Nucleotide Sequence Variation Research Articles

Viral Diversity in Mixed Tree Fruit Production Systems Determined through Bee-Mediated Pollen Collection

Commercially cultivated Prunus species are commonly grown in adjacent or mixed orchards and can be infected with unique or commonly shared viruses. Apple (Malus domestica), another member of the Rosacea and distantly related to Prunus, can share the same growing regions and common pathogens. Pollen can be a major route for virus transmission, and analysis of the pollen virome in tree fruit orchards can provide insights into these virus pathogen complexes from mixed production sites. Commercial honey bee (Apis mellifera) pollination is essential for improved fruit sets and yields in tree fruit production systems. To better understand the pollen-associated virome in tree fruits, metagenomics-based detection of plant viruses was employed on bee and pollen samples collected at four time points during the peak bloom period of apricot, cherry, peach, and apple trees at one orchard site. Twenty-one unique viruses were detected in samples collected during tree fruit blooms, including prune dwarf virus (PDV) and prunus necrotic ringspot virus (PNRSV) (Genus Ilarvirus, family Bromoviridae), Secoviridae family members tomato necrotic ringspot virus (genus Nepovirus), tobacco necrotic ringspot virus (genus Nepovirus), prunus virus F (genus Fabavirus), and Betaflexiviridae family member cherry virus A (CVA; genus Capillovirus). Viruses were also identified in composite leaf and flower samples to compare the pollen virome with the virome associated with vegetative tissues. At all four time points, a greater diversity of viruses was detected in the bee and pollen samples. Finally, the nucleotide sequence diversity of the coat protein regions of CVA, PDV, and PNRSV was profiled from this site, demonstrating a wide range of sequence diversity in pollen samples from this site. These results demonstrate the benefits of area-wide monitoring through bee pollination activities and provide new insights into the diversity of viruses in tree fruit pollination ecosystems.

Nucleotide sequence variants, gene expression and serum profile of immune and antioxidant markers associated with bacterial diarrhea susceptibility in Barki lambs

BackgroundDespite the fact that diarrhea is more accurately described as a clinical symptom than a disease. Diarrhea is one of the most important issues in ovine medicine, particularly in lambs, and because of high morbidity and mortality rate, sluggish growth performance, and veterinary costs, it is believed to be a major source of economic loss. Salmonella and enterotoxigenic Escherichia coli are the most common and commercially significant agents responsible for diarrhea.ObjectiveThe objective of this study was to monitor the nucleotide sequence variations, gene expression, serum inflammatory and oxidative stress biomarkers in diarrheic lambs. Another aim was to identify different pathotypes and virulence genes of Salmonella and E. coli causing diarrhea.MethodologyBlood samples were taken from 50 Barki who were diarrheal and 50 who appeared to be healthy, and then divided in 3 portions, with EDTA added to the first part for CBC, DNA and RNA extraction. The second sample received 5000 I.U. of heparin calcium, and a clean plain tube was used for the third component. The second and third sections were centrifuged to extract serum and plasma until the biochemical and immunological analysis was completed. Fecal samples were collected for bacteriological examination, and the bacteria were identified by PCR analysis. PCR-DNA sequencing was conducted for immune (SELL, JAK2, SLC11A1, IL10, FEZF1, NCF4, LITAF, SBD2, NFKB, TNF-α, IL1B, IL6, LGALS, and CATH1), antioxidant (SOD1, CAT, GPX1, GST, Nrf2, Keap1, HMOX1, and NQO1), and GIT health (CALB1, GT, and MUC2) genes in healthy and diarrheic lambs.ResultsVirulent genetic markers of pathogenic characteristics of E. coli (astA, Vt2e (Stx2e), CFA/I, groES and luxS) and Salmonella (invA, SopB, bcfC and avrA) were detected in all diarrheic lambs. PCR-DNA sequencing of immune, antioxidant and intestinal health genes found eleven single nucleotide polymorphisms (SNPs) linked to either diarrhea resistance or susceptibility in Barki lambs. Transcript levels of immune, antioxidant, and GIT health (CALB1, GT, and MUC2) genes varied between healthy and diarrheic lambs. Nucleotide sequence variation of the genes under inquiry between reference sequences in GenBank and those of the animals under investigation verified all identified SNPs. Significant (P = 0.001) erythrocytosis, neutrophilic leukocytosis, with lymphocytopenia were observed in diarrheic lambs. Significant (P = 0.001) increases in serum IL-1α, IL-1β, IL-6, TNF-α (90.5 ± 1.7, 101.8 ± 1.7, 72.3 ± 6.6, 71.26 ± 4.89 Pg/ml, respectively), serum Fb, Cp, Hp, SAA (230.7 ± 12.4 mg/dl, 6.5 ± 0.07 mg/dl, 2.5 ± 0.09 g/dl, 7.4 ± 0.4 mg/L, respectively), free radicals (MDA, NO), cortisol (6.91 ± 0.18 μg/dl) and growth hormone, with significant (P = 0.001) decreases in serum IL-10 (81.71 ± 1.05 Pg/ml), antioxidants (CAT, GPx), insulin, triiodothyronine (T3) and thyroxine (T4) in diarrheic lambs.ConclusionsThe study's findings provided credence to the theory that marker-assisted selection (MAS) could be used to predict and prevent diarrhea in Barki sheep by selecting lambs based on SNPs in genes linked to inflammation, antioxidants, and intestinal health. In order to establish an efficient management protocol and determine the most susceptible risk period for disease occurrence, gene expression profiles of the genes under investigation, pro-inflammatory cytokines and acute phase proteins may also be utilized as proxy biomarkers for lamb enteritis.

Mitochondrial DNA sequence-based identification of two subterranean termite species, from Riyadh Province, Kingdom of Saudi Arabia.

Termites are economically important wood-destroying and agricultural pests. The termite fauna almost consists of 2900 described species in 286 genera worldwide. In the present study, hundreds of termite samples from 42 different locations in the Riyadh province were collected. These samples were previously used for morphometric identification and reported two subterranean termite species, Coptotermes heimi and Psammotermes hypostoma, in the family Rhinotermitidae. In the present study, these samples were analysed using DNA barcoding with the mitochondrial cytochrome c oxidase subunit 1 gene to confirm the conventional taxonomical identification on a molecular basis. The obtained COI gene sequences of all 42 termite specimens were submitted to GenBank (accession numbers: ON529959-ON529969, OP825131-OP825132, and OP890882-OP890910). Eleven of the 42 samples were thus identified as C. heimi and the remaining 31 samples as P. hypostoma, which were phylogenetically analysed. All the 11 C. heimi sequences were grouped in a single clade, indicating close relatedness. While 31 sequences of P. hypostoma constituted two clades in the phylogenetic tree. Pairwise nucleotide sequence identity and divergence analysis showed that C. heimi sequences showed high nucleotide identities of 87.6-99.5% and less divergence ranging from 0.5% to 13.6%. Similarly, sequences of P. hypostoma also showed high nucleotide identity of 78.6-100% and low divergence among them ranging from 0-10.7%. A further application, significance, and shortcomings of COI-based DNA barcoding have been discussed. DNA barcoding using the COI gene is a reliable tool to distinguish C. heimi and P. hypostoma genotypes.

Characterisation of Ovine KRTAP19-3 and Its Impact on Wool Traits in Chinese Tan Sheep.

Wool, a natural fibre derived from sheep, can present a challenge to wool processing and manufacturing industries because of the variation in fibre traits. Genetic improvement offers one solution to this challenge, and having a better understanding of the genes that affect wool fibre traits is therefore important. Here, we describe ovine KRTAP19-3, a new member of the KAP19 gene family. Phylogenetic analysis revealed its relationship to other known KRTAP19 gene sequences, and an analysis of the nucleotide sequence variation in KRTAP19-3 from 288 sheep of a variety of breeds revealed six unique variant sequences. Among these variants, eleven single nucleotide polymorphisms (SNPs) were detected, with six located in the coding region. Three of these coding region SNPs were non-synonymous and would result in amino acid changes. Associations were observed between the presence of specific sequence variants in Chinese Tan sheep and wool trait variation, particularly an increase in fibre diameter variability in the heterotypic hair fibres. These findings enhance our understanding of the genes that encode sheep wool proteins.

Is polyphagy of a specific cryptic Bemisia tabaci species driving the high whitefly populations on cassava in eastern Africa?

AbstractSince the 1990s, the cryptic whitefly (Bemisia tabaci) has been linked to severe viral disease pandemics affecting cassava, a crucial staple crop in eastern Africa. This surge in whitefly populations has also been observed in other crops and uncultivated plants. While previous surveys have connected the increase on cassava to two specific populations, SSA1 and SSA2, the dynamics behind the population growth on other plants remain unclear. Additionally, other B. tabaci species, including EA1, IO, MED, SSA9, and SSA10, have been found on cassava in smaller numbers. This study aimed to identify the host plants that support the growth and development of different B. tabaci in Uganda by collecting fourth-instar nymphs from cassava and 20 other common host plants. Host transfer experiments were conducted to test the ability of seven species (EA1, MEAM1, MED-Africa Silver Leafing (ASL), SSA1-subgroup1, SSA1-Hoslundia, SSA6, and SSA12) to develop on cassava. The identities of the nymphs were determined using partial mitochondrial cytochrome oxidase 1 sequences. Twelve B. tabaci species were identified, including two novel species, based on the 3.5% nucleotide sequence divergence. Cassava was colonised by SSA1-SG1, SSA1-SG2, and SSA2. The most prevalent species were SSA1-SG1, MED-ASL, and SSA13, which were also the most polyphagous, colonising multiple plant species. Several whitefly species colonised specific weeds, such as Aspilia africana and Commelina benghalensis. The polyphagous nature of these species supports continuous habitats and virus reservoirs. Effective management of whitefly populations in eastern Africa requires an integrated approach that considers their polyphagy and the environmental factors sustaining host plants.

Genetic diversity and epidemiological insights into cutaneous leishmaniasis in Pakistan: a comprehensive study on clinical manifestations and molecular characterization of Leishmania species.

Cutaneous leishmaniasis (CL) stands out as a significant vector-borne endemic in Pakistan. Despite the rising incidence of CL, the genetic diversity of Leishmania species in the country's endemic regions remains insufficiently explored. This study aims to uncover the genetic diversity and molecular characteristics of Leishmania species in CL-endemic areas of Baluchistan, Khyber Pakhtunkhwa (KPK), and Punjab in Pakistan. Clinical samples from 300 CL patients were put to microscopic examination, real-time ITS-1 PCR, and sequencing. Predominantly affecting males between 16 to 30years of age, with lesions primarily on hands and faces, the majority presented with nodular and plaque types. Microscopic analysis revealed a positivity rate of 67.8%, while real-time PCR identified 60.98% positive cases, mainly L. tropica, followed by L. infantum and L. major. Leishmania major (p = 0.009) showed substantially greater variation in nucleotide sequences than L. tropica (p = 0.07) and L. infantum (p = 0.03). Nucleotide diversity analysis indicated higher diversity in L. major and L. infantum compared to L. tropica. This study enhances our understanding of CL epidemiology in Pakistan, stressing the crucial role of molecular techniques in accurate species identification. The foundational data provided here emphasizes the necessity for future research to investigate deeper into genetic diversity and its implications for CL control at both individual and community levels.

Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring

BackgroundGenome-wide comparisons of populations are widely used to explore the patterns of nucleotide diversity and sequence divergence to provide knowledge on how natural selection and genetic drift affect the genome. In this study we have compared whole-genome sequencing data from Atlantic and Pacific herring, two sister species that diverged about 2 million years ago, to explore the pattern of genetic differentiation between the two species.ResultsThe genome comparison of the two species revealed high genome-wide differentiation but with islands of remarkably low genetic differentiation, as measured by an FST analysis. However, the low FST observed in these islands is not caused by low interspecies sequence divergence (dxy) but rather by exceptionally high estimated intraspecies nucleotide diversity (π). These regions of low differentiation and elevated nucleotide diversity, termed high-diversity regions in this study, are not enriched for repeats but are highly enriched for immune-related genes. This enrichment includes genes from both the adaptive immune system, such as immunoglobulin, T-cell receptor and major histocompatibility complex genes, as well as a substantial number of genes with a role in the innate immune system, e.g. novel immune-type receptor, tripartite motif and tumor necrosis factor receptor genes. Analysis of long-read based assemblies from two Atlantic herring individuals revealed extensive copy number variation in these genomic regions, indicating that the elevated intraspecies nucleotide diversities were partially due to the cross-mapping of short reads.ConclusionsThis study demonstrates that copy number variation is a characteristic feature of immune trait loci in herring. Another important implication is that these loci are blind spots in classical genome-wide screens for genetic differentiation using short-read data, not only in herring, likely also in other species harboring qualitatively similar variation at immune trait loci. These loci stood out in this study because of the relatively high genome-wide baseline for FST values between Atlantic and Pacific herring.

Distinct evolutionary lineages of Schistocephalus parasites infecting co-occurring sculpin and stickleback fishes in Alaska.

Sculpins (coastrange and slimy) and sticklebacks (ninespine and threespine) are widely distributed fishes cohabiting 2 south-central Alaskan lakes (Aleknagik and Iliamna), and all these species are parasitized by cryptic diphyllobothriidean cestodes in the genus Schistocephalus. The goal of this investigation was to test for host-specific parasitic relationships between sculpins and sticklebacks based upon morphological traits (segment counts) and sequence variation across the NADH1 gene. A total of 446 plerocercoids was examined. Large, significant differences in mean segment counts were found between cestodes in sculpin (mean = 112; standard deviation [s.d.] = 15) and stickleback (mean = 86; s.d. = 9) hosts within and between lakes. Nucleotide sequence divergence between parasites from sculpin and stickleback hosts was 20.5%, and Bayesian phylogenetic analysis recovered 2 well-supported clades of cestodes reflecting intermediate host family (i.e. sculpin, Cottidae vs stickleback, Gasterosteidae). Our findings point to the presence of a distinct lineage of cryptic Schistocephalus in sculpins from Aleknagik and Iliamna lakes that warrants further investigation to determine appropriate evolutionary and taxonomic recognition.

Prognostic significance of <I>TLR3</I> and <I>TLR9</I> gene polymorphism in assessing the severity of COVID-19

Objective: to study polymorphic variants of TLR3 (rs3775291) and TLR9 (rs352140) genes in patients with COVID-19 depending on the severity of the disease and their significance for determining the risk of severe course of COVID-19.Materials and Methods: genetic analysis of polymorphism of TLR3 (rs3775291) and TLR9 genes (rs352140) was performed in 164 patients with COVID-19, who were divided by degree of severity into three groups: Group 1 with mild, Group 2 with moderate and Group 3 with severe and extremely severe degrees of severity. The control group consisted of 40 healthy donors. Statistical processing of the obtained results was carried out using STATISTICA 12.0 programs (Stat Soft, USA). To assess the difference of groups by qualitative characteristics, the χ2 criterion with Yates correction was used, and in case of violation of its conditions, the χ2 criterion was applied. Yates correction, and if the conditions of its applicability were violated, the two-sided Fisher’s two-sided criterion (RF). The difference between the groups was considered statistically significant at р<0,05. The strength of associations was evaluated in the values of the odds ratio index odds ratio (OR) and 95% confidence interval.> ˂ 0,05. The strength of associations was evaluated in the values of the odds ratio index odds ratio (OR) and 95% confidence interval.Results: the frequency of the ST genotype was significantly higher and the frequency of the TT genotype of the rs3775291 allele of the TLR3 gene was significantly lower in patients with the manifest form of COVID-19 compared with the control group. Frequency analysis of TLR9 (rs352140) in COVID-19 patients showed significantly higher values of the ST genotype and lower values of the CC genotype compared to healthy individuals. Comparative analysis between groups of hospitalized patients depending on severity revealed higher frequency of ST genotype and lower frequency of TT genotype of TLR3 (rs3775291) and TLR9 (rs352140) genes in patients with severe and extremely severe condition.Conclusion: reliable differences in the frequency of occurrence of genotypes of TLR3 (rs3775291) and TLR9 (rs352140) genes in patients with the manifest form of COVID-19 compared to healthy people were revealed. The analysis of nucleotide sequence variants of the studied genes in hospitalized patients depending on the degree of severity also showed significant differences in the frequency of genotypes. Thus, in patients with severe and extremely severe COVID-19, a significant difference in the frequency of occurrence of ST and TT genotypes of TLR3 (rs3775291) and TLR9 (rs352140) genes was revealed compared to patients with mild and moderate COVID-19, which may further have prognostic value in assessing the severity of the disease.

Production performance analysis of sheep MSTN gene C2361T locus

The myostatin (MSTN) gene exhibits significant nucleotide sequence variations in sheep, impacting growth characteristics and muscular traits of the body. However, its influence on specific growth traits in some sheep remains to be further elucidated. This study utilized single nucleotide polymorphism sequence analysis to investigate the role of the MSTN gene in meat production performance across four sheep breeds: Charolais sheep, Australian White sheep, crossbreeds of Australian White and Small-tailed Han, and crossbreeds of Charolais and Small-tailed Han. At a SNP locus of the MSTN gene, the C2361T site was identified, with three genotypes detected: CC, CT, and TT, among which CC predominated. Gene substitution effect analysis revealed that replacing C with T could elevate the phenotypic value. Comparative analysis of data from different genotypes within the same breed highlighted the superiority of CC and TT genotypes in phenotypic values, underscoring the significance of specific genotypes in influencing key traits. Contrasting the performance of different genotypes across breeds, Charolais sheep and Charolais Han hybrids demonstrated superiority across multiple indicators, offering valuable insights for breeding new sheep varieties. Analysis of gender effects on growth characteristics indicated that ewes exhibited significantly wider chest, waist, and hip widths compared to rams, while rams displayed better skeletal growth and muscle development. Additionally, the MSTN gene also exerted certain effects on lamb growth characteristics, with the CC genotype closely associated with weight. These findings not only contribute crucial insights for sheep breeding but also pave the way for future research exploring the interaction of this gene with others.

Assessment of the association of the rs12329760 polymorphism of the <i>TMPRSS2</i> gene with acute coronary syndrome in patients with new coronavirus infection

Introduction. Cardiovascular diseases (СVD) rank first in terms of morbidity and mortality not only in the Russian Federation but throughout the world. Since the end of 2019 a pandemic of Severe Acute Respiratory Syndrome (SARS) or new coronavirus infection (NCI) has spread throughout the world, which contributed to the development and course of CVD. Therefore, genetic markers began to be considered as factors potentially influencing CVD, its development and severity. Objective: To evaluate the association of the nucleotide sequence variant rs12329760 of the TMPRSS2 gene with acute coronary syndrome in patients who have had a new coronavirus infection.Material and methods. The study included 100 patients (women – 50, men – 50) with ACS and previous NCI, who were selected on the basis of a positive PCR test for the presence of SARS-CoV-2 in the anamnesis, hospitalized at the regional vascular center No. 7 of the City Clinical Hospital No. 2 of the city of Novosibirsk. Women age was 59.5 ± 7.2 years, men age was 53.5 ± 9.3 years. The diagnosis of ACS was established according to a set of criteria proposed and established by the Russian Society of Cardiology and in accordance with the updated clinical recommendations of the Ministry of Health of the Russian Federation of 2020. Patients underwent clinical and instrumental examination, coronary angiography with possible stenting, as provided for in the standards of medical care and clinical guidelines. The nucleotide sequence variant rs12329760 of the TMPSS2 gene was determined in patients using PCR with further analysis of restriction fragment length polymorphism. The comparison group consisted of 200 patients with ACS without previous NCI (no positive PCR test, no positive antibodies).Results. Carriage of CC, СТ, TT, genotype variants of the nucleotide sequence rs12329760 of the TMPSS2 gene are not associated with an increased risk of developing ACS in patients with previous NCI. When comparing the frequencies of the rs12329760 genotypes of the TMPSS2 gene in groups with ACS with NCI and ACS without NCI, no statistically significant differences were obtained. In the group with ACS with NCI, carriage of the homozygous genotype was more common (p = 0.011).Conclusions. Variants of the nucleotide sequence rs12329760 of the TMPSS2 gene are not associated with ACS with previous NCI.

Exploring genetic polymorphisms and transcript levels of antioxidant and metabolic markers for prediction and monitoring diarrhea in Holstein dairy calves

ABSTRACT The objective of this study was to investigate the genetic polymorphisms and transcript levels of antioxidant and metabolic markers for diarrhea monitoring in Holstein dairy calves. For DNA and RNA extraction, blood samples were taken from 100 female calves (50 with diarrhea and 50 appearing healthy). DNA sequencing and real time PCR for and metabolic genes were performed to identify genetic variants linked to diarrhea susceptibility. Results revealed that there were nucleotide sequence variations in the investigated genes between healthy and diarrheal calves. Keap1, HMOX1, CMPK2, ASPG, FPGT, TNNI3 K, and LPCAT1 were considerably more highly expressed in diarrheic calves than resistant ones. The Nrf2, PRDX2, and PRDX6 genes, however, produced a different pattern. This study provides a practical control strategy to lessen newborn diarrhea in Holstein dairy calves and emphasizes the significance of nucleotide variations along with antioxidant and metabolic gene expression patterns as proxy markers of diarrhea susceptibility/resistance.

Exploring COVID-19 causal genes through disease-specific Cis-eQTLs

Genome-wide association study (GWAS) analysis has exposed that genetic factors play important roles in COVID-19. Whereas a deeper understanding of the underlying mechanism of COVID-19 was hindered by the lack of expression of quantitative trait loci (eQTL) data specific for disease. To this end, we identified COVID-19-specific cis-eQTLs by integrating nucleotide sequence variations and RNA-Seq data from COVID-19 samples. These identified eQTLs have different regulatory effect on genes between patients and controls, indicating that SARS-CoV-2 infection may cause alterations in the human body's internal environment. Individuals with the TT genotype in the rs1128320 region seemed more susceptible to SARS-CoV-2 infection and developed into severe COVID-19 due to the abnormal expression of IFITM1. We subsequently discovered potential causal genes, of the result, a total of 48 genes from six tissues were identified. siRNA-mediated depletion assays in SARS-CoV-2 infection proved that 14 causal genes were directly associated with SARS-CoV-2 infection. These results enriched existing research on COVID-19 causal genes and provided a new sight in the mechanism exploration for COVID-19.

Plant virus diversity in bee and pollen samples from apple (Malus domestica) and sweet cherry (Prunus avium) agroecosystems.

Honey bee (Apis mellifera) pollination is widely used in tree fruit production systems to improve fruit set and yield. Many plant viruses can be associated with pollen or transmitted through pollination, and can be detected through bee pollination activities. Honey bees visit multiple plants and flowers in one foraging trip, essentially sampling small amounts of pollen from a wide area. Here we report metagenomics-based area-wide monitoring of plant viruses in cherry (Prunus avium) and apple (Malus domestica) orchards in Creston Valley, British Columbia, Canada, through bee-mediated pollen sampling. Plant viruses were identified in total RNA extracted from bee and pollen samples, and compared with profiles from double stranded RNA extracted from leaf and flower tissues. CVA, PDV, PNRSV, and PVF coat protein nucleotide sequences were aligned and compared for phylogenetic analysis. A wide array of plant viruses were identified in both systems, with cherry virus A (CVA), prune dwarf virus (PDV), prunus necrotic ringspot virus (PNRSV), and prunus virus F (PVF) most commonly detected. Citrus concave gum associated virus and apple stem grooving virus were only identified in samples collected during apple bloom, demonstrating changing viral profiles from the same site over time. Different profiles of viruses were identified in bee and pollen samples compared to leaf and flower samples reflective of pollen transmission affinity of individual viruses. Phylogenetic and pairwise analysis of the coat protein regions of the four most commonly detected viruses showed unique patterns of nucleotide sequence diversity, which could have implications in their evolution and management approaches. Coat protein sequences of CVA and PVF were broadly diverse with multiple distinct phylogroups identified, while PNRSV and PDV were more conserved. The pollen virome in fruit production systems is incredibly diverse, with CVA, PDV, PNRSV, and PVF widely prevalent in this region. Bee-mediated monitoring in agricultural systems is a powerful approach to study viral diversity and can be used to guide more targeted management approaches.

Validation of genetic risk scores for hypertension in the Central Russian population

Aim. To validate and evaluate the accuracy of 4 genetic risk scores (GRSs) for hypertension (HTN), previously created on European samples, on a population sample of the Ivanovo Oblast.Material and methods. For genetic analysis, targeted next-generation sequencing was used on a sample of the Central Russia (n=1682) based on the biobank collection. Four GRSs associated with HTN, previously developed for the European population, were selected for validation. The coefficient of determination and the area under the ROC curve were used as quality metrics for regression models. Additional validation was carried out to include all nucleotide sequence variants, regardless of linkage disequilibrium level. A combined GRS was compiled based on coefficients from individual GRSs using the clumping + thresholding (C+T) method.Results. The study demonstrated that the predictive value of previously developed GRSs when used for Central Russian population is lower than in the original studies. The proportion of explained variance was 0,5-0,8%. The best predictive ability (proportion of explained variance — 2,5%) was demonstrated using previously developed GRSs (Evangelou E, et al., 2018), which includes the largest number of nucleotide sequence variants (n=852).Conclusion. GRSs for HTN, developed on European samples, is not recommended for Russian population without preliminary validation. To create original GRSs, combining statistical parameters (β-coefficients and p-value) from different GRS is not recommended.

Differential amplification of the subtelomeric satellite DNA JcSAT1 in the genus Jatropha L. (Euphorbiaceae).

Satellite DNAs (satDNAs) are highly repetitive sequences that occur in virtually all eukaryotic genomes and can undergo rapid copy number and nucleotide sequence variation among relatives. After chromosomal mapping of the satDNA JcSAT1, it was found a large accumulation at subtelomeres of Jatropha curcas (subgenus Curcas), but an absence of these monomers in J. integerrima (subgenus Jatropha). This fact suggests a dynamic scenario for this satellite repeat in Jatropha genomes. Here, we used a multitasking approach (sequence analysis, DNA blotting and chromosomal mapping) to investigate the molecular organization and chromosomal abundance and distribution of JcSAT1 in a broader group of species from the subgenus Jatropha (J. gossypiifolia, J. mollissima, J. podagrica, and J. multifida) in addition to J. curcas, with the aiming of understanding the evolution of this satDNA. Based on the analysis of BAC clone sequences of J. curcas, a large array (~ 30kb) of 80 homogeneous monomers of JcSAT1 was identified in BAC 23J11. The monomer size was conserved (~ 358bp) and contained a telomeric motif at the 5' end. PCR amplification coupled with a Southern blot revealed the presence of JcSAT1-like sequences in all species examined. However, a large set of genome copies was identified only in J. curcas, where a ladder-like pattern with multimers of different sizes was observed. In situ hybridization of BAC 23J11 confirmed the subtelomeric pattern for J. curcas, but showed no signals on chromosomes of species from the subgenus Jatropha. Our data indicate that JcSAT1 is a highly homogeneous satDNA that originated from a region near the telomeres and spread throughout the chromosomal subtermini, possibly due to frequent ectopic recombination between these regions. The abundance of JcSAT1 in the genome of J. curcas suggests that an amplification event occurred either at the base of the subgenus Curcas or at least in this species, although the repeat is shared by all species of the genus studied so far.

Genetic Status of Exotic Chinese Carp Hypophthalmichthys molitrix and Hypophthalmichthys nobilis through Mitochondrial Gene Cytochrome C Oxidase Subunit I (COI) in Bangladesh

The use of mitochondrial gene Cytochrome C Oxidase subunit I (mtCOI) has emerged as a promising technique in study of genetic variation and phylogenetic relationship of different group of fishes. This work reports the first example of the study of genetic status of two exotic Chinese carp, silver carp, Hypophthalmichthys molitrix and bighead carp, Hypophthalmichthys nobilis in Bangladesh through the analyses of mtCOI gene. The highest nucleotide sequence divergence occurred between sequenced H. nobilis N3 and reference H. molitrix from India which was 1.208 and the lowest nucleotide divergence occurred in sequenced H. nobilis N1 and sequenced H. molitrix M3 with their reference counterparts from Bangladesh, India and China (0.002). The phylogenetic tree analysis showed that one of the H. nobilis (H. nobilis N3) formed a sister group with H. molitrix M2 with 100% sequence similarities. Otherwise, all sequenced and reference H. molitrix and H. nobilis showed separate clade in the tree. Therefore, we can conclude that the exotic H. molitrix and H. nobilis maintain distinct population status with lower genetic variation. However, we should take essential measures to reduce inbreeding in future.

Dual RNA-sequencing of Fusarium head blight resistance in winter wheat.

Fusarium head blight (FHB) is a devastating fungal disease responsible for significant yield losses in wheat and other cereal crops across the globe. FHB infection of wheat spikes results in grain contamination with mycotoxins, reducing both grain quality and yield. Breeding strategies have resulted in the production of FHB-resistant cultivars, however, the underlying molecular mechanisms of resistance in the majority of these cultivars are still poorly understood. To improve our understanding of FHB-resistance, we performed a transcriptomic analysis of FHB-resistant AC Emerson, FHB-moderately resistant AC Morley, and FHB-susceptible CDC Falcon in response to Fusarium graminearum. Wheat spikelets located directly below the point of inoculation were collected at 7-days post inoculation (dpi), where dual RNA-sequencing was performed to explore differential expression patterns between wheat cultivars in addition to the challenging pathogen. Differential expression analysis revealed distinct defense responses within FHB-resistant cultivars including the enrichment of physical defense through the lignin biosynthesis pathway, and DON detoxification through the activity of UDP-glycosyltransferases. Nucleotide sequence variants were also identified broadly between these cultivars with several variants being identified within differentially expressed putative defense genes. Further, F. graminearum demonstrated differential expression of mycotoxin biosynthesis pathways during infection, leading to the identification of putative pathogenicity factors.

Genetic diversity of a recovering European roller (Coracias garrulus) population from Serbia.

The European Roller (Coracias garrulus), a long-distance migratory bird, faced a considerable decline in breeding pairs throughout Europe at the end of the 20th century. Due to conservation efforts and the installation of nesting boxes, the population of the European Roller in Serbia has made a remarkable recovery. Here, we used the variability of nucleotide sequences of the mitochondrial DNA (mtDNA) control region and 10 microsatellite loci to assess the genetic diversity and structuring, phylogeographic patterns and demographic history of this species using 224 individuals from Serbia. Our results showed moderate level of genetic diversity (HO = 0.392) and a slightly elevated level of inbreeding and homozygosity (FIS = 0.393). Genetic structuring based on microsatellite data indicated three genetic clusters, but without a clear spatial pattern. High haplotype diversity (Hd = 0.987) of the mtDNA control region sequences was detected, and neutrality tests indicated a recent demographic expansion. The phylogeographic analysis, which also included previously published sequences of the mtDNA control region, supported the subdivision into two distinct European and Asian haplogroups (ΦST = 0.712). However, the results of our study showed that a larger number of haplotypes sampled in Serbia are clustered in the Asian haplogroup as compared to previous studies, indicating a historically continuous distribution of this species and possibly a wider distribution of the subspecies Coracias garrulus semenovwi. Our results suggest that the European Roller population in Serbia is genetically stable, with no evidence of recent bottlenecks, and emphasize the importance of artificial nest boxes for promoting and maintaining population dynamics of European Rollers.

<i>DEPDC5</i>-related familial focal epilepsy

Focal epilepsy is the most common type of epilepsy accounting for 60–70% of all cases of this pathology. We present two familial cases of focal epilepsy associated with a nucleotide sequence variant in DEPDC5 gene. Clinical and ancestry examination was performed by using instrumental (magnetic resonance imaging, video-electroencephalography) and genetic testing methods. The nucleotide sequence variants in DEPDC5 gene were found in two probands and paired fathers with epilepsy. Focal cortical dysplasia was detected only in the father of Proband 1 as well as Proband 2 with resistant epilepsy and severe cognitive deficit. Hence, such clinical cases confirm that pathogenic variants in DEPDC5 gene are related with familial focal epilepsy, which clinical manifestation may depend on the type of identified mutation. The study of genotype-phenotype correlations is necessary to apply proper therapy. Before surgical treatment of epilepsy, the genetic testing by whole exome or whole genome sequencing should be performed.