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

Poster (download) Yury Malovichko1, Maria Belousova2, Elena Lukasheva3, Daria Gorbach4, Ekaterina Romanovskaya5, Christian Ihling6, Andrej Frolov7, Anton Nizhnikov8, Kirill Antonets91All-Russian Research Institute of Agricultural Microbiology, yu.malovichko@arriam.ru2All-Russian Research Institute of Agricultural Microbiology, m.belousova@arriam.ru3St. Petersburg State University, elena_lukasheva@mail.ru4St. Petersburg State University, daria.gorba4@yandex.ru5St. Petersburg State University, e.romanovskaya@spbu.ru6Martin-Luther Universität Halle-Wittenberg, christian.ihling@pharmazie.uni-halle.de7Martin-Luther Universität Halle-Wittenberg, Andrej.Frolov@ipb-halle.de8All-Russian Research Institute of Agricultural Microbiology, a.nizhnikov@arriam.ru9All-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.

Read More

Genome Assembly and Annotation of Nothobranchius rachovii killifish

Zulfiia Guvatova1, George Krasnov2, Anastasiya Snezhkina3, Artemy Tokarev4, Maria Fedorova5, Anna Kudryavtseva61Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, guvatova.zulfiya@mail.ru2Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, gskrasnov@mail.ru3Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, leftger@rambler.ru4Artemy Tokarev Veterinary biology faculty MSAVM&B – MVA named after K.I. Skryabin Moscow, Russia, artemiy.tokarev@mail.ru5Laboratory of Postgenomic Research Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, fedorowams@yandex.ru6Center 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.

Read More

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

Zulfiia Guvatova1, George Krasnov2, Sergey Simanovsky3, Alexander Frolov4, Nataliya Gladysh5, Anna Kudryavtseva61Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, guvatova.zulfiya@mail.ru2Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, gskrasnov@mail.ru3Laboratory 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.com4Laboratory for Ecological Monitoring of Nuclear Power Plant (NPP) Regions and Bioindication Russia A.N. Severtsov Institute of Ecology and Evolution Moscow, Russia, frolov@mail.ru5Veterinary biology faculty MSAVM&B – MVA named after K.I. Skryabin Moscow, Russia, natalyagladish@gmail.com6Center 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.

Read More

Comparative analysis of repeatome composition of four allopolyploid Poaceae species

Elizaveta Kolganova11All-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.

Read More

Functioning of unique nitrile-detoxifying system in soil xenobiotic degrader Rhodococcus rhodochrous: a whole-genome transcriptomic approach

Konstantin V Lavrov1, Andrey D Novikov2, Tatyana I Kalinina3, Artem S Kasianov4, Alexander S Yanenko51NRC “Kurchatov institute – GosNIIgenetika”, lavrov.ko@gmail.com2NRC “Kurchatov institute – GosNIIgenetika”, alexm19@mail.ru3NRC “Kurchatov institute – GosNIIgenetika”, tatyana.i.kalinina@googlemail.com4Vavilov Institute of General Genetics, artem.kasianov@gmail.com5NRC “Kurchatov institute – GosNIIgenetika”, yanenko@genetika.ru Organic nitriles are significant participants of interactions between soil living organisms, thus their synthesis and degradation are of interest. Using transcriptomic approach, we revealed a genetic cascade, realizing nitrile degradation in powerful nitrile degrader – Rhodococcus rhodochrous. We also hypothesized a genetic “network” for nitrile/amide utilization, connected with cobalt homeostasis.

Read More
  • June 29, 2020
  • N/A

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

Poster (download) Mikhail Ponomarenko1, Irina Chadaeva2, Dmitry Oshchepkov3, Dmitry Rasskazov4, Alexander Osadchuk5, Ludmila Osadchuk61Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, pon@bionen.nsc.ru2Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, ichadaeva@bionet.nsc.ru3Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, diman@bionet.nsc.ru4Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, rassk@bionen.nsc.ru5Animal Genetics Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, osadchuk@bionet.nsc.ru6Animal 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.

Read More

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

Video (download) Gulnara R. Svishcheva1, Evgeny S. Tiys2, Sofya G. Feoktistova3, Elizaveta E. Elgaeva4, Sodbo Sharapov5, Yakov A. Tsepilov61Institute of cytology and genetics, gulsvi@mail.ru2Institute of cytology and genetics, tiys@bionet.nsc.ru3Institute of cytology and genetics, sayfutdinovas@gmail.com4Institute of cytology and genetics, elizabeth.elgaeva@gmail.com5Institute of cytology and genetics, sharapovsodbo@gmail.com6Novosibirsk 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.

Read More

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

Poster (download) 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.

Read More

Patterns of maternal and paternal inheritance in Russian populations

Poster (download) Anton Logachev1, Daisuke Hirata2, Gaik Tamazian31St. Petersburg State University, a.logachev@spbu.ru2St. Petersburg State University, d.khirata@spbu.ru3St. 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.

Read More