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

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Genomics, transcriptomics, bioinformatics symposium

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Genomics, transcriptomics, bioinformatics symposiumPredicting elongation efficiency of gene translation for annotation of bacterial genomes: a case study for biosynthetic gene clusters of nonribosomal peptides

Predicting elongation efficiency of gene translation for annotation of bacterial genomes: a case study for biosynthetic gene clusters of nonribosomal peptides

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/414.pdf”]
A.I. Klimenko1, Yu.G. Matushkin2, D.A. Afonnikov3
1Kurchatov Genomics Center, Institute of Cytology and Genetics, klimenko@bionet.nsc.ru
2ICG SB RAS, mat@bionet.nsc.ru
3ICG SB RAS, NSU, ada@bonet.nsc.ru

The gene expression levels for bacteria are largely determined by the efficiency of translation elongation. We have performed bioinformatic elongation efficiency analysis of NRP biosynthetic gene clusters (BGCs) obtained from ANTISMASH-DB using whole-genome sequences of bacterial genomes that are available at NCBI Genbank. The analysis has provided the information about distribution of nonribosomal peptide biosynthetic gene clusters in bacteria and their putative translation elongation efficiency.

Genomics, transcriptomics, bioinformatics symposiumExpression of DNA reparation genes in anhydrobiotic insect Polypedilum vanderplanki

Expression of DNA reparation genes in anhydrobiotic insect Polypedilum vanderplanki

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Alexander Nesmelov1, Sabina Kondratyeva2, Taisiya Voronina3
1IFMB KFU, Kazan, Russia, nesmelov@gmail.com
2IFMB KFU, Kazan, Russia, sabinakondr@gmail.com
3IFMB KFU, Kazan, Russia, vorotaisiya@gmail.com

Anhydrobiosis is survival of complete body desiccation, tightly linked to the ability to cope with a massive DNA damage. However, in anhydrobiotic midge Polypedilum vanderplanki this ability is not accompanied by a huge induction of genes of DNA reparation system which is typical for many other anhydrobiosis-related genes in this insect.

Genomics, transcriptomics, bioinformatics symposiumComparative genomics and quantitative proteomics reveal differentially produced proteins underlying virulence and host specificity in Bacillus thuringiensis

Comparative genomics and quantitative proteomics reveal differentially produced proteins underlying virulence and host specificity in Bacillus thuringiensis

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/402.pdf”]
Yury Malovichko1, Maria Belousova2, Elena Lukasheva3, Daria Gorbach4, Ekaterina Romanovskaya5, Christian Ihling6, Andrej Frolov7, Anton Nizhnikov8, Kirill Antonets9
1All-Russian Research Institute of Agricultural Microbiology, yu.malovichko@arriam.ru
2All-Russian Research Institute of Agricultural Microbiology, m.belousova@arriam.ru
3St. Petersburg State University, elena_lukasheva@mail.ru
4St. Petersburg State University, daria.gorba4@yandex.ru
5St. Petersburg State University, e.romanovskaya@spbu.ru
6Martin-Luther Universität Halle-Wittenberg, christian.ihling@pharmazie.uni-halle.de
7Martin-Luther Universität Halle-Wittenberg, Andrej.Frolov@ipb-halle.de
8All-Russian Research Institute of Agricultural Microbiology, a.nizhnikov@arriam.ru
9All-Russian Research Institute of Agricultural Microbiology, k.antonets@arriam.ru

Bacillus thuringiensis is a Gram-positive spore-forming bacterium known for its insecticidal activities. Although its features of high virulence and exceptional host specificity are wiely known and have conditioned its use as a source of novel biopesticides, molecular mechanisms underlying these traits remain elusive and are usually attributed to its repertoire of proteinaceous toxins. In this work we used combined proteogenomic approach to dissect <>. We used three different strains of B. thuringiensis belonging to the var. thuringiensis, darmstadtiensis and israeliensis and one derivate of B. thuringiensis var israeliensis, which lost the ability to produce Cry-toxins. By using hybrid Oxford Nanopore and Illumina sequencing we achieved replicon-level genome assemblies of the studied strains which, upon annotation, facilitated comparison of virulence factor repertoires and putative reasons of virulence loss in derivate strain, Further application of quantitative HPLC-Orbitrap-MS and proteome level-comparison between vegetative and sporulating cultures allowed us to identify the proteins, which were differentially produced in the strains at each stage. While proteins differentially produced at vegetative stage related mostly to cell metabolism with few virulence factors captured, those identified in spores included different spore coat proteins, flotillin-like proteins involved in in cell differentiation, exosporium proteins and a wide set of virulence factors including proteinaceous Cry toxins. Taking together the data obtained in this study indicate the impact of the accessory genes produced at various stages of colony development on pathogenicity-associated phenotypic traits in strains with different host ranges. To our knowledge, this is the first proteogenomic study of B. thuringiensis aimed to compare both genomic and proteomic profiles between serovars.

Genomics, transcriptomics, bioinformatics symposiumGenome Assembly and Annotation of Nothobranchius rachovii killifish

Genome Assembly and Annotation of Nothobranchius rachovii killifish

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Zulfiia Guvatova1, George Krasnov2, Anastasiya Snezhkina3, Artemy Tokarev4, Maria Fedorova5, Anna Kudryavtseva6
1Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, guvatova.zulfiya@mail.ru
2Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, gskrasnov@mail.ru
3Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, leftger@rambler.ru
4Artemy Tokarev Veterinary biology faculty MSAVM&B – MVA named after K.I. Skryabin Moscow, Russia, artemiy.tokarev@mail.ru
5Laboratory of Postgenomic Research Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, fedorowams@yandex.ru
6Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, rhizamoeba@mail.ru

Nothobranchius rachovii is a species of freshwater annual killifish native to Africa. This organism is an attractive model in aging studies because of short lifetime and rapid maturation. In this study, we present draft genome assembly of this organism based on Nanopore reads and polished with Illumina reads. We tested four popular Nanopore reads assemblers (Flye, MaSuRCA, Shasta, wtdbg2) and two polishers (Pilon and MaSuRCA-polish tool). We selected the best combination of these tools in terms of contig length and assembly completeness.

Genomics, transcriptomics, bioinformatics symposiumComparison of Brain Transcriptome Profiles of Short-lived and Long-lived Species of Nothobranchius

Comparison of Brain Transcriptome Profiles of Short-lived and Long-lived Species of Nothobranchius

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Zulfiia Guvatova1, George Krasnov2, Sergey Simanovsky3, Alexander Frolov4, Nataliya Gladysh5, Anna Kudryavtseva6
1Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, guvatova.zulfiya@mail.ru
2Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, gskrasnov@mail.ru
3Laboratory for Ecological Monitoring of Nuclear Power Plant (NPP) Regions and Bioindication Russia A.N. Severtsov Institute of Ecology and Evolution Moscow, Russia, sergey.a.simanovsky@gmail.com
4Laboratory for Ecological Monitoring of Nuclear Power Plant (NPP) Regions and Bioindication Russia A.N. Severtsov Institute of Ecology and Evolution Moscow, Russia, frolov@mail.ru
5Veterinary biology faculty MSAVM&B – MVA named after K.I. Skryabin Moscow, Russia, natalyagladish@gmail.com
6Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, rhizamoeba@mail.ru

Annual fishes of the genus Nothobranchius from East Africa are promising vertebrate model in comparative and ageing studies. Nothobranchius show accelerated growth and age-related changes at all levels of organization. The present work aims to compare brain transcriptome profiles of short-lived N. rachovii with longer-lived N. korthausae and N. guntheri.

Genomics, transcriptomics, bioinformatics symposiumComparative analysis of repeatome composition of four allopolyploid Poaceae species

Comparative analysis of repeatome composition of four allopolyploid Poaceae species

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Elizaveta Kolganova1
1All-Russia Research Institute of Agriculture biotechnology Moscow, Russia, liza.colg@gmail.com

Repeating evidence, including satellite DNA and transposable elements, highlights most of the genomes of most organisms. Despite this, our knowledge of the elements of evolution is boring. These repetitions are often collapsed and underrepresented. Here, we analyzed tandem repeats and the composition of transposing elements in four allopolyploid Poaceae species using short Illumina readings and clustering based on reclassified plots. The four genomes differ in retrotransposons and the prevalence of tandem repeats. The detailed composition of the repitome and evolutionary implications of this data will be discussed.

Genomics, transcriptomics, bioinformatics symposiumDisruptive natural selection by male reproductive potential prevents underexpression of the genes encoding proteins on the human Y chromosome as a self-domestication syndrome

Disruptive natural selection by male reproductive potential prevents underexpression of the genes encoding proteins on the human Y chromosome as a self-domestication syndrome

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/98.pdf”]
Mikhail Ponomarenko1, Irina Chadaeva2, Dmitry Oshchepkov3, Dmitry Rasskazov4, Alexander Osadchuk5, Ludmila Osadchuk6
1Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, pon@bionen.nsc.ru
2Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, ichadaeva@bionet.nsc.ru
3Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, diman@bionet.nsc.ru
4Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, rassk@bionen.nsc.ru
5Animal Genetics Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, osadchuk@bionet.nsc.ru
6Animal Genetics Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, losadch@bionet.nsc.ru

We performed an in silico genome-wide analysis of all SNPs located within 70 bp proximal promoters in front of the all experimentally knowns starts of protein-coding transcripts from human Y chromosome within the framework of the current release #151 of the dbSNP database and GRCh38/hg38 assembly of the human reference genome, which are publicly available using the UCSC Genome Browser. As a result, we first found disruptive natural selection by male reproductive potential preventing underexpression of the Y-linked proteins under this study as if self-domestication would have happened during the human origing and evolution that could cause male fertility disorders as self-domestication syndrome.

Genomics, transcriptomics, bioinformatics symposiumA new method for combining of genetically correlated traits by maximizing of their shared heritability

A new method for combining of genetically correlated traits by maximizing of their shared heritability

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Gulnara R. Svishcheva1, Evgeny S. Tiys2, Sofya G. Feoktistova3, Elizaveta E. Elgaeva4, Sodbo Sharapov5, Yakov A. Tsepilov6
1Institute of cytology and genetics, gulsvi@mail.ru
2Institute of cytology and genetics, tiys@bionet.nsc.ru
3Institute of cytology and genetics, sayfutdinovas@gmail.com
4Institute of cytology and genetics, elizabeth.elgaeva@gmail.com
5Institute of cytology and genetics, sharapovsodbo@gmail.com
6Novosibirsk State University, drosophila.simulans@gmail.com

Genetic correlations between phenotypic traits are widely observed phenomena. Many groups of traits have a significant level of shared genetic background. In this work, we suggested a new method for extraction of shared genetic component for genetically correlated phenotypic traits. We applied the method to GWAS results for anthropometric traits.

Genomics, transcriptomics, bioinformatics symposiumGenome-wide association study of Parkinson’s disease using MAX3 test

Genome-wide association study of Parkinson’s disease using MAX3 test

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Georgii Ozhegov1, Dmitry Poverin2, Sergey Medvedev3, Suren Zakian4, Yuri Vyatkin5, Sergey Postovalov6
1Kazan Federal University, Kazan, Russia; Novel Software Systems, Ltd., Novosibirsk, Russia, georgii_provisor@mail.ru
2Novosibirsk State Technical University, Novosibirsk, Russia, foxlandg@gmail.com
3Federal Research Center Institute of Cytology and Genetics, Novosibirsk, Russia, medvedev@bionet.nsc.ru
4Federal Research Center Institute of Cytology and Genetics, Novosibirsk, Russia, zakian@bionet.nsc.ru
5Novosibirsk State University, Novosibirsk, Russia; Novel Software Systems, Ltd., Novosibirsk, Russia, yuri@nprog.ru
6Novosibirsk State Technical University, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia, postovalovsn@gmail.com

Whole exomes for a set of patients with Parkinson’s disease (PD) were sequenced to conduct a genome-wide association study (GWAS) using MAX3 test to find novel genomic variants associated with the disease. As a result, several new variants were identified.

Genomics, transcriptomics, bioinformatics symposiumPatterns of maternal and paternal inheritance in Russian populations

Patterns of maternal and paternal inheritance in Russian populations

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/139.pdf”]
Anton Logachev1, Daisuke Hirata2, Gaik Tamazian3
1St. Petersburg State University, a.logachev@spbu.ru
2St. Petersburg State University, d.khirata@spbu.ru
3St. Petersburg State University, g.tamazian@spbu.ru

Genome Russia (GR) study is a national collaboration to expand our understanding of demographic history of peoples of Russia, to get deep insight into population genetics and to create a detailed genetic map of a country. Here we report analyses of matrilineal and patrilineal inheritance derived from whole genome sequencing data collected in the framework of the project. We examined sequences of 171 Y-chromosomes and 322 mtDNA ascertained from 14 ethnicities. We determined haplogroups for both Y-chromosomes and mtDNA sequences and estimated their distribution across the country. We performed phylogenetic and population genetic analyses for mtDNA and Y-chromosomes separately and then compared the results to reveal genetic history of indigenous groups living in Russia.