Genotypic diversity and clonal structure of Erigeron annuus (Asteraceae) in Lithuania

This study was conducted to assess the clonal structure and genetic diversity of alien herbaceous plant species Erigeron annuus. The global warming and changes in agriculture practice in the past few decades were favourable for the expansion of this species in Lithuania. We used RAPD and ISSR assays to assess genetic variation within and among 29 populations of E. annuus. A total of 278 molecular markers were revealed. Our study detected reduced level of genetic diversity of invasive populations of E. annuus. Significant differences in DNA polymorphism among populations of E. annuus were also found. Some populations of this species are composed of genetically identical plants, while others were polymorphic. Clonal diversity of study populations ranged from 0.083 to 0.4 for both DNA marker systems. The Simpsons diversity index values ranged from 0.0 to 0.636. The average number of genotypes per population established using both assays was about 1.7. Out of 328 E. annuus individuals only 16 showed unique RAPD and 14 unique ISSR banding patterns. The remaining plants were clones of different size. The most common genotype of E. annuus identified in our study was represented by predominate in nine populations.Keywords: Clonal structure, DNA markers, Erigeron annuus, invasive plants, ISSR, RAPDGenetische Vielfalt und Klonstruktur von Erigeron annuus (Asteraceae) in LitauenZusammenfassungDie Untersuchungen verfolgen das Ziel, die genetische Struktur der nicht-einheimischen Pflanzenart Erigeron annuus auszuwerten. Globale Erwärmung sowie Veränderungen in der landwirtschaftlichen Praxis der letzten Jahrzehnte waren bedeutsam für die Verbreitung dieser Art in Litauen. Für die Feststellung der genetischen Verteilungsvielfalt in den 29 E. annuus Populationen haben wir uns der RAPD und ISSR -Methoden bedient. Insgesamt wurden 117 RAPD - und 161 ISSR - Loci festgestellt. Die Untersuchungen haben die verringerte genetische Vielfalt der E. annuus Populationen aufgezeigt. Außerdem wurden bedeutende DNR polymorphe Unterschiede zwischen E. annuus Populationen angetroffen. Einige Populationen dieser Art bestanden aus genetisch identischen Pflanzen, während die anderen polymorphem waren. Die Klonvielfalt der untersuchten Populationen schwankte zwischen 0.083 und 0.4 bei der Verwendung von beiden DNR-Signifikanten. Die durchschnittliche Genotypen Zahl in der Population betrug etwa 1.7 bei der Verwendung von beiden Signifikanten. Nach der Untersuchung der 328 E. annuus Individuen wurden 16 unikale RAPD - und 14 unikale ISSR - Phänotypen festgestellt. Die übriggebliebenen Pflanzen waren Klonen von unterschiedlicher Größe. Der am meisten verbreitete E. annuus Genotyp wurde in neun Populationen ermittelt.Stichwörter: DNS- Marker, Erigeron annuus, ISSR, Klonstruktur, invasive Pflanzen, RAP

Comparison of genetic diversity in two alien plant species

Bunias orientalis and Erigeron annuus are two alien herbal plant species invading native ecosystems in Lithuania. Both species have similar introduction and invasion history but differ in their life history traits and strategies of reproduction. We used random amplified polymorphic DNA (RAPD) data to compare the genetic diversity in invasive populations of these species. 42 RAPD bands were identified in B. orientalis and 70 RAPD bands in E. annuus. All six populations of B. orientalis were polymorphic, while only four of eight study populations of E. annuus were polymorphic. The highest differences between species were established at the level of RAPD phenotypes. 67 RAPD phenotypes were found among 90 plants of B. orientalis but only 10 RAPD phenotypes were identified among 89 plants of E. annuus. This study shows that the level of genetic diversity in populations of different invasive species at the same geographic area may vary considerably. Keywords: Bunias orientalis, Erigeron annuus, genetic diversity, RAPD phenotypeVergleich der genetischen Vielfalt von zwei nicht-einheimischen PflanzenartenBunias orientalis und Erigeron annuus sind zwei nicht-einheimische Pflanzenarten, die in litauische natürliche Ökosysteme eindringen. Eindringungs- und Invasionswege beider Arten sind ähnlich. Unterschiede liegen in den Entwicklungs- und Reproduktionsbesonderheiten. In dieser Arbeit haben wir anhand der Ergebnisse von random amplified polymorphic DNA (RAPD) die genetische Vielfalt von verschiedenen Populationen dieser nicht-einheimischen Arten verglichen. 42 RAPD Banden wurden bei B. orientalis und 70 bei E. annuus festgestellt. Alle sechs B. orientalis-Populationen waren polymorph; bei E. annuus waren es nur vier von acht Populationen. Die größte Differenz zwischen den Arten zeigten die RAPD-Phänotypen. Bei 90 B. orientalis-Pflanzen wurden 67 RAPD-Phänotypen identifiziert aber nur 10 RAPD-Phänotypen bei 89 E. annuus-Pflanzen. Die Ergebnisse zeigen, dass die genetische Vielfalt der nicht-einheimischen Pflanzenarten auf demselben geographischen Territorium wesentliche Unterschiede aufweisen kann. Stichwörter: Bunias orientalis, Erigeron annuus, genetische Vielfalt, RAPD-Phänotype

CyberGenomics: Application of behavioral genetics in cybersecurity

Cybersecurity (CS) is a contemporary field for research and applied study of a range of aspects from across multiple disciplines. A cybersecurity expert has an in-depth knowledge of technology but is often also recognized for the ability to view technology in a non-standard way. This paper explores how CS specialists are both a combination of professional computing-based skills and genetically encoded traits. Almost every human behavioral trait is a result of many genome variants in action altogether with environmental factors. The review focuses on contextualizing the behavior genetics aspects in the application of cybersecurity. It reconsiders methods that help to identify aspects of human behavior from the genetic information. And stress is an illustrative factor to start the discussion within the community on what methodology should be used in an ethical way to approach those questions. CS positions are considered stressful due to the complexity of the domain and the social impact it can have in cases of failure. An individual risk profile could be created combining known genome variants linked to a trait of particular behavior using a special biostatistical approach such as a polygenic score. These revised advancements bring challenging possibilities in the applications of human behavior genetics and CS.publishedVersio

Diversity analysis of pathogenic genomic variants and genes that cause the autosomal recessive diseases using whole exome sequencing

In thesis analysed data reveals which pathogenic genome variants appear in healthy individuals from the general Lithuanian population and which of them have statistically significantly higher frequency in the Lithuanian population, in comparison with other populations. To achieve aim of the study, the Lithuanian exome data from the project “Genetic diversity of the population of Lithuania and changes of its genetic structure related with evolution and common diseases” were used. As a source of known pathogenic variants, the data from ClinVar database were used. In all studied individuals, 321 unique SNV (single nucleotide variant) and 30 unique INDEL were identified as pathogenic. Each person, in average, had 45 SNV genomic variants that were identified as pathogenic. There were identified 15 pathogenic genomic variants that are inherited in autosomal recessive manner and statistically significantly differ from other European populations, 10 of them had a higher frequency and 5 had a lower frequency than the frequencies of Europeans. There were determined 103 pathogenic variants, which differed statistically from the global frequencies of respective genomic variants. Two pathogenic variants of studied data were found only in Žemaitija and one only in Aukštaitija. Study of genome pathogenic variants in healthy individuals can have practical benefits for Lithuanian population diagnostics and interpretation results of ClinVar pathogenic variant database is important for all that use this database

Patogeninių genomo variantų ir jų genų, lemiančių autosomines recesyviąsias ligas, įvairovės analizė, panaudojant viso egzomo sekoskaitą

In thesis analysed data reveals which pathogenic genome variants appear in healthy individuals from the general Lithuanian population and which of them have statistically significantly higher frequency in the Lithuanian population, in comparison with other populations. To achieve aim of the study, the Lithuanian exome data from the project “Genetic diversity of the population of Lithuania and changes of its genetic structure related with evolution and common diseases” were used. As a source of known pathogenic variants, the data from ClinVar database were used. In all studied individuals, 321 unique SNV (single nucleotide variant) and 30 unique INDEL were identified as pathogenic. Each person, in average, had 45 SNV genomic variants that were identified as pathogenic. There were identified 15 pathogenic genomic variants that are inherited in autosomal recessive manner and statistically significantly differ from other European populations, 10 of them had a higher frequency and 5 had a lower frequency than the frequencies of Europeans. There were determined 103 pathogenic variants, which differed statistically from the global frequencies of respective genomic variants. Two pathogenic variants of studied data were found only in Žemaitija and one only in Aukštaitija. Study of genome pathogenic variants in healthy individuals can have practical benefits for Lithuanian population diagnostics and interpretation results of ClinVar pathogenic variant database is important for all that use this database

Особенности растений арабидопсиса и кормовых бобов от многократных воздействий селективными дозами некоторых химических соединений

Vytauto Didžiojo universitetasŽemės ūkio akademij

Challenges in exome analysis by LifeScope and its alternative computational pipelines

Background: Every next generation sequencing (NGS) platform relies on proprietary and open source computational tools to analyze sequencing data. NGS tools for Illumina platforms are well documented which is not the case with AB SOLiD systems. We applied several computational and variant calling pipelines to analyse targeted exome sequencing data obtained using AB SOLiD 5500 system. Our investigated tools comprised proprietary LifeScope’s pipeline in combination with open source color-space competent mapping programs and a variant caller. We present instrumental details of the pipelines that were used and quantitative comparative analysis of variant lists generated by LifeScope’s pipeline versus open source tools. Results: Sufficient coverage of targeted regions was achieved by all investigated pipelines. High variability was observed in identities of variants across the mapping programs. We observed less than 50 % concordance of variant lists produced by approaches based on different mapping algorithms. We summarized different approaches with regards to coverage (DP) and quality (QUAL) properties of the variants provided by GATK and found that LifeScope’s computational pipeline is superior. Fusion of information on mapping profiles (pileup) at genomic positions of variants in several different alignments proved to be a useful strategy to assess questionable singleton variants. Conclusions: We quantitatively supported a conclusion that Lifescope’s pipeline is superior for processing sequencing data obtained by AB SOLiD 5500 system. Nevertheless the use of alternative pipelines is encouraged because aggregation of information from other mapping and variant calling approaches helps to resolve questionable calls and increases the confidence of the call. It was noted that a coverage threshold for variant to be considered for further analysis has to be chosen in data-driven way to prevent a loss of important information

Application of barley tweaky spike mutants for the study of effects of plant immunity‐related substances

Barley developmental mutants tweaky spike (tw) with disturbed auxin pathways possess a unique feature of an increased level of mouldy germinating grains (MGG), which serves as a convenient model to investigate the effects of plant immunity‐related substances. The effects of the auxin 2,4‐dichlorophenoxyacetic acid (2,4‐D), auxin inhibitors, salicylic acid (SA), and trans‐cinnamic acid (TCA) were studied using the tw‐WT system in surface‐sterilized and unsterilized germinating grains under high rates of natural infection. Significant differences among the allelic tw mutants were revealed at the natural MGG level and in response to 2,4‐D, SA, and TCA. The most effective means against MGG were sterilization and TCA. 2,4‐D inhibited root growth in tw and tw2 mutants, occurring only in unsterilized and not sterilized germinating grains, while the opposite was observed for TCA and SA. The tw mutations influenced variations in the seed‐borne fungal spectra, decreasing the frequency of Bipolaris sorokiniana and increasing Fusarium spp. Hypochlorite‐based surface sterilization methods should be used with caution in studies where the action of exogenous 2,4‐D will be analysed in germinating grains. Auxin pathway disturbances specific for pleiotropic tw mutants are generally restricted to organogenesis but not to germination events

The prevalence of rare variants potentially important for the response to medicines used for CVD treatment in the Lithuanian population

Cardiovascular disease (CVD) is one of the leading causes of death among Europeans and around the world. Major factors that are considered relevant for the efficacy or adverse drug reactions (ADRs) caused by drugs used for CVD treatment have been identified through GWAS studies mostly using low density common variant genotyping arrays. In this study whole exome sequencing (WES) was carried out to identify genomic variants relevant for CVD treatment. The study group included 98 (49 males and 49 females) self-reported healthy unrelated individuals from the Lithuanian population with at least three generations of Lithuanian ethnicity and residency in the same ethnolinguistic region. After performing WES genetic loci of 55 genes that were reported as relevant to the efficacy or ADRs caused by drugs used for CVD treatment were analyzed using LifeScopeTM and ANNOVAR software. The analysis of small indels in the selected regions revealed 13 exonic frameshift indels and a single intronic splice site variant that may affect the efficacy or cause ADRs in patients treated for CVD. Over 400 potentially relevant SNVs in different frequencies were detected in the genes reported to be important for CVD treatment. The strength of evidence analysis identified 14 SNVs most likely to be relevant for CVD treatment. The frequency distribution of several variant alleles that have been shown to be highly important for CVD treatment in the CYP2D6 (rs16947) and ADRB1 (rs1801253) as well as several variants in the CYP2C9 and NAT2 genes were determined to be significantly (p<0.05) different from other Caucasian populations showing the potential benefit of pharmacogenomic testing prior to treatment in the Lithuanian population. The research was carried out under the LITGEN project. LITGEN project (VP1-3.1-ŠMM-07-K-01-013) was funded by the European Social Fund under the Global Grant measure