Development of Microsatellite Genetic Markers in Siberian larch (Larix sibirica Ledeb.) Based on the De Novo Whole Genome Sequencing

This special issue of the journal is devoted to the outstanding population geneticist Yuri Petrovich Altukhov, who paid much attention in his research to the development of molecular genetic markers for pop- ulation studies. Over the past time markers and methods of their development have undergone significant change. Thanks to modern methods of whole genome sequencing, it has become possible to develop markers of very different types – selectively neutral, as well as functional. Among them, microsatellite markers remain the most informative, convenient, reproducible, relatively inexpensive, and polymorphic. Whole genome sequencing greatly facilitates their discovery and development. This paper is devoted to the development of new microsatellite markers for a very important species of boreal forest – Siberian larch (Larix sibirica Ledeb.). Using a draft assembly of the larch genome, several thousand contigs containing microsatellite loci with di-, tri, tetra- and pentanucleotide motifs were selected. A total of 59 pairs of PCR primers were tested for loci with dinucleotide motifs as the most variable. From them, 11 pairs were finally selected for 11 loci with dinucleotide repeats, which showed a high level of polymorphism and can be used in various population genetic studies and to identify the origin of wood and plant material. This study was done at the Laboratory of Forest Genomics of the Genome Research and Education Center of the Siberian Federal University with the support of the Department of Forest Genetics and Forest Tree Breeding of the Georg-August University of Göttingen, the Department for Monitoring of Forest Genetic Resources of the Forest Protection Center of the Krasnoyarsk Territory, and the Laboratory of Forest Genetics and Selection of the V. N. Sukachev Institute of Forest of the Siberian Branch of the Russian Academy of Sciences within the framework of the project “Genomics of the key boreal forest conifer species and their major phytopathogens in the Russian Federation” funded by the Government of the Russian Federation (grant no. 14.Y26.31.0004)

Організаційно-економічні основи розвитку соціальної відповідальності промисловго підприємства

Сучасний етап розвитку суспільства характеризується суттєвими змінами в усіх сферах соціального та економічного життя. Довготривалий економічний спад після відновлення незалежності України обумовив зниження соціальної активності підприємств, а сучасні кризові тенденції негативно позначаються на виконанні соціальних функцій державою. Це, поряд з постійними трансформаційними процесами, призводить до зниження якості життя й негативно впливає на розвиток економіки. Впровадження принципів соціальної відповідальності в бізнес- процеси виступає чинником подальшого розвитку підприємства та набуває першочергового значення при вирішенні ряду соціальних проблем. При цитуванні документа, використовуйте посилання http://essuir.sumdu.edu.ua/handle/123456789/1581

Animal models for COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the aetiological agent of coronavirus disease 2019 (COVID-19), an emerging respiratory infection caused by the introduction of a novel coronavirus into humans late in 2019 (first detected in Hubei province, China). As of 18 September 2020, SARS-CoV-2 has spread to 215 countries, has infected more than 30 million people and has caused more than 950,000 deaths. As humans do not have pre-existing immunity to SARS-CoV-2, there is an urgent need to develop therapeutic agents and vaccines to mitigate the current pandemic and to prevent the re-emergence of COVID-19. In February 2020, the World Health Organization (WHO) assembled an international panel to develop animal models for COVID-19 to accelerate the testing of vaccines and therapeutic agents. Here we summarize the findings to date and provides relevant information for preclinical testing of vaccine candidates and therapeutic agents for COVID-19

Intraspecific Genetic Differentiation of the Cajanderi Larch (Larix cajanderi) in the North-East Asia

The study of intraspecific genetic differentiation of the Cajanderi larch (Larix cajanderi) was carried out in the north-east of Asia – in Magadan region and on the Kamchatka Peninsula. Genetic diversity of the larch was investigated using eight nuclear microsatellite loci. SSR analysis revealed high level of genetic diversity of the Cajanderi larch in the Far North-East of Asia. Significant genetic differences between L. cajanderi samples from Magadan region and Kamchatka suggests early isolation of the larch on the peninsula

Phylogenetic position of whitefish Coregonus lavaretus (L.) from Teletskoye Lake (Siberia) based on complete mitochondrial DNA

The taxonomy of the European whitefish species complex Coregonus lavaretus (L.) is extremely intricate. Owing to wide distribution from Central Europe to water bodies in Chukotka and high biological plasticity, many forms with different taxonomic status have been described. Teletskoye Lake is inhabited by two endemic whitefishes: Pravdin's whitefish Coregonus lavaretus pravdinellus and Teletskoye whitefish C. smitti. Previously, a total of 106 mitogenomes of whitefishes from the C. lavaretus complex from different populations of the Baltic and North seas were sequenced; however, there are no such data for whitefishes from Siberia. We obtain the mitochondrial genomes of C. smitti and C. l. pravdinellus, 16 738 bp in length, with high coverage. The mitogenomes differ in 46 positions (0.27%). Comparative analysis of C. lavaretus mitogenomes from water bodies of Europe and Teletskoye Lake confirms the common origin of the populations from the eastern part of the Baltic Sea and water bodies of Siberia. In addition, analysis of the complete mitogenomes of C. smitti and C. l. pravdinellus does not confirm their different taxonomic status, at least on the basis of mtDNA

Development of Nuclear Microsatellite Markers with Long (Tri-, Tetra-, Penta-, and Hexanucleotide) Motifs for Three Larch Species Based on the de novo Whole Genome Sequencing of Siberian Larch (Larix sibirica Ledeb.)

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.Siberian larch (Larix sibirica Ledeb.) is one of the major boreal tree species in Eurasia and has a considerable economic and ecological value. Despite that importance, the development and use of microsatellite markers in this species remain limited. Microsatellite markers are considered to be a valuable tool for estimation of population diversity and structure. Availability of a draft reference assembly of the Siberian larch genome allowed us to identify 1015 microsatellite loci or simple sequence repeats (SSRs) with tri-, tetra-, penta-, and hexanucleotide motifs. For 60 of them PCR primers were designed and tested for amplification in L. sibirica and for their within-genus transferability to L. gmelinii (Rupr.) Rupr. and L. cajanderi Mayr. Here, we present a set of 14 reliable and polymorphic new nuclear SSR markers that can be used for further population genetic studies, breeding programs, and timber origin identification

Development of Cytoplasmatic SSR-Markers for Population Genetic Studies of the Siberian Stone Pine (Pinus Sibirica Du Tour)

Three chloroplast and one mitochondrial DNA markers were developed and used for genotyping of 60 trees in two populations of the Siberian stone pine (Pinus sibirica Du Tour). Two chloroplast loci were monomorphic in both populations, and one polymorphic with two alleles. Therefore, four chloroplast haplotypes were revealed totally. A mitochondrial DNA marker had two alleles or haplotypes (mitotypes)

The effect of individual genetic heterozygosity on general homeostasis, heterosis and resilience in Siberian larch (Larix sibirica Ledeb.) using dendrochronology and microsatellite loci genotyping

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала.The genetic mechanisms underlying the relationship of individual heterozygosity (IndHet) with heterosis and homeostasis are not fully understood. Such an understanding, however, would have enormous value as it could be used to identify trees better adapted to environmental stress. Dendrochronology data, in particular the individual average radial increment growth of wood measured as the average tree ring width (AvTRW) and the variance of tree ring width (VarTRW) were used as proxies for heterosis (growth rate measured as AvTRW) and homeostasis (stability of the radial growth of individual trees measured as VarTRW), respectively. These traits were then used to test the hypothesis that IndHet can be used to predict heterosis and homeostasis of individual trees. Wood core and needle samples were collected from 100 trees of Siberian larch (Larix sibirica Ledeb.) across two populations located in Eastern Siberia. DNA samples were obtained from the needles of each individual tree and genotyped for eight highly polymorphic microsatellite loci. Then mean IndHet calculated based on the genotypes of eight loci for each tree was correlated with the statistical characteristics of the measured radial growth (AvTRW and VarTRW) and the individual standardized chronologies. The analysis did not reveal significant relationships between the studied parameters. In order to account for the strong dependence of the radial growth on tree age the age curves were examined. An original approach was employed to sort trees into groups based on the distance between these age curves. No relationship was found between these groups and the groups formed based on heterozygosity. However, further work with more genetic markers and increased sample sizes is needed to test this novel approach for estimating heterosis and homeostasis

Preliminary Results of De Novo Whole Genome Sequencing of the Siberian Larch (Larix sibirica Ledeb.) and the Siberian Stone Pine (Pinus sibirica Du Tour)

The Illumina HiSeq2000 DNA sequencing generated 2 906 977 265 high quality paired-end nucleotide sequences (reads) and 576 Gbp for Siberian larch (Larix sibirica Ledeb.) that corresponds to 48X coverage of the larch genome (12.03 Gbp), and 3 427 566 813 reads and 679 Gbp for Siberian stone pine (Pinus sibirica Du Tour) that corresponds to 29X coverage of its genome (23.6 Gbp). These data are not enough to assemble and annotate whole genomes, but the obtained nucleotide sequences have allowed us to discover and develop effective highly polymorphic molecular genetic markers, such as microsatellite loci that are required for population genetic studies and identification of the timber origin. Sequence data can be used also to discover single nucleotide polymorphisms (SNPs). Genomic studies of Russian boreal forests and major phytopathogens associated with them will also allow us to identify biomarkers that can be used for solving important scientific and economic problems related to the conservation of forest genetic resources and breeding more resilient and fast growing trees with improved timber and resistance to diseases and adverse environmental factors