patient's blood samples were collected at the Heart Center of the First Affiliated Hospital of Xinjiang Medical University. In the Xinjiang Han population, 100 cases of hyperlipidemia and 80 cases of the control group were selected. The two groups were age and gendermatched. Quantitative methylation analysis of CpG sites in the gene promoter regions of six genes was performed by Solexa high-throughput sequencing. Results: The DNA methylation levels of 23 CpG sites in six genes were shown to be associated with hyperlipidemia, and a total of 20 DNA methylation haplotypes showed statistically significant differences between the two groups. When compared with the control group, the dyslipidemia group had significantly higher levels of methylation in the GRINA gene (2.68 vs 2.36, P = 0.04). Additionally, we also discovered a significant methylation haplotype of GRINA (P = 0.017). Conclusion: The findings of this study reveal that the DNA methylation of GRINA increases the risk for dyslipidemia in humans. [ABSTRACT FROM AUTHOR]

Moving forward, the inclusion of a larger number of microtia/OAVS-related genes or the use of whole-exome sequencing should identify new variants that can be considered in future gene-gene interaction studies [[62]]. One significant gene-gene interaction related to the presentation of microtia/OAVS was identified: that between the non-synonymous p.(Pro1099Arg) I TCOF1 i variant and the synonymous p.(Leu858=) I SALL1 i variant (Figure 1). Keywords: gene-gene interactions; microtia; Mexican population; Multifactor Dimensionality Reduction (MDR); next-generation sequencing; OAVS EN gene-gene interactions microtia Mexican population Multifactor Dimensionality Reduction (MDR) next-generation sequencing OAVS 1723 11 11/17/22 20221101 NES 221101 1. Conclusions Although gene-gene interactions are known to play an important role in the etiology of many complex diseases, no previous study has addressed gene interactions in patients with microtia/OAVS. [Extracted from the article]

Morinda officinalis How is well-known as a valuable medicinal plant found in some regions of Vietnam. This species is mainly used for treating male impotence, irregular menstruation, and rheumatoid arthritis. This study aimed to identify the species of and genetic diversity in three M. officinalis populations: one each in Quang Binh (QB), Thua Thien Hue (TTH), and Quang Nam (QN). In this study, four DNA barcoding markers (ITS1, ITS2, matK, and rbcL) were used to identify the species and 22 microsatellite markers were applied for population structure and diversity analyses. The results showed that the sequences of gene regions studied in M. officinalis had a high similarity (>95%) to the ITS1, ITS2, matK, and rbcL sequences of M. officinalis on BLAST. Of the four DNA barcoding markers used, ITS1 and ITS2 showed higher efficiency in DNA amplification of M. officinalis. From this study, 27 GenBank codes were published on BLAST. The results also revealed high levels of genetic diversity in populations. The average observed and expected heterozygosity values were HO = 0.513 and HE = 0.612, respectively. The average FST value was 0.206. Analysis of molecular variance (AMOVA) showed 70% variation within populations and 30% among populations. The population structure of M. officinalis inferred in STRUCTURE revealed that the optimum number of genetic groups for the admixture model was K = 2. These findings provided vital background information for future studies in the conservation of M. officinalis in both ex situ and in situ plans. [ABSTRACT FROM AUTHOR]

Background: Voltage‐gated sodium channels are essential for the generation and conduction of electrical impulses in excitable cells. Sodium channel Nav1.7, encoded by the SCN9A‐gene, has been of special interest in the last decades because missense gain‐of‐function mutations have been linked to a spectrum of neuropathic pain conditions, including inherited erythermalgia (IEM), paroxysmal extreme pain disorder (PEPD), and small fiber neuropathy (SFN). Methods: In this case report, we present a 61‐year‐old woman who was referred to our tertiary referral center in a standard day care setting with suspicion of SFN. We performed additional investigations: skin biopsy to determine the intra‐epidermal nerve fiber density (IENFD), quantitative sensory testing (QST), and blood examination (including DNA analysis) for possible underlying conditions. Results: The patient showed a clinical picture that fulfilled the criteria of IEM, PEPD, and SFN. DNA analysis revealed the heterozygous variant c.554G > A in the SCN9A‐gene (OMIM 603415). This variant has already been described in all three human pain conditions separately, but never in one patient having symptoms of all three conditions. Because its pathogenicity has never been functionally confirmed, the variant is classified as a variance of unknown significance (VUS)/risk factor. This suggests that another genetic and/or environmental substrate plays a role in the development of neuropathic conditions like described. Conclusion: We have described this as the SCN9A‐pain triangle phenomenon. Treatment should focus on pain management, genetic counseling, and improving/maintaining quality of life by treating symptoms and, if indicated, starting a rehabilitation program. [ABSTRACT FROM AUTHOR]

Background: Ticks (order Ixodida) are ectoparasites, vectors and reservoirs of many infectious agents affecting humans and domestic animals. However, the lack of information on tick genomic diversity leaves significant gaps in the understanding of the evolution of ticks and associated bacteria. Results: We collected > 20,000 contemporary and historical (up to 60 years of preservation) tick samples representing a wide range of tick biodiversity across diverse geographic regions in China. Metagenomic sequencing was performed on individual ticks to obtain the complete or near-complete mitochondrial (mt) genome sequences from 46 tick species, among which mitochondrial genomes of 23 species were recovered for the first time. These new mt genomes data greatly expanded the diversity of many tick groups and revealed five cryptic species. Utilizing the same metagenomic sequence data we identified divergent and abundant bacteria in Haemaphysalis, Ixodes, Dermacentor and Carios ticks, including nine species of pathogenetic bacteria and potentially new species within the genus Borrelia. We also used these data to explore the evolutionary relationship between ticks and their associated bacteria, revealing a pattern of long-term co-divergence relationship between ticks and Rickettsia and Coxiella bacteria. Conclusions: In sum, our study provides important new information on the genetic diversity of ticks based on an analysis of mitochondrial DNA as well as on the prevalence of tick-borne pathogens in China. It also sheds new light on the long-term evolutionary and ecological relationships between ticks and their associated bacteria. [ABSTRACT FROM AUTHOR]

The goal of our study was to estimate genetic diversity of Arabian horses from Polish state studs which could have changed due to the extensive use of foreign sires in Polish breeding after 1989. The analysis focused on 1,388 Arabian mares born from 1996 to 2013 in the Białka, Janów Podlaski and Michałów studs. Basic parameters of pedigree, mitochondrial DNA and microsatellite analyses were considered in the study. In the pedigree analysis, changes in the gene pool over the years were noted through the considerable increase of contribution of new founders' genes and the considerable decrease of inbreeding level. The microsatellite analysis confirmed progressive changes in the gene pool but, contrary to expectations, only three new microsatellite alleles were detected, and a decreased level of heterozygosity was observed. In turn, mtDNA analysis showed a stable genetic situation in the studs throughout the period analysed. The results of the analyses present a diverse picture of the population, which is clearly divided into the three subpopulations of Białka, Janów Podlaski and Michałów, although the pictures presented differed depending on the analytical methods used. Genetic differences among the studs should be considered a positive feature of the Polish population. In order to preserve the present level of population genetic diversity, changes in breeding policy are needed that aim to stop the loss of genes of the historical ancestors of Polish Arabian horses. [ABSTRACT FROM AUTHOR]

Simple Summary: Multiple myeloma (MM) is characterized by an expansion of plasma cells in the bone marrow (BM). The genetics of MM are highly complex with multiple mutations and genetic subpopulations of tumor cells that arise during the disease evolution, affecting prognosis and treatment response. Standard bone marrow DNA analysis requires an invasive sample collection and does not always reflect the complete mutation profile. Therefore, we examined the possibility to use peripheral blood-based liquid biopsies as an alternative DNA source for mutation profiling. By comparing DNA from circulating tumor cells with circulating tumor-derived vesicles and cell-free DNA (cfDNA), we found that the latter provided the best concordance with bone marrow DNA and also showed mutations derived from myeloma cell populations that were undetectable in bone marrow. Our comparative study indicates that cfDNA is the preferable circulating biomarker for genetic characterization in MM and can provide additional information compared to standard BM analysis. The analysis of bone marrow (BM) samples in multiple myeloma (MM) patients can lead to the underestimation of the genetic heterogeneity within the tumor. Blood-derived liquid biopsies may provide a more comprehensive approach to genetic characterization. However, no thorough comparison between the currently available circulating biomarkers as tools for mutation profiling in MM has been published yet and the use of extracellular vesicle-derived DNA for this purpose in MM has not yet been investigated. Therefore, we collected BM aspirates and blood samples in 30 patients with active MM to isolate five different DNA types, i.e., cfDNA, EV-DNA, BM-DNA and DNA isolated from peripheral blood mononucleated cells (PBMNCs-DNA) and circulating tumor cells (CTC-DNA). DNA was analyzed for genetic variants with targeted gene sequencing using a 165-gene panel. After data filtering, 87 somatic and 39 germline variants were detected among the 149 DNA samples used for sequencing. cfDNA showed the highest concordance with the mutation profile observed in BM-DNA and outperformed EV-DNA, CTC-DNA and PBMNCs-DNA. Of note, 16% of all the somatic variants were only detectable in circulating biomarkers. Based on our analysis, cfDNA is the preferable circulating biomarker for genetic characterization in MM and its combined use with BM-DNA allows for comprehensive mutation profiling in MM. [ABSTRACT FROM AUTHOR]

Purpose: Alström Syndrome (AS) is an autosomal recessive hereditary disease with the characteristics of multiorgan dysfunction. Due to the heterogeneity of clinical manifestations of AS, genetic testing is crucial for the diagnosis of AS. Herein, we used whole-exome sequencing (WES) to determine the genetic causes and characterize the clinical features of three affected patients in two Chinese families with Alström Syndrome.Materials and Methods: Three affected patients (initially diagnosed as achromatopsia). and five asymptomatic members were recruited for both genetic and clinical tests. The complete ophthalmic examinations and systemic examinations were performed on all participants. Whole exome sequencing (WES) was performed for mutation detection. The silico analysis was also applied to predict the pathogenesis of identified pathogenic variants.Results: In family 1, the proband showed low vision, hyperopia, photophobia, nystagmus, and total color blindness. DNA analysis revealed that she carried a compound heterozygote with two novel pathogenic variants in the ALMS1 gene NM_015120.4:c.10379del (NP_055935.4:p.(Asp2252Tyr)) and NM_015120.4:c.11641_11642del (NP_055935.4:p.(Val3881ThrfsTer11)). Further systemic examinations showed short stature, acanthosis nigricans, and sensorineural hearing loss. In family 2, two affected siblings presented the low vision, hyperopia, photophobia, nystagmus, and total color blindness. DNA analysis revealed that they carried a same compound heterozygote with two novel pathogenic variants in the ALMS1 gene NM_015120.4:c.10379del (NP_055935.4:p.(Asn3460IlefsTer49)), NM_015120.4:c.10819C > T (NP_055935.4:p.(Arg3607Trp)). Further systemic examinations showed obesity and mild abnormalities of lipid metabolism. According to the genetic testing results and further systemic analysis, the three affected patients were finally diagnosed as Alström Syndrome (AS).Conclusions: We found two new compound heterozygous pathogenic variants of the ALMS1 gene and determined the diagnosis as Alström Syndrome in three patients of two Chinese families. Our study extends the genotypic and phenotypic spectrums for ALMS1 -AS and emphasizes the importance of gene testing in assisting the clinical diagnosis for cases with phenotypic diversities, which would help the AS patients with early diagnosis and treatment to reduce future systemic damage. [ABSTRACT FROM AUTHOR]

Simple Summary: Salivary gland cancer (SGC) is a rare and heterogeneous cancer for which limited treatment options are available in the palliative treatment setting. Characterization of the SGC genetic landscape to identify actionable aberrations is therefore important. This research aimed to comprehensively assess the prevalence of various types of actionable aberrations, including gene fusions, in a large cohort of patients with different SGC subtypes. The combined approach using RNA- and DNA-based targeted next-generation sequencing panels revealed the presence of gene fusions in half of the cases, including several fusions not previously described in SGC. Targets for genetically matched therapies were identified in 28.3–81.8% of cases, depending on the SGC subtype (overall 53.7% of the cases). This highlights the potential of molecular diagnostics to select systemic treatment in SGC. Introduction: Salivary gland cancer (SGC) is a rare cancer for which systemic treatment options are limited. Therefore, it is important to characterize its genetic landscape in search for actionable aberrations, such as NTRK gene fusions. This research aimed to identify these actionable aberrations by combining NGS-based analysis of RNA (gene fusions) and DNA (single and multiple nucleotide variants, copy number variants, microsatellite instability and tumor mutational burden) in a large cohort of SGC patients. Methods: RNA and DNA were extracted from archival tissue of 121 patients with various SGC subtypes. Gene fusion analysis was performed using a customized RNA-based targeted NGS panel. DNA was sequenced using a targeted NGS panel encompassing 523 cancer-related genes. Cross-validation of NGS-based NTRK fusion detection and pan-TRK immunohistochemistry (IHC) was performed. Results: Fusion transcripts were detected in 50% of the cases and included both known (MYB-NFIB, MYBL1-NFIB, CRTC1-MAML2) and previously unknown fusions (including transcripts involving RET, BRAF or RAD51B). Only one NTRK fusion transcript was detected, in a secretory carcinoma case. Pan-TRK IHC (clone EPR17341) was false positive in 74% of cases. The proportion of patients with targets for genetically matched therapies differed among subtypes (salivary duct carcinoma: 82%, adenoid cystic carcinoma 28%, mucoepidermoid carcinoma 50%, acinic cell carcinoma 33%). Actionable aberrations were most often located in PIK3CA (n = 18, 15%), ERBB2 (n = 15, 12%), HRAS and NOTCH1 (both n = 9, 7%). Conclusions: Actionable genetic aberrations were seen in 53.7% of all SGC cases on the RNA and DNA level, with varying percentages between subtypes. [ABSTRACT FROM AUTHOR]

Background: Autosomal dominant polycystic kidney disease (ADPKD), one of the common inherited disorders in humans, is characterized by the development and enlargement of renal cysts, often leading to end-stage renal disease (ESRD). In this study, Iranian ADPKD families were subjected to high-throughput DNA sequencing to find potential causative variants facilitating the way toward risk assessment and targeted therapy. Methods: Our protocol was based on the targeted next generation sequencing (NGS) panel previously developed in our center comprising 12 genes involved in PKD. This panel has been applied to investigate the genetic causes of 32 patients with a clinical suspicion of ADPKD. Results: We identified a total of 31 variants for 32 individuals, two of which were each detected in two individuals. Twenty-seven out of 31 detected variants were interpreted as pathogenic/likely pathogenic and the remaining 4 of uncertain significance with a molecular diagnostic success rate of 87.5%. Among these variants, 25 PKD1/2 pathogenic/likely pathogenic variants were detected in 32 index patients (78.1%), and variants of uncertain significance in four individuals (12.5% in PKD1/2). The majority of variants was identified in PKD1 (74.2%). Autosomal recessive PKD was identified in one patient, indicating the similarities between recessive and dominant PKD. In concordance with earlier studies, this biallelic PKD1 variant, p.Arg3277Cys, leads to rapidly progressive and severe disease with very early-onset ADPKD. Conclusion: Our findings suggest that targeted gene panel sequencing is expected to be the method of choice to improve diagnostic and prognostic accuracy in PKD patients with heterogeneity in genetic background. [ABSTRACT FROM AUTHOR]

Wild Foeniculum vulgare populations from the region of Istria have been subjected to a genetic and chemical study. Headspace-gas chromatography analysis of volatile secondary metabolites and PCR-RFLP analysis of the ribosomal DNA internal transcribed spacer region has been chosen to analyze the chemical and genetic traits of single plants, respectively. Large intrapopulation and interpopulation differences have been observed in both chemical profiles and restriction patterns of PCR products. The data from chemical and genetic analyses were pooled and used to assess allele frequencies of three putative genetic loci on individual populations. The pooled allele frequencies were used to determine interpopulation distances for phenogram reconstruction. The combined use of chemical and genetic datasets for genetic variation analysis proved to be a more comprehensive approach for such a study, compared to the use of single datasets, even using such relatively simple analytical tools. [ABSTRACT FROM AUTHOR]