CRISPR/Cas9-mediated multiple guide RNA-targeted mutagenesis in the potato.

CRISPR/Cas9 technology has become the most efficient method for genome editing in many plant species, including important industrial crops such as potatoes. This study used three target regions (T1, T2, and T3) in gbss exon I, whose sequences were first inserted into the BbsI sites in the appropriate guide RNA (gRNA) vector (pEn-Chimera, pMR203, pMR204, and pMR205), and then localized between the AtU6 promoter and the gRNA scaffold sequence. Expression vectors were constructed by introducing gRNA genes into the pMR287 (pYUCas9Plus) plasmids using the MultiSite Gateway system by attR and attL sites. The three target regions of mutant potato lines were analyzed. The use of CRISPR/Cas9-mediated multiple guide RNA-targeted mutagenesis allowed tri- or tetra-allelic mutant potato lines to be generated. Multiple nucleotide substitutions and indels within and around the three target sites caused a frameshift mutation that led to a premature stop codon, resulting in the production of gbss-knockout plants. Mutation frequencies and analysis of mutation patterns suggested that the stably transformed Cas9/multiple guide RNA expression constructs used in this study can induce targeted mutations efficiently in the potato genome. Full knockout of the gbss gene was analyzed by CAPS, Sanger sequencing and iodine staining. The present study demonstrated successful CRISPR/Cas9-mediated multiple guide RNA-targeted mutagenesis in the potato gbss gene by Agrobacterium-mediated transformation, resulting in an amylose-free phenotype.

Cytoprotective Activity of Newly Synthesized 3-(Arylmethylamino)-6-Methyl-4-Phenylpyridin-2(1H)-Ones Derivatives.

Currently, studies are being conducted on the possible role of the cytoprotective effect of biologically active substances in conditions of cerebral hypoxia or cardiomyopathies. At the same time, oxidative stress is considered one of the important mechanisms of cellular cytotoxicity and a target for the action of cytoprotectors. The aim of this study is to search for derivatives of 3-(arylmethylamino)-6-methyl-4-phenylpyridin-2(1H)-ones. The probability of cytoprotective action was assessed by measuring cell viability using two tests (with neutral red dye and MTT test). It was found that some derivatives of 3-(arylmethylamino)-6-methyl-4-phenylpyridin-2(1H)-ones under the conditions of our experiment had a pronounced cytoprotective activity, providing better cell survival in vitro, including the MTT test and conditions of blood hyperviscosity. To correlate the obtained results in vitro, molecular docking of the synthesized derivatives was also carried out. The standard drug omeprazole (co-crystallized with the enzyme) was used as a standard. It was shown that all synthesized derivatives of 3-(arylmethylamino)-6-methyl-4-phenylpyridin-2(1H)-ones had higher affinity for the selected protein than the standard gastro-cytoprotector omeprazole. The studied derivatives of 3-(arylmethylamino)-6-methyl-4-phenylpyridin-2(1H)-ones also fully satisfy Lipinski's rule of five (RO5), which increases their chances for possible use as orally active drugs with good absorption ability and moderate lipophilicity. Thus, the results obtained make it possible to evaluate derivatives of 3-(arylmethylamino)-6-methyl-4-phenylpyridin-2(1H)-ones as having a relatively high cytoprotective potential.

Genomic analysis of Latin American-Mediterranean family of Mycobacterium tuberculosis clinical strains from Kazakhstan.

The human-adapted strains of the Mycobacterium tuberculosis complex (MTBC) comprise seven phylogenetic lineages originally associated with their geographical distribution. Here, we report the genomes of three drug-resistant clinical isolates of the Latin American-Mediterranean (LAM) family collected in Kazakhstan. We utilised whole-genome sequencing to study the distribution and drug resistance of these isolates. Phylogenetic analysis grouped the genomes described in this study with the sequences from Russia, Uzbekistan, and Kazakhstan belonging to the LAM family. One isolate has acquired extensive drug resistance to seven antituberculosis drugs. Our results suggest at least two multi-drug resistant (MDR)/extensively drug-resistant (XDR)-associated genotypes of the LAM family circulate in Kazakhstan.

FastPCR: An in silico tool for fast primer and probe design and advanced sequence analysis.

Polymerase chain reaction (PCR) is one of the most important laboratory techniques used in molecular biology, genetics and molecular diagnostics. The success of a PCR-based method largely depends on the correct nucleic acid sequence analysis in silico prior to a wet-bench experiment. Here, we report the development of an online Java-based software for virtual PCR on linear or circular DNA templates and multiple primer or probe search from large or small databases. Primer or probe sensitivity and specificity are predicted by searching a database to find sequences with an optimal number of mismatches, similarity and stability. The software determines primer location, orientation, efficiency of binding and calculates primer melting temperatures for standard and degenerate oligonucleotides. The software is suitable for batch file processing, which is essential for automation when working with large amounts of data. The online Java software is available for download at http://primerdigital.com/tools/pcr.html. Accession numbers for the sequences resulting from this study: EU140956 EU177767 EU867815 EU882730 FJ975775-FJ975780 HM481419 HM481420 KC686837-KC686839 KM262797.

Synthesis, Computational Study, and In Vitro α-Glucosidase Inhibitory Action of 1,3,4-Thiadiazole Derivatives of 3-Aminopyridin-2(1H)-ones.

This article reports on the synthesis of nine promising new 1,3,4-thiadiazole derivatives based on 3-aminopyridones, containing various acidic linkers. The synthesis was carried out by cyclizing the corresponding thiohydrazides 4a-c and anhydrides of glutaric, maleic, and phthalic acids upon heating in acetic acid solution. The conducted bio-screening of the synthesized new 1,3,4-thiadiazole derivatives containing different acidic linkers (butanoic, acrylic, and benzoic acids) showed that they have significant inhibitory activity against α-glucosidase (up to 95.0%), which is 1.9 times higher than the value for the reference drug acarbose (49.5%). Moreover, one of the 1,3,4-thiadiazole derivatives with a benzoic acid linker-2-(5-((6-Methyl-2-oxo-4-(thiophen-2-yl)-1,2-dihydropyridin-3-yl)carbamoyl)-1,3,4-thiadiazol-2-yl)benzoic acid (9'b)-showed an IC50 value of 3.66 mM, nearly 3.7 times lower than that of acarbose (IC50 = 13.88 mM). High inhibitory activity was also shown by 1,3,4-thiadiazole derivatives with a butanoic acid linker (compounds 7b, 7c)-with IC50 values of 6.70 and 8.42 mM, respectively. A correlation between the structure of the compounds and their activity was also established. The results of molecular docking correlated well with the bioanalytical data. In particular, the presence of a butanoic acid linker and a benzoic fragment in compounds 7b, 7c, and 9b increased their binding affinity with selected target proteins compared to other derivatives 3-6 (a-c). Calculations according to Lipinski's rule of five also showed that the synthesized compounds 7b, 7c, and 9b fully comply with Ro5 and meet all criteria for good permeability and acceptable oral bioavailability of potential drugs. These positive bioanalytical results will stimulate further in-depth studies, including in vivo models.

An impact of N-glycosylation on biochemical properties of a recombinant α-amylase from Bacillus licheniformis.

Amylases are enzymes that are known to hydrolyze starch. High efficiency of amylolytic enzymes allows them to compete in the industry with the technology of chemical hydrolysis of starch. A Bacillus licheniformis strain with high amylolytic activity was isolated from soil and designated as T5. The gene encoding α-amylase from B. licheniformis T5 was successfully expressed in both Escherichia coli (rAmyT5-E) and Pichia pastoris (as rAmyT5-P). According to the study, the recombinant α-amylases rAmyT5-E and rAmyT5-P exhibited the highest activity at pH 6.0 and temperatures of 70 and 80 °C, respectively. Over 80% of the rAmyT5-E enzyme activity was preserved following incubation within the pH range of 5-9; the same was true for rAmyT5-P after incubation at pH 6-9. N-glycosylation reduced the thermal and pH stability of the enzyme. The specific activity and catalytic efficiency of the recombinant AmyT5 α-amylase were also diminished by N-glycosylation.

Theileria and Babesia infection in cattle - First molecular survey in Kazakhstan.

Central Asia, including Kazakhstan, is an endemic area of Theileria and Babesia infections in cattle. Current data on the geographic distribution, prevalence, and genetic diversity of these pathogens in vertebrate hosts are lacking in Kazakhstan. The present study aimed to fill this gap, using molecular techniques for the first time. A cross-sectional survey was performed on adult cattle from 40 villages in nine administrative districts of the provinces of Turkistan and Zhambyl, southern Kazakhstan, in summer 2020. A total of 766 blood samples were screened for Theileria annulata (enolase gene), Theileria orientalis (major piroplasm surface protein gene, MPSP) and Babesia spp. (18 S ribosomal RNA gene) using polymerase chain reaction. The genetic variability of Theileria spp. was assessed by sequencing one amplicon from each village. All Babesia spp. positive amplicons were sequenced to identify the species involved. The overall prevalence of infections with T. annulata, T. orientalis and Babesia spp. was 83.0% (40 villages positive), 33.3% (31 villages) and 13.5% (36 villages), respectively. Co-infections with two or three species were present in 48.9% of all positive cattle. Theileria annulata showing a high polymorphism of the enolase gene occurred with similar frequency in both provinces. Theileria orientalis was detected for the first time in Kazakhstan being significantly (P = 0.014) more prevalent in Zhambyl than in Turkistan. Fourteen genotypes of T. orientalis were identified; two belonged to the moderately virulent MPSP-type 1 ('Chitose') and the others to MPSP-type 3 ('Buffeli') which is considered avirulent. The prevalence of Babesia infection was significantly (P < 0.000) higher in Turkistan than in Zhambyl. An unequivocal identification of the species involved was possible in 127 sequenced samples: Babesia occultans was the most common species, followed by Babesia bigemina and Babesia major, the latter being the first record in the country. The results show that Theileria and Babesia infections in cattle are widespread and occur with remarkably high prevalence in the southern Kazakhstan. They also provide first data on the genetic diversity of the species involved.

Generation of Peptides for Highly Efficient Proximity Utilizing Site-Specific Biotinylation in Cells.

Protein tags are peptide sequences genetically embedded into a recombinant protein for various purposes, such as affinity purification, Western blotting, and immunofluorescence. Another recent application of peptide tags is in vivo labeling and analysis of protein-protein interactions (PPI) by proteomics methods. One of the common workflows involves site-specific in vivo biotinylation of an AviTag-fused protein in the presence of the biotin ligase BirA. However, due to the rapid kinetics of labeling, this tag is not ideal for analysis of PPI. Here we describe the rationale, design, and protocol for the new biotin acceptor peptides BAP1070 and BAP1108 using modular assembling of biotin acceptor fragments, DNA sequencing, transient expression of proteins in cells, and Western blotting methods. These tags were used in the Proximity Utilizing Biotinylation (PUB) method, which is based on coexpression of BAP-X and BirA-Y in mammalian cells, where X or Y are candidate interacting proteins of interest. By changing the sequence of these peptides, a low level of background biotinylation is achieved, which occurs due to random collisions of proteins in cells. Over 100 plasmid constructs, containing genes of transcription factors, histones, gene repressors, and other nuclear proteins were obtained during implementation of projects related to this method.

Associations of Reported Genetic Risk Loci with Sporadic Brain Arteriovenous Malformations: Meta-analysis.

An arteriovenous malformation (AVM) is an abnormal nidus of blood vessels that is characterized by a direct connection between arteries and veins without intervening in the capillary network. The exact underlying cause of sporadic AVMs is unknown, but many studies have reported genetic associations between genes that contribute to angiogenesis, vasculogenesis, and inflammation. Eleven studies retrieved from Medline Complete, PubMed, and Google Scholar up to February 2022 were included. Heterogeneity was assessed using I2 and Q-tests. Publication bias was also assessed for the shortlisted CDKN2B-AS1 rs1333040 (T > C), ACVRL1 rs2071219 (A > G), and rs11169953 (C > T) polymorphisms. The rs1333040 polymorphism showed a lower association with sporadic brain AVM for T versus C in an allelic model (OR = 0.59, 95% confidence interval [CI] = 0.41-0.84). In the recessive model, rs2071219 for AA + AG vs. GG was OR = 0.62, 95% CI = 0.43-0.9. In the recessive model, rs11169953 CC + CT vs. TT was OR = 0.56, 95% CI = 0.33-0.95. In summary, the results of this study support the association between CDKN2B-AS1 and ACVRL1 polymorphisms and sporadic brain arteriovenous malformations. This study summarized the existing information and showed the need for more replication studies on the genetic basis of sporadic AVM. In the future, more genome-wide studies should be conducted to validate and fill existing gaps in knowledge about the mechanisms of sporadic AVM development.

Comparative Characterization and Identification of Poly-3-hydroxybutyrate Producing Bacteria with Subsequent Optimization of Polymer Yield.

In this work, the strains Bacillus megaterium RAZ 3, Azotobacter chrocococcum Az 3, Bacillus araybhattay RA 5 were used as an effective producer of poly-3-hydroxybutyrate P(3HB). The purpose of the study was to isolate and obtain an effective producer of P(3HB) isolated from regional chestnut soils of northern Kazakhstan. This study demonstrates the possibility of combining the protective system of cells to physical stress as a way to optimize the synthesis of PHA by strains. Molecular identification of strains and amplification of the phbC gene, transmission electron microscope (TEM), extracted and dried PHB were subjected to Fourier infrared transmission spectroscopy (FTIR). The melting point of the isolated P(3HB) was determined. The optimal concentration of bean broth for the synthesis of P(3HB) for the modified type of Bacillus megaterium RAZ 3 was 20 g/L, at which the dry weight of cells was 25.7 g/L-1 and P(3HB) yield of 13.83 g/L-1, while the percentage yield of P(3HB) was 53.75%. The FTIR spectra of the extracted polymer showed noticeable peaks at long wavelengths. Based on a proof of concept, this study demonstrates encouraging results.

Macroporous Cell-Laden Gelatin/Hyaluronic Acid/Chondroitin Sulfate Cryogels for Engineered Tissue Constructs.

Cryogels are a unique macroporous material for tissue engineering. In this work, we study the effect of hyaluronic acid on the physicochemical properties of cryogel as well as on the proliferation of a 3D model of mesenchymal stem cells. The functional groups of the synthesized cryogels were identified using Fourier transform infrared spectroscopy. With an increase in the content of hyaluronic acid in the composition of the cryogel, an increase in porosity, gel content and swelling behavior was observed. As the hyaluronic acid content increased, the average pore size increased and more open pores were formed. Degradation studies have shown that all cryogels were resistant to PBS solution for 8 weeks. Cytotoxicity assays demonstrated no toxic effect on viability of rat adipose-derived mesenchymal stem cells (ADMSCs) cultured on cryogels. ADMSC spheroids were proliferated on scaffolds and showed the ability of the cryogels to orient cell differentiation into chondrogenic lineage even in the absence of inductive agents. Thus, our results demonstrate an effective resemblance to extracellular matrix structures specific to cartilage-like microenvironments by cryogels and their further perspective application as potential biomaterials.

Isolation of Bacillus sp. A5.3 Strain with Keratinolytic Activity.

Environmental safety and economic factors necessitate a search for new ways of processing poultry farm feathers, which are 90% ß-keratin and can be used as a cheap source of amino acids and peptones. In this study, feather-decomposing bacteria were isolated from a site of accumulation of rotten feathers and identified as Bacillus. Among them, the Bacillus sp. A5.3 isolate showed the best keratinolytic properties. Scanning electron microscopy indicated that Bacillus sp. A5.3 cells closely adhere to the feather surface while degrading the feather. It was found that Bacillus sp. A5.3 secretes thermostable alkaline proteolytic and keratinolytic enzymes. Zymographic analysis of the enzymatic extract toward bovine serum albumin, casein, gelatin, and ß-keratin revealed the presence of proteases and keratinases with molecular weights 20-250 kDa. The proteolytic and keratinolytic enzymes predominantly belong to the serine protease family. Proteome analysis of the secreted proteins by nano-HPLC coupled with Q-TOF mass spectrometry identified 154 proteins, 13 of which are proteases and peptidases. Thus, strain Bacillus sp. A5.3 holds great promise for use in feather-processing technologies and as a source of proteases and keratinases.

Cloning, expression, and characterization of a recombinant xylanase from Bacillus sonorensis T6.

Xylanase is one of industrial enzymes with diverse applications including the paper-bleaching industry and feed additives. Here, a strain having xylanolytic activity and identified as Bacillus sonorensis T6 was isolated from soil. A secretory enzyme was identified by mass-spectrometry as a xylanase of glycosyl hydrolase family 11, with a molecular weight of 23.3 kDa. The xylanase gene of Bacillus sonorensis T6 was cloned and expressed in Escherichia coli (yielding an enzyme designated as rXynT6-E) and in Pichia pastoris (yielding rXynT6-P). The recombinant xylanases were found to have optimal activity at 47-55°C and pH 6.0-7.0. The recombinant xylanase expressed in P. pastoris has 40% higher thermal stability than that expressed in E. coli. The recombinant xylanases retained 100% of activity after 10 h incubation in the pH range 3-11 and 68% of activity after 1 h at pH 2.0. The xylanase activities of rXynT6-E and rXynT6-P under optimal conditions were 1030.2 and 873.8 U/mg, respectively. The good stability in a wide range of pH and moderate temperatures may make the xylanase from Bacillus sonorensis T6 useful for various biotechnological applications, e.g., as an enzyme additive in the feed industry.

Whole-Exome Sequencing Reveals Pathogenic SIRT1 Variant in Brain Arteriovenous Malformation: A Case Report.

Arteriovenous malformations of the brain (bAVMs) are plexuses of pathological arteries and veins that lack a normal capillary system between them. Intracranial hemorrhage (hemorrhagic stroke) is the most frequent clinical manifestation of AVM, leading to lethal outcomes that are especially high among children and young people. Recently, high-throughput genome sequencing methods have made a notable contribution to the research progress in this subject. In particular, whole-exome sequencing (WES) methods allow the identification of novel mutations. However, the genetic mechanism causing AVM is still unclear. Therefore, the aim of this study was to investigate the potential genetic mechanism underlying AVM. We analyzed the WES data of blood and tissue samples of a 30-year-old Central Asian male diagnosed with AVM. We identified 54 polymorphisms in 43 genes. After in-silica overrepresentation enrichment analysis of the polymorphisms, the SIRT1 gene variant (g.67884831C>T) indicated a possible molecular mechanism of bAVM. Further studies are required to evaluate the functional impact of SIRT1 g.67884831C>T, which may warrant further replication and biological investigations related to sporadic bAVM.

Cloning and characterization of the major AP endonuclease from Staphylococcus aureus.

Apurinic/apyrimidinic (AP) endonucleases are key enzymes involved in the repair of abasic sites and DNA strand breaks. Complete genome analysis of Staphylococcus aureus identified a single AP endonuclease, SaNfo, which is a member of the endonuclease IV family exemplified by Escherichia coli Nfo. At present, it remains unknown whether SaNfo possesses DNA repair activities similar to its counterparts from E. coli and other bacteria. Here, we report that the purified SaNfo protein contains efficient AP endonuclease and nucleotide incision repair (NIR) activities. Optimal reaction conditions for SaNfo-catalysed AP endonuclease activity are high ionic strength and Mn2+ concentration, pH in range 7.5-9.0 and the temperature optimum of 37-45 °C. Cell-free extracts of S. aureus exhibited efficient AP site cleavage and NIR activities. Heterologous expression of SaNfo strongly reduces the sensitivity of AP endonuclease-deficient E. coli xth nfo strain to methylmethanesulfonate and H2O2. Site-directed mutagenesis showed that the Glu258 residue is critical for the SaNfo enzyme function. The AP endonuclease but not the NIR activity of SaNfo were stimulated by the ß-clamp (SaDnaN dimer), suggesting that it might participate in the organization of BER in S. aureus. Overall, our data confirm that the activity, substrate specificity and in vivo functionality of S. aureus Nfo are consistent with this protein being the major AP endonuclease for the repair of DNA damage generated by endogenous and host-imposed factors.

Optimization of polymerase chain reaction for the identification of Roe deer, Saiga, and Siberian stag living in Kazakhstan.

Background and Aim: One of the reasons for the decline in the number of wild species of artiodactyls is poaching and the illegal trading of animal products. Molecular genetic identification of animals from a biological sample effectively proves poaching cases and illegal trade of animal products. This study aimed to develop a polymerase chain reaction (PCR) test that allows for species identification of artiodactyl animals that are most often subject to poaching. Materials and Methods: Genomic DNA was extracted from meat and blood samples of animals killed by poachers using commercial kits. Three pairs of primers were designed and used to amplify the cytochrome b gene fragment of Roe deer, Saiga antelope, and Siberian stag. Results: The proposed protocol allows amplification of specific PCR products of 542 bp with Roe deer DNA, 587 bp with Saiga DNA, and 525 bp with Siberian stag DNA. Specificity analysis showed no cross activity with DNA from other animal species. The detection limit of PCR ranged from 15.6 pg to 1.9 pg of DNA in 25 mL of the reaction mixture. Conclusion: Sequencing the amplified products and subsequent comparison with the corresponding reference sequence showed a similarity ranging from 99.99% to 100%. The PCR based on the developed primers demonstrated high sensitivity and specificity when using DNA from homogeneous and heterogeneous animals.

Highly pathogenic avian influenza virus of the A/H5N8 subtype, clade 2.3.4.4b, caused outbreaks in Kazakhstan in 2020.

Background: Large poultry die-offs happened in Kazakhstan during autumn of 2020. The birds' disease appeared to be avian influenza. Northern Kazakhstan was hit first and then the disease propagated across the country affecting eleven provinces. This study reports the results of full-genome sequencing of viruses collected during the outbreaks and investigation of their relationship to avian influenza virus isolates in the contemporary circulation in Eurasia. Methods: Samples were collected from diseased birds during the 2020 outbreaks in Kazakhstan. Initial virus detection and subtyping was done using RT-PCR. Ten samples collected during expeditions to Northern and Southern Kazakhstan were used for full-genome sequencing of avian influenza viruses. Phylogenetic analysis was used to compare viruses from Kazakhstan to viral isolates from other world regions. Results: Phylogenetic trees for hemagglutinin and neuraminidase show that viruses from Kazakhstan belong to the A/H5N8 subtype and to the hemagglutinin H5 clade 2.3.4.4b. Deduced hemagglutinin amino acid sequences in all Kazakhstan's viruses in this study contain the polybasic cleavage site (KRRKR-G) indicative of the highly pathogenic phenotype. Building phylogenetic trees with the Bayesian phylogenetics results in higher statistical support for clusters than using distance methods. The Kazakhstan's viruses cluster with isolates from Southern Russia, the Russian Caucasus, the Ural region, and southwestern Siberia. Other closely related prototypes are from Eastern Europe. The Central Asia Migratory Flyway passes over Kazakhstan and birds have intermediate stops in Northern Kazakhstan. It is postulated that the A/H5N8 subtype was introduced with migrating birds. Conclusion: The findings confirm the introduction of the highly pathogenic avian influenza viruses of the A/Goose/Guangdong/96 (Gs/GD) H5 lineage in Kazakhstan. This virus poses a tangible threat to public health. Considering the results of this study, it looks justifiable to undertake measures in preparation, such as install sentinel surveillance for human cases of avian influenza in the largest pulmonary units, develop a human A/H5N8 vaccine and human diagnostics capable of HPAI discrimination.

Activated leukocyte cell adhesion molecule/cluster of differentiation 166 rs10933819 (G>A) variant is associated with familial intracranial aneurysms.

Rupture of intracranial aneurysms (IAs) is the most common cause of subarachnoid hemorrhage (SAH). Currently, there is sufficient evidence to indicate that inflammatory responses contribute to aneurysm rupture. Moreover, the familial occurrence of SAH suggests that genetic factors may be involved in disease susceptibility. In the present study, a clinically proven case of IA in a patient who is a heterozygous mutation carrier of the activated leukocyte cell adhesion molecule (ALCAM)/cluster of differentiation 166 (CD166) gene, is reported. Genomic DNA was extracted from two siblings diagnosed with SAH and other available family members. A variant prioritization strategy that focused on functional prediction, frequency, predicted pathogenicity, and segregation within the family was employed. Sanger sequencing was also performed on the unaffected relatives to assess the segregation of variants within the phenotype. The verified mutations were sequenced in 145 ethnicity-matched healthy individuals. Based on whole exome sequencing data obtained from three individuals, two of whom were diagnosed with IAs, the single-nucleotide variant rs10933819 was prioritized in the family. Only one variant, rs10933819 (G>A), in ALCAM co-segregated with the phenotype, and this mutation was absent in ethnicity-matched healthy individuals. Collectively, ALCAM c1382 G>A p.Gly229Val was identified, for the first time, as a pathogenic mutation in this IA pedigree.

Ancient Components and Recent Expansion in the Eurasian Heartland: Insights into the Revised Phylogeny of Y-Chromosomes from Central Asia.

In the past two decades, studies of Y chromosomal single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) have shed light on the demographic history of Central Asia, the heartland of Eurasia. However, complex patterns of migration and admixture have complicated population genetic studies in Central Asia. Here, we sequenced and analyzed the Y-chromosomes of 187 male individuals from Kazakh, Kyrgyz, Uzbek, Karakalpak, Hazara, Karluk, Tajik, Uyghur, Dungan, and Turkmen populations. High diversity and admixture from peripheral areas of Eurasia were observed among the paternal gene pool of these populations. This general pattern can be largely attributed to the activities of ancient people in four periods, including the Neolithic farmers, Indo-Europeans, Turks, and Mongols. Most importantly, we detected the consistent expansion of many minor lineages over the past thousand years, which may correspond directly to the formation of modern populations in these regions. The newly discovered sub-lineages and variants provide a basis for further studies of the contributions of minor lineages to the formation of modern populations in Central Asia.

Genetic Polymorphism of 27 Y-STR Loci in the Western Kazakh Tribes from Kazakhstan and Karakalpakstan, Uzbekistan.

Data on the genetic polymorphism of 27 Y-STR in Kazakhs of the Junior Zhuz has been presented and analyzed in relation to forensic features. A total of 464 representatives of the Western Kazakh tribes of Kazakhstan (Western Kazakhs, n = 405) and Uzbekistan (Karakalpakstan Kazakhs, n = 59) were examined by the Yfiler Plus set. The data are available in the YHRD under accession numbers YA006010 and YA006009. Genetic analysis (AMOVA and MDS) did not show significant differences between the two groups (Kazakhstan and Karakalpakstan Kazakhs) in terms of Y-chromosome diversity. Both groups are characterized by haplogroup C2a1a2 as a founder effect, which dominated two of the three tribes: Alimuly (67%), Baiuly (74.6%), and Zhetiru (25.8%). At the same time, the phylogenetic network for each tribe found its own clusters within C2a1a2. Western Kazakhs and Karakalpakstan Kazakhs present high values of unique haplotypes (84.44% and 96.61%), discrimination capacity (90.37% and 98.30%), and haplotype diversity (0.9991 and 0.9994). A set of 27 Y-STR loci distinguishes closely related individuals within the Western Kazakh tribes quite well. It is suitable for forensic application, and is also optimal for population genetics studies.