International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”

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Bioinformatics and systems biology of plants symposium

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Bioinformatics and systems biology of plants symposiumComparative analysis of flax (Linum usitatissimum L.) genomes and transcriptomes

Comparative analysis of flax (Linum usitatissimum L.) genomes and transcriptomes

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/379.pdf”]
Elena Pushkova1, George Krasnov2, Roman Novakovskiy3, Liubov Povkhova4, Artemy Beniaminov5, Nadezhda Bolsheva6, Tatiana Rozhmina7, Alexey Dmitriev8, Nataliya Melnikova9
1Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, pushkova18@gmail.com
2Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, gskrasnov@mail.ru
3Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, 0legovich46@mail.ru
4Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, Russia, povhova.lv@phystech.edu
5Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, abeniaminov@mail.ru
6Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, nlbolsheva@mail.ru
7Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Federal Research Center for Bast Fiber Crops, Torzhok, Russia, tatyana_rozhmina@mail.ru
8Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, alex_245@mail.ru
9Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, mnv-4529264@yandex.ru

Flax (Linum usitatissimum L.) is an agriculturally important plant that has a wide range of applications in industry, and the direction of cultivar application is determined by its genetic characteristics. The present work aimed to obtain high-quality sequences of flax genomes and transcriptomes for genetically diverse cultivars and lines, which have breeding value and different direction of use. Six cultivars/lines (LM98, #3896, Diplomat, Atlant, Universal, Alizee) were selected for the present work. We have developed an optimal method for the extraction of pure high-molecular-weight DNA from flax plants and performed genome and transcriptome sequencing. From 6 to 10 Gb was obtained for each of the studied flax cultivars/lines on the Oxford Nanopore platform and 20-25 million reads on the Illumina platform. Transcriptome sequencing of different flax tissues was also performed. Genome assembly using Flye resulted in the N50 value from 200 kb to 1 Mb depending on the genotype. Genome annotation was then performed. The obtained genome assemblies are the basis for molecular genetic studies in flax and allow assessment of the differences in L. usitatissimum cultivars/lines at the genome-wide level.

Bioinformatics and systems biology of plants symposiumComparative genomic analysis of male and female poplars

Comparative genomic analysis of male and female poplars

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/378.pdf”]
Elena Pushkova1, George Krasnov2, Roman Novakovskiy3, Nadezhda Bolsheva4, Nataliya Melnikova5, Alexey Dmitriev6
1Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, pushkova18@gmail.com
2Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, gskrasnov@mail.ru
3Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, 0legovich46@mail.ru
4Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, nlbolsheva@mail.ru
5Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, mnv-4529264@yandex.ru
6Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, alex_245@mail.ru

In the genomic analysis of trees, species belonging to the Populus genera serve as model objects. In our work, we carried out sequencing of the genome of male and female plants of Populus x sibirica, which are widespread in the Moscow region. Achieve high quality de novo In assemblies, we used a combination of two platforms, namely Oxford Nanopore and Illumina, to obtain long and high-precision short read operations, respectively. In general, using the MinION sequencer, we got 18 GB with an average N50 of 25 kb for each genotype, while using the HiSeq 2500 tool, we got from 36 to 52 million paired 125 + 125 readings for male and female plants. The Shasta assembler provided the best assembly results: N50 values ​​were around 0.5 MB, and integrity was above 95% according to BUSCO. Analysis of the high-quality genomes of male and female P. x sibirica trees makes it possible to identify genes associated with poplar sex, which will facilitate the determination of its sex determination mechanism.

Bioinformatics and systems biology of plants symposiumAnalysis of repeatomes in Cannabaceae family

Analysis of repeatomes in Cannabaceae family

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/362.pdf”]
Julia Bocharkina1, Olga Razumova2, Gennady Karlov3
1Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia; Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia, julia.bocharkina@skoltech.ru
2Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia, razumovao@gmail.com
3Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia, karlovg@gmail.com

Analysis of repeatomes in the Cannabaceae family was done. There were found family-specific, species-specific and sex-specific clusters. Primers were created and checked.

Bioinformatics and systems biology of plants symposiumRegulation of Transcription Activity of MAKR4 in Arabidopsis thaliana L.

Regulation of Transcription Activity of MAKR4 in Arabidopsis thaliana L.

No Comment on Regulation of Transcription Activity of MAKR4 in Arabidopsis thaliana L.

Korosteleva Anastasia1, Novikova Daria2, Mironova Victoria3
1Novosibirsk State University, kartzeva.kar@gmail.com
2Institute of Cytology and Genetics SB RAS, da6ik777@gmail.com
3Institute of Cytology and Genetics SB RAS, kviki@bionet.nsc.ru

Auxin has a crucial influence on genes expression. In this work, we show that transcriptional activity of an auxin-sensitive gene MAKR4 (MEMBRANE ASSOSIATED KINASE REGULATOR 4) depends on the composite elements in its upstream regulatory region. Analysis of such elements could clarify the understanding of the regulation of this gene and other auxin-sensitive genes.

Bioinformatics and systems biology of plants symposiumEffects of anthocyanin-rich grain diet on growth and metastasis of Lewis lung carcinoma in mice

Effects of anthocyanin-rich grain diet on growth and metastasis of Lewis lung carcinoma in mice

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/55.pdf”]
Michael V. Tenditnik1, Maria A. Tikhonova2, Ekaterina A. Litvinova3, Nelly A. Popova4, Tamara G. Amstislavskaya5, Elena K. Khlestkina6
1Scientific Research Institute of Physiology and Basic Medicine Novosibirsk, Russia, m.v.tenditnik@physiol.ru
2Scientific Research Institute of Physiology and Basic Medicine Novosibirsk, Russia, tikhonovama@physiol.ru
3Scientific Research Institute of Physiology and Basic Medicine Novosibirsk, Russia, litvinovaea@physiol.ru
4Federal Research Center “Institute of Cytology and Genetics” Novosibirsk, Russia, nelly@bionet.nsc.ru
5Scientific Research Institute of Physiology and Basic Medicine Novosibirsk, Russia, Amstislavskaya@yandex.ru
6N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources St. Petersburg, Russia, Federal Research Center “Institute of Cytology and Genetics” Novosibirsk, Russia, khlest@bionet.nsc.ru

Abstract Currently functional nutrition has developed intensively. Functional foods are a valuable addition to existing dietary therapy. Such products are enriched with biologically active substances. Anthocyanins attract particular attention due to multiple beneficial properties including antitumor activity. Here we used two wheat near-isogenic lines created at the Institute of Cytology and Genetics SB RAS [1] that have almost similar genomes with the exception of a small part of chromosome 2A, which contains the Pp3/TaMyc1 gene regulating anthocyanin biosynthesis, to assess the effect of an anthocyanin-rich grain diet on the development and metastasis of the Lewis lung carcinoma (LLC), as well as the accompanying immune response in C57BL/6 mice. Mice were kept at a grain or standard diet for four month prior tumor transplantation. A decrease in the number of metastases in the lungs and the size of the tumor in the groups at a grain diet, regardless of the content of anthocyanins, was revealed. However, the highest percentage of animals without metastases was observed at an anthocyanin-rich grain diet. The LLC transplantation caused a significant increase in plasma levels of pro-inflammatory cytokines (IL-6 and LIF) in mice at a standard diet, but not in animals at grain diets. Thus, the anthocyanin-rich diet helps to reduce the severity of the tumor process. The antitumor effects of grain diets are probably mediated by modulation of signaling pathways associated with IL-6 cytokines.

Acknowledgment

The study was supported by Russian Science Foundation (grant No. 16-14-00086).

References
  • I. Gordeeva, O. Y. Shoeva, and E. K.Khlestkina, “Marker-assisted development of bread wheat near-isogenic lines carrying various combinations of purple pericarp (Pp) alleles,” Euphytica, vol. 203, pp. 469-476, 2015.
Bioinformatics and systems biology of plants symposiumSTUDY OF THE ROOT TRANSCRIPTOME OF BREAD WHEAT USING HIGH-THROUGHPUT RNA SEQUENCING (RNA-SEQ)

STUDY OF THE ROOT TRANSCRIPTOME OF BREAD WHEAT USING HIGH-THROUGHPUT RNA SEQUENCING (RNA-SEQ)

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Alexandr Vikhorev1, Nikolay Shmakov2, Anastasia Glagoleva3, Elena Khlestkina4, Olesya Shoeva5
1Novosibirsk State University, vikhorev@bionet.nsc.ru
2Institute of Cytology and Genetics SB RAS, shmakov@bionet.nsc.ru
3Institute of Cytology and Genetics SB RAS, glagoleva@bionet.nsc.ru
4All-Russian Institute of Plant Recources, khlest@bionet.nsc.ru
5Institute of Cytology and Genetics SB RAS, olesya_ter@bionet.nsc.ru

Bread wheat (Triticum aestivum L.) is the most important crop in the world. It provides about 20% of the total calories consumed by humans. For a long time, wheat selection was mainly based on phenotypic traits of the shoot, but the roots were given little attention. As a result, the root system of modern wheat varieties has weakened. Therefore, the study of genetic control of wheat roots development is an urgent issue. In this study, sequencing of RNA libraries from roots and coleoptile of Russian spring variety “Saratovskaya, 29” was performed. De novo transcriptome was assembled. 31,488 up-regulated, 35,851 down-regulated and 18,040 roots-specific transcripts were found. The subsequent analysis of genes with differential expression will allow choosing the candidate genes for development of wheat varieties with resistant root system.

Bioinformatics and systems biology of plants symposiumAnalysis of agronomic traits of mungbean (Vigna radiata) accessions from the World Vegetable Gene Bank (Taiwan)

Analysis of agronomic traits of mungbean (Vigna radiata) accessions from the World Vegetable Gene Bank (Taiwan)

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/249.pdf”]
Alena Sokolkova1, Marina Burlyaeva2, Tatjana Valiannikova3, Margarita A. Vishnyakova4, Roland Schafleitner5, Cheng-Ruei Lee6, Chau-Ti Ting7, Sergey V. Nuzhdin8, Maria G. Samsonova9, Eric von Wettberg10
1Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia, alyonasok@yandex.ru
2Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia, m.burlyaeva@vir.nw.ru
3Kuban Branch of Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), Krasnodar region, Russia, fitolaka61@yandex.ru
4Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia, m.vishnyakova@vir.nw.ru
5World Vegetable Center, Shanhua, Tainan 74199, Taiwan, roland.schafleitner@worldveg.org
6National Taiwan University, Taipei 106, Taiwan, chengrueilee@ntu.edu.tw
7National Taiwan University, Taipei 106, Taiwan, ctting@ntu.edu.tw
8University of Southern California, Program in Molecular and Computational Biology, Dornsife College of Letters Arts & Sciences, Los Angeles, CA 90089 USA, snuzhdin@usc.edu
9Peter the Great St. Petersburg Polytechnic University, Department of Applied Mathematics, St. Petersburg, Russia, m.g.samsonova@gmail.com
10University of Vermont, Department of Plant and Soil Science, Burlington, VT 05405, USA, eric.bishop-von-wettberg@uvm.edu

The World Vegetable Gene Bank, in Taiwan, houses a unique genebank of mungbean. Here we analyze the genomes of 293 accessions that represent the major market classes. GWAS analysis conducted on phenotypic data obtained in Astrakhan experimental station of VIR in 2019 and multi-environmental GWAS analysis with phenotypic data obtained in different locations and time periods (Taiwan 1984, Taiwan 2018, India 2016, Kuban 2018, Astrakhan 2019) identified a large number of genome intervals and potential gene candidates that may affect important agronomic traits. To find out the effects of different climatic conditions on phenotypic traits, the data was subjected to AMMI and GGE biplot analyses. Phenotyping the mini-core collection of mungbean in different climatic locations can estimate phenology traits such as maturation. Uncovering SNPs for these traits will speed breeding efforts for production of mungbean suitable for cultivation in temperate regions.

Bioinformatics and systems biology of plants symposiumGenomic analysis of Vavilov\’s historic chickpea landraces using GWAS, AMMI and GGE biplot analyses

Genomic analysis of Vavilov\’s historic chickpea landraces using GWAS, AMMI and GGE biplot analyses

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/247.pdf”]
Alena Sokolkova1, Sergey V. Bulyntsev2, Peter L. Chang3, Noelia Carrasquila-Garcia4, Eric von Wettberg5, Margarita A. Vishnyakova6, Douglas R. Cook7, Sergey V. Nuzhdin8, Maria G. Samsonova9
1Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia, alyonasok@yandex.ru
2Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia, s_bulyntsev@mail.ru
3University of Southern California, Program in Molecular and Computational Biology, Dornsife College of Letters Arts & Sciences, Los Angeles, CA 90089 USA, peterc@usc.edu
4University of California Davis, Department of Plant Pathology, Davis, CA 95616 USA, noecarras@ucdavis.edu
5University of Vermont, Department of Plant and Soil Science, Burlington, VT 05405, USA, eric.bishop-von-wettberg@uvm.edu
6Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia, m.vishnyakova@vir.nw.ru
7University of California Davis, Department of Plant Pathology, Davis, CA 95616 USA, drcook@ucdavis.edu
8University of Southern California, Program in Molecular and Computational Biology, Dornsife College of Letters Arts & Sciences, Los Angeles, CA 90089 USA, snuzhdin@usc.edu
9Peter the Great St. Petersburg Polytechnic University, Department of Applied Mathematics, St. Petersburg, Russia, m.g.samsonova@gmail.com

The Vavilov seed bank contains numerous landraces collected nearly hundred years ago, before intensive breeding of most crops, and thus is a potential reservoir of historic crop adaptations. Here we analyze the genomes of 407 of Vavilov\’s original landraces, sampled from major historic centers of chickpea cultivation and secondary diversification. We performed GWAS to find associations between VIR’s chickpea accessions and phenotypic data obtained in Kuban experimental station of VIR in 2017 under infectious conditions. To find out the effects of infectious conditions on phenotypic traits, the data was subjected to AMMI and GGE biplot analyses.

Bioinformatics and systems biology of plants symposiumIdentification of an AP2/ERF Transcription Factor Controlling the Synthesis of Barley Epicuticular Wax

Identification of an AP2/ERF Transcription Factor Controlling the Synthesis of Barley Epicuticular Wax

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/246.pdf”]
Ekaterina Kolosovskaya1, Sophia Gerasimova2, Anna Korotkova3, Christian Hertig4, Sergey Morozov5, Elena Chernyak6, Dmitriy Domrachev7, Vikhorev Alexander8, Nikolay Shmakov9, Alexey Kochetov10, Jochen Kumlehn11, Elena Khlestkina12
1ICG SB RAS, Novosibirsk, Russia, kolosovskaya@bionet.nsc.ru
2ICG SB RAS, Novosibirsk, Russia NSU, Novosibirsk, Russia, gerson@bionet.nsc.ru
3ICG SB RAS, Novosibirsk, Russia, korotkova@bionet.nsc.ru
4Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Germany, hertig@ipk-gatersleben.de
5Novosibirsk Institute of Organic Chemistry, SB RAS Novosibirsk, Russia, moroz@nioch.nsc.ru
6Novosibirsk Institute of Organic Chemistry, SB RAS Novosibirsk, Russia, chernyak@nioch.nsc.ru
7Novosibirsk Institute of Organic Chemistry, SB RAS Novosibirsk, Russia, dmitry@nioch.nsc.ru
8ICG SB RAS, Novosibirsk, Russia NSU, Novosibirsk, Russia, vikhorev@bionet.nsc.ru
9ICG SB RAS, Novosibirsk, Russia, shmakov@bionet.nsc.ru
10ICG SB RAS, Novosibirsk, Russia NSU, Novosibirsk, Russia, ak@bionet.nsc.ru
11Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Germany, kumlehn@ipk-gatersleben.de
12ICG SB RAS, Novosibirsk, Russia NSU, Novosibirsk, Russia Vavilov Institute of Plant Genetic Resources (VIR) Saint Petersburg, Russia, khlest@bionet.nsc.ru

Site-directed mutagenesis provides ample opportunity for reverse genetics, which allows us to establish a relationship between a gene and its function. In the present study, the role of the HvWIN1 barley (Hordeum vulgare) gene in the formation of epicuticular wax was identified by taking a targeted knockout approach using RNA-guided Cas9 endonuclease technology.

Bioinformatics and systems biology of plants symposiumRetrotransposons of Arabidopsis thaliana expressed in wild-type plants

Retrotransposons of Arabidopsis thaliana expressed in wild-type plants

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Sofya Gvaramiya1, Murad Omarov2, Ilya Kirov3
1Department of marker-assisted and genomic selection of plant All-Russia Research Institute of Agricultural Biotechnology, sofia.gvaramia@gmail.com
2Department of marker-assisted and genomic selection of plant All-Russia Research Institute of Agricultural Biotechnology, muradok98@gmail.com
3Department of marker-assisted and genomic selection of plant All-Russia Research Institute of Agricultural Biotechnology, kirovez@gmail.com

Mobile genetic elements are widely spread across the genomes of plants and animals. Of them, retrotransposons occupy substantial part of the genome. They had a huge impact on host genome evolution. However, their current activity in plant cell is thought to be very low on both RNA and cDNA (mobilome) levels because multiple silencing pathways. To get deeper insight into the mechanisms of mobilome formation we carried out identification of transcribed TEs of model plant, Arabidopsis thaliana. Using bioinformatics and ‘wet’ approaches we found evidence of expression of 6 TEs of A.thaliana. This opens a door for further functional studies of how some TEs can overcome the genome defense against retrotransposon activity.