Genetic Diversity in Natural Populations of Rhodiola Species of Different Adaptation Strategies

Representatives of the Crassulaceae family’s genus Rhodiola are succulents, making them distinctive in a changing environment. One of the most significant tools for analyzing plant resources, including numerous genetic processes in wild populations, is the analysis of molecular genetic polymorphism. This work aimed to look at the polymorphisms of allelic variations of the superoxide dismutase (SOD) and auxin response factor (ARF) gene families, as well as the genetic diversity of five Rhodiola species, using the retrotransposons-based fingerprinting approach. The multi-locus exon-primed intron-crossing (EPIC-PCR) profiling approach was used to examine allelic variations in the SOD and ARF gene families. We implemented the inter-primer binding site (iPBS) PCR amplification technique for genome profiling, which demonstrated a significant level of polymorphism in the Rhodiola samples studied. Natural populations of Rhodiola species have a great capacity for adaptation to unfavorable environmental influences. The genetic variety of wild populations of Rhodiola species leads to their improved tolerance of opposing environmental circumstances and species evolutionary divergence based on the diversity of reproductive systems

Facilitated sequence assembly using densely labeled optical DNA barcodes:A combinatorial auction approach

<div><p>The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard “foreign” contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.</p></div

Analysis of TaqMan Array Cards Data by an Assumption-Free Improvement of the maxRatio Algorithm Is More Accurate than the Cycle-Threshold Method

<div><p>Quantitative PCR diagnostic platforms are moving towards increased sample throughput, with instruments capable of carrying out thousands of reactions at once already in use. The need for a computational tool to reliably assist in the validation of the results is therefore compelling. In the present study, 328 residual clinical samples provided by the Public Health England at Addenbrooke's Hospital (Cambridge, UK) were processed by TaqMan Array Card assay, generating 15 744 reactions from 54 targets. The amplification data were analysed by the conventional cycle-threshold (CT) method and an improvement of the <i>maxRatio</i> (MR) algorithm developed to filter out the reactions with irregular amplification profiles. The reactions were also independently validated by three raters and a consensus was generated from their classification. The inter-rater agreement by Fleiss' kappa was 0.885; the agreement between either CT or MR with the raters gave Fleiss' kappa 0.884 and 0.902, respectively. Based on the consensus classification, the CT and MR methods achieved an assay accuracy of 0.979 and 0.987, respectively. These results suggested that the assumption-free MR algorithm was more reliable than the CT method, with clear advantages for the diagnostic settings.</p></div

Связь цитогенетических показателей с молекулярно-генетическими различиями у видов рода Rhododendron l. при интродукции

Currently, woody plants attract special attention given the prospects of their involving in bio- and genomic technologies to address challenges of sustainable environment, biodiversity, food security and production of raw materials. Thence, studies of cytogenetic characteristics of woody plants are increasingly relevant. The change in a number of cytogenetic characteristics, in particular, mitotic activity, which may increase and decrease depending on the intensity of stress loads, an increase in the pathology of mitosis, etc., has been shown. However, attempts to identify the similarities and differences in cytogenetic characteristics in woody plants on the basis of the results of molecular genetic comparison weren’t conducted yet. Sequences of the internal transcribed spacer (ITS) regions of nuclear ribosomal NA were used to generate a phylogenetic hypothesis for disjuncting of wood species of the genus Aralia (J. Wen, 2000), to specify of Rhododendron systematic state (T.V. Baranova et al., 2014) and other genera of the family Ericaceae (O. Schwery et al., 2015). Cluster analysis of nucleotide sequences and construction of the dendrogram were carried out using the ML (Maximum Likelihood, Nearest-Neighbor-Interchange) method in the MEGA software. Germination of Rhododendron seeds was carried out in Petri dishes at room temperature. Roots were stained with acetohematoxylin, rinsed with distilled water, and suppressed micro-preparations were prepared using Goyer’s fluid. Nucleotide sequences of the ITS1-ITS2 spacer of the parent plants and cytogenetic parameters (mitotic activity, level and spectrum of pathological mitoses, number of cells with residual nucleoli in the metaphase-telophase mitosis stage) we obtained from seed progeny in four Rhododendron species introduced into the conditions of the Central Black Earth region of Russia. The identity of the nucleotide sequence of the spacer ITS1-ITS2 in species of the genus Rhododendron leads to their greater similarity in the aggregate of cytogenetic indices. However, there is no complete analogy of cytogenetic characteristics in the species studied that have the identical sequence ITS1-ITS2. On the basis of this comparison, it can be assumed that genetic similarity in the studied Rhododendron species causes the similarity of cytogenetic indices. According to mitotic activity in the root meristem of the seedlings, two groups can be distinguished among the seed progeny, i.e. with a high value of mitotic activity, namely Rhododendron dauricum (7.6±0.3 %) and Rh. mucronulatum (7.7±0.7 %), and with low value, namely Rh. sichotense (5.6±0.7 %) and Rh. ledebourii (6.1±0.6%). The greatest cytogenetic instability is noted in Rh. ledebourii (5.2±1.1 %, the level of pathologies of mitosis in this species is maximal), in three other species it was lower (from 3.5±0.5 % for Rh. sichotense to 1.6±0.4 % for Rh. dauricum mitosis pathologies). A higher level of cells with a residual nucleolus at the stage of metaphase—telophase mitosis indicates a greater intensity of synthetic processes associated with adaptation in conditions of introduction. For this indicator, we can distinguish two groups: i) Rh. sichotense (13.3±1.2 %) with a high level of cells with a residual nucleolus at the stage of metaphase—telophase of mitosis, and ii) Rh. mucronulatum (9.1±1.1 %), Rh. dauricum (10.2±1.0 %) and Rh. ledebourii (10.9±1.3 %) with low values. Despite the difference in cytogenetic parameters in the seed offspring of the studied species, a cluster analysis of the totality of the characteristics of the course of mitosis and nucleolar activity made it possible to distinguish two groups: 1) Rh. mucronulatum and Rh. dauricum; 2) Rh. ledebourii and Rh. sichotense.The cytogenetic characteristics of the seed offspring of the species studied are species-specific.Peer reviewe

Molecular genetic identification of Scots pine and Siberian larch populations in Perm Krai based on polymorphism of ISSR-PCR markers : Молекулярно-генетическая идентификация популяций сосны обыкновенной и лиственницы сибирской в Пермском крае на основании полиморфизма ISSR-маркеров

The use of DNA-fingerprinting of forest-forming woody plants is considered the most promising tool for genetic control of wood’s geographic origin, the formation of a reliable management system for harvesting and turnover of lumber. The purpose of this work was to search for identification markers, genotyping trees, and molecular genetic identification of previously not studied 2 populations of the Siberian larch Larix sibirica Ledeb. and 4 populations of Scots pine Pinus sylvestris L. of different regions of the Perm Krai. To DNA extraction, from each plant specimens wood were individually obtained and a modified method of extracting DNA from wood was used. In total, the analysis used the DNA of 114 Scots pine trees and 55 Siberian larch trees. For genetic testing, we used ISSR (Inter Simple Sequence Repeats)-method of DNA polymorphism analysis. Genetic identification was performed based on the original author's method proposed by S. V. Boronnikova and I. V. Boboshina (2014). As a result of molecular genetic analysis, 74 ISSR markers were found and analyzed in populations of Scots pine, 85 ISSR markers were identified in populations of the Siberian larch, and the share of polymorphic loci in both species was high. As a result of molecular genetic identification, identification of species and polymorphic ISSR-markers and their combinations were found that characterize the belonging of trees to a species, as well as to a specific population. Molecular genetic formulas and barcodes for each individual population of two species have been compiled. The effectiveness, stability, and reproducibility of detected identification markers and their combinations have been proven through anonymous testing. The data obtained are the basis for determining the place of origin of wood, which will allow us to recommend measures to counter illegal logging and reduce the damage to the budget of logging regions of Russia, such as the Perm Krai.Peer reviewe

Use of retrotransposon markers to analyse genetic diversity of wild emmer wheat (Triticum dicoccoides)

vokBEL/KG

Vitamin D Status, VDR, and TLR Polymorphisms and Pulmonary Tuberculosis Epidemiology in Kazakhstan

Background: Tuberculosis (TB) and vitamin D deficiency remain major public health problems in Kazakhstan. Due to the high incidence of pulmonary tuberculosis in the country and based on the importance of vitamin D in the modulation of the immune response and the association of its deficiency with many health conditions, the aim of our research was to study the vitamin D status, VDR and TLR gene polymorphisms, and pulmonary tuberculosis epidemiology in Kazakhstan. Methods: A case-control study included 411 individuals diagnosed with pulmonary TB and 686 controls with no family history of pulmonary tuberculosis. Concentrations of serum vitamin D (25-(OH)D) levels were measured by electrochemiluminescence immunoassay. The gene polymorphisms were determined by real-time polymerase chain reaction (PCR) allelic discrimination assay using TaqMan probes. The association between the risk of pulmonary TB and polymorphisms was evaluated using multimodal logistic regression and assessed with the ORs, corresponding to 95% Cis, and the significance level was determined as p < 0.05. Results: 1097 individuals were recruited from 3 different regions of Kazakhstan. Biochemical data showed vitamin D deficiency (25-(OH)D < 20 ng/mL) was present in both groups, with the case group accounting for almost 95% and 43.7% in controls. Epidemiological data revealed that socioeconomic factors such as BMI < 25 kg/m2 (p < 0.001), employment (p < 0.001), diabetes (p < 0.001), and vitamin D deficiency (p < 0.001) were statistically different between case and control groups. Logistic regression analysis, adjusted by sex, age, BMI, residence, employment, smoking, alcohol consumption, and diabetes, showed that T/T polymorphism of the VDR gene (rs1544410, OR = 1.97, 95% CI: 1.04–3.72, p = 0.03) and A/A polymorphism of the TLR8 gene (rs3764880, OR = 2.44, 95% CI: 1.20–4.98, p = 0.01) were associated with a high risk of developing pulmonary tuberculosis. Conclusions: Vitamin D deficiency remains prevalent in our study cohort and is associated with TB progression. Socioeconomic determinants such as unemployment, BMI under 25 kg/m2, and diabetes are the main risk factors for the development of pulmonary TB in our study. A/A polymorphism of TLR8 (rs3764880) and T/T polymorphism (BsmI, rs1544410) of VDR genes may act as biomarkers for pulmonary tuberculosis in the Kazakh population