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

Category

Genomics,  bioinformatics  and evolution symposium

Showing: 11 - 20 of 28 RESULTS
Genomics,  bioinformatics  and evolution symposiumMitochondrial genetics of amphipods: revealing mechanisms of diversity

Mitochondrial genetics of amphipods: revealing mechanisms of diversity

No Comment on Mitochondrial genetics of amphipods: revealing mechanisms of diversity

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/432.pdf”]
Elena V. Romanova1, Yurij S. Bukin2, Kirill V. Mikhailov3, Maria D. Logacheva4, Elena A. Sirotinina5, Vladimir V. Aleoshin6, Dmitry Yu. Sherbakov7
1Laboratory of Molecular Systematics LIN SB RAS, elena_romanova@lin.irk.ru
2Laboratory of Molecular Systematics LIN SB RAS, bukinyura@mail.ru
3Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, kv.mikhailov@gmail.com
4Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, maria.log@gmail.com
5Laboratory of Molecular Systematics LIN SB RAS, haleo.inc@gmail.com
6Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, aleshin@genebee.msu.su
7Laboratory of Molecular Systematics LIN SB RAS, dysh007@gmail.com

We performed a thorough analysis of mitochondrial (mt) genomes of amphipods with the focus on endemic Baikalian species. Possible causes and mechanisms explaining an unusually high variability in mt genomes of Baikalian amphipods in comparison to that of non-Baikalian species are discussed.

Genomics,  bioinformatics  and evolution symposiumOrthoWeb – web application for macro- and microevolutionary analysis of genes

OrthoWeb – web application for macro- and microevolutionary analysis of genes

No Comment on OrthoWeb – web application for macro- and microevolutionary analysis of genes

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/409.pdf”]
Zakhar Mustafin, Alexey Mukhin, Dmitry Afonnikov, Yury Matushkin, Sergey Lashin1
1Kurchatov Genomics Center, ICG SB RAS, Novosibirsk, Russia, mustafinzs@bionet.nsc.ru

Problems of macro- and microevolution remain key problems of biology. Phylostratigraphic analysis became one of the most popular methods for studying macroevolutionary characteristic of genes. It is based on estimation of the divergence time among orthologous genes. Along with methods of microevolutionary analysis (for example, dN/dS ratio estimation), phylostratigraphic methods are increasingly included into the methodological arsenal of evolutionary bioinformatics. There are some software packages used for computational analysis of the evolution by using different phylostratigraphic and microevolutionary indices, but they require users to know some additional software or programming languages. Here we present OrthoWeb software to calculate such indices using web browser only.

Genomics,  bioinformatics  and evolution symposiumComparative Genomic Analysis of Moderate Bacteriophages of Alfalfa Root Nodule Bacteria

Comparative Genomic Analysis of Moderate Bacteriophages of Alfalfa Root Nodule Bacteria

No Comment on Comparative Genomic Analysis of Moderate Bacteriophages of Alfalfa Root Nodule Bacteria

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/389.pdf”]
Kozlova A.P.1, Muntyan V.S.2, Afonin A.M.3, Antonova E.V.4, Muntyan A.N.5, Kabilov M.R.6, Roumiantseva M.L.7, Dzyubenko E.A.8
1All-Russian research institute for agricultural microbiology, Pushkin, Saint-Petersburg, Russia, alexsandrak95@mail.ru
2All-Russian research institute for agricultural microbiology, Pushkin, Saint-Petersburg, Russia, vucovar@yandex.ru
3All-Russian research institute for agricultural microbiology, Pushkin, Saint-Petersburg, Russia, afoninalexeym@gmail.com
4Institute of Plant and Animal Ecology, Ural Division of Russian Academy of Sciences, Ekaterinburg, Russia, selena@ipae.uran.ru
5All-Russian research institute for agricultural microbiology, Pushkin, Saint-Petersburg, Russia, allmuntyan@gmail.com
6ICBFM SB RAS, Novosibirsk, Russia, kabilov@niboch.nsc.ru
7All-Russian research institute for agricultural microbiology, Pushkin, Saint-Petersburg, Russia, mroumiantseva@yandex.ru
8Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) Ministry of science and higher education, Saint-Petersburg, Russia, elena.dzyubenko@gmail.com

The bacteriophage AP300 infecting Sinorhizobium meliloti was isolated from soil sample В from В mountainous region of Dagestan, which belongs to the Caucasus Center for Legume Variety in the frame of the grant RSFВ 17-16-01095. The AP300 genome was annotated and its similarity to bacteriophage vB MloP_Lo5R7ANS (NC_025431; Podoviridae family) infecting Mesorhizobium loti strains was revealed. In the chromosomes of 4 strains of Sinorhizobium meliloti isolated in geographically different regions from soils and nodules of alfalfa plants, intact vB MloP_Lo5R7ANS-like prophages were detected.В The 46.39-57.14% ORFsВ of AP300 and 4 prophages were homologous to ORFsВ of vB MloP_Lo5R7ANS. The 18 ORFs from mentioned above ORFs were identified in all studied sequences and they wereВ similar to those in vB MloP_Lo5R7ANS. The other 7.22-15.79% ORFsВ were homologous to other phages. ORFs encodingВ virion components: head, capsid, tail, virion, integrase were detected in soil bacteriophage AP300 and in all studied В prophages determined in rhizobia symbionts of alfalfa.

Genomics,  bioinformatics  and evolution symposiumIntraspecific genetic variability of enhancers in the craniofacial tissue

Intraspecific genetic variability of enhancers in the craniofacial tissue

No Comment on Intraspecific genetic variability of enhancers in the craniofacial tissue

Elena Minkina1, Natalia Akberova2, Elena Shagimardanova3, Igor Adameyko4, Oleg Gusev5
1Institute of Fundamental Medicine and Biology, KFU, Kazan, Russia, minkinaea@gmail.com
2Institute of Fundamental Medicine and Biology, KFU, Kazan, Russia, nakberova@mail.ru
3Institute of Fundamental Medicine and Biology, KFU, Kazan, Russia, rjuka@mail.com
4Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden, igor.adameyko@ki.se
5RIKEN, Yokohama, Japan, gaijin.ru@gmail.com

The craniofacial morphology is determined by a combination of complex polygenic traits, and trait variability may also be influenced by changes in the final expression of key genes due to polymorphisms in regulatory regions. We found that craniofacial enhancers show greater values ​​of the genetic diversity compared to other tissues.

Genomics,  bioinformatics  and evolution symposiumGenetic aspects of internet-dependence in teenagers

Genetic aspects of internet-dependence in teenagers

No Comment on Genetic aspects of internet-dependence in teenagers

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/56.pdf”]
Marina Smolnikova1, Sergey Tereshchenko2
1Scientific Research Institute of Medical Problems of the North FRC KSC SB RAS, smarinv@yandex.ru
2Scientific Research Institute of Medical Problems of the North FRC KSC SB RAS, legise@mail.ru

The rapid emergence and spread of Internet addiction in adolescent populations, combined with a rapid change in consumed content due to mobile access availability and the new access devices, are new challenges for classical psychology and fundamental medicine that require urgent solutions. The presence of the genetic component of Internet addiction was convincingly shown in different populations, but to date the specific genes involved in the mechanisms of such heritability have not been well identified. The aim of the study was to investigate the role of candidate neurotransmitters and to perform a population analysis of candidate genes polymorphisms for the Internet addiction formation. As a result of the analysis, 7 Internet-dependent adolescents and 39 adolescents with a tendency to Internet-dependent behavior were identified. The frequencies of genotype distribution in the population sampling of Caucasians (n = 302) В were obtained: * CC 59.6%, * CT 40.4%, * TT 0% (rs1800497 DRD2); * AA 23.8%, AG 52.4%, * GG 23.8% (rs4680 COMT); * CC 37.4%, * CG 46.0%, * GG 16.6% (rs2229910 NTRK3). The results will help to open new perspectives in assessing the fundamental neurobiological causes for the Internet addiction and the personalization of therapeutic approaches in Internet dependent adolescents.

Genomics,  bioinformatics  and evolution symposiumFMO superfamily protein phylogeny and the origin of YUCCA family.

FMO superfamily protein phylogeny and the origin of YUCCA family.

No Comment on FMO superfamily protein phylogeny and the origin of YUCCA family.

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/335.pdf”]
Igor Turnaev1, Valentin Suslov2, Konstantin Gunbin3, Dmitriy Afonnikov4
1Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, turn@bionet.nsc.ru
2Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, valya@bionen.nsc.ru
3Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, genkvg@bionen.nsc.ru
4Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, ada@bionen.nsc.ru

We performed a comparative analysis of phylogeny, conservative sites, protein domains, and the presence in taxa of FMOs and BVMOs proteins. Earlier in the FMOs, the following protein groups were distinguished: type I FMO, type II FMO, YUCCAs. According to the results of our analysis, we propose that the type II FMO group is, in turn, divided into two groups: FMO IIA type and type IIB FMO. Type IIB FMO proteins represent a new special group in a number of parameters (site consensus, composition of protein domains, presence in taxa and, apparently, functions) significantly different from all other FMOs proteins and type IIA FMO proteins, in particular. While type IIA FMO proteins exhibit properties typical of the FMO subclass. The type IIB FMO protein group is likely to represent a new family of proteins. These proteins are of interest for biocatalysis.

Genomics,  bioinformatics  and evolution symposiumAnalysis of sequenced chromosome-specific libraries of gekkonids sheds light to large scale genome reshuffling in reptiles

Analysis of sequenced chromosome-specific libraries of gekkonids sheds light to large scale genome reshuffling in reptiles

No Comment on Analysis of sequenced chromosome-specific libraries of gekkonids sheds light to large scale genome reshuffling in reptiles

Katerina Tishakova1, Dmitry Prokopov2, Ilya Kichigin3, Anna Molodtseva4, LukГЎЕЎ Kratochvil5, Artem Lisachov6, Vladimir Trifonov7
1Novosibirs State University, Novosibirsk, Russia; Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia, k.tishakova@g.nsu.ru
2Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia, dprokopov@mcb.nsc.ru
3Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia, kig@mcb.nsc.ru
4Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia, rada@mcb.nsc.ru
5Charles University, Prague, Czech Republic, lukkrat@email.cz
6Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia, lisachov@bionet.nsc.ru
7Novosibirs State University, Novosibirsk, Russia; Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia, vlad@mcb.nsc.ru

Representatives of Infraorder Gekkota demonstrate relatively low chromosomal evolution and rapidly evolved sex chromosome systems. Using low-coverage chromosome sequencing, we sequenced chromosome-specific libraries of Gekko japonicus and putative sex chromosome of Hemidactylus platyurus to compare with annotated genomes of squamate reptiles. We found evolutionary long conservation of macro-chromosome and high dynamic of micro-chromosomes. Also, we discovered homologues synteny blocks between sex chromosomes of species from different infraorder.

Genomics,  bioinformatics  and evolution symposiumMultigene phylogenies for the earthworm Eisenia nordenskioldi (Lumbricidae, Annelida)

Multigene phylogenies for the earthworm Eisenia nordenskioldi (Lumbricidae, Annelida)

No Comment on Multigene phylogenies for the earthworm Eisenia nordenskioldi (Lumbricidae, Annelida)

Sergei V. Shekhovtsov1, Alexandra A. Shipova2, Tatiana V. Polyboyarova3, Sergei E. Peltek4
1Institute of Cytology and Genetics SB RAS, shekhovtsov@bionet.nsc.ru
2Institute of Cytology and Genetics SB RAS, shipova@bionet.nsc.ru
3Institute of Cytology and Genetics SB RAS, poluboyarova@bionet.nsc.ru
4Institute of Cytology and Genetics SB RAS, peltek@bionet.nsc.ru

Eisenia nordenskioldi is a polymorphic earthworm species with two subspecies and high cryptic genetic diversity. We performed transcriptome sequencing for eleven genetic lineages of this species and built phylogenies based on different extracted datasets. We demonstrated that, contrary to previous studies, E. nordenskioldi is monophyletic, but both of its subspecies are polyphyletic. E. nordenskioldi was split into two groups of lineages, representing the northwestern and southeastern parts of its range.

Genomics,  bioinformatics  and evolution symposiumPhylogenetic Analysis of Poxviridae Genomes Using K-mer Approach

Phylogenetic Analysis of Poxviridae Genomes Using K-mer Approach

No Comment on Phylogenetic Analysis of Poxviridae Genomes Using K-mer Approach

Tatyana Nepomnyashchikh1, Denis Antonets2, Tatyana Tregubchak3, Alexander Shvalov4, Elena Gavrilova5, Rinat Maksyutov6
1SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, nepom@vector.nsc.ru
2SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, antonec@yandex.ru
3SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, tregubchak_tv@vector.nsc.ru
4SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, shvalov_an@vector.nsc.ru
5SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, gavrilova_ev@vector.nsc.ru
6SRC VB “Vector” Rospotrebnadzor, Koltsovo, Russia, maksyutov_ra@vector.nsc.ru

Abstract There is a growing interest towards alignment-free approaches that use k-mers as genomic features. Large sizes of poxvirus genomes, their complex organization with repetitive regions and recombination sites, makes it difficult to produce accurate whole genome alignments especially for distantly related species. K-mer based trees built for 663 whole genome sequences were found to be in good agreement with alignment-based ones and correspond well to currently accepted taxonomy and evolution of poxviruses.

Genomics,  bioinformatics  and evolution symposiumApplication of ITS1 and ITS2 for population genetic studies of sturgeons (Acipenseridae)

Application of ITS1 and ITS2 for population genetic studies of sturgeons (Acipenseridae)

No Comment on Application of ITS1 and ITS2 for population genetic studies of sturgeons (Acipenseridae)

Guzel Davletshina1, Sergey Kliver2, Elena Interesova3, Dmitry Prokopov4, Vladimir Trifonov5
1IMCB SB RAS, Novosibirsk, Russia; ICG SB RAS, Novosibirsk, Russia, guzel@mcb.nsc.ru
2IMCB SB RAS, Novosibirsk, Russia, skliver@mcb.nsc.ru
3TSU, Tomsk, Russia, e.interesova@ngs.ru
4ICG SB RAS, Novosibirsk, Russia, dprokopov@mcb.nsc.ru
5IMCB SB RAS, Novosibirsk, Russia; NSU, Novosibirsk, Russia, vlad@mcb.nsc.ru

The order Acipenseridae is a very interesting group for evolutionary genetics: all species have unique morphology, inter-specific hybrids are widely occurring and there are variations between species in ploidy levels. Most acipenserids are endangered due to poaching and special efforts are required for the maintenance of natural populations. The genetic studies of acipenserids are still limited, although these are needed for successful farming. ITS – is the DNA spacer located between the small subunit and large subunit rRNA genes. The genes encoding ribosomal RNAs are located one after another in tandem and are repeated several hundred times, so we use new generation sequencing to estimate the frequency of occurrence of SNPs in the genome of one organism. ITS1 and ITS2 are used as phylogenetic markers to study the relationships between highly diverged taxonomic groups [1]. Despite high interest to different sturgeon species, acipenserid ITS1 and ITS2 sequences are missing in the GenBank depository, and most sturgeon population studies are performed using mitochondrial markers. Here we study the structure of ITS1 and ITS2 in several sturgeon species and demonstrate efficiency of these nuclear markers for species identification and interspecific hybrids confirmation.