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

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Genomics,  bioinformatics  and evolution symposium

Showing: 1 - 10 of 28 RESULTS
Genomics,  bioinformatics  and evolution symposiumGenetic diversity of the flat leeches (Hirudinea, Glossiphoniidae) in Western Siberia

Genetic diversity of the flat leeches (Hirudinea, Glossiphoniidae) in Western Siberia

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/356.pdf”]
Nadezhda Bolbat1, Lyudmila Fedorova2, Irina Kaygorodova3
1Irkutsk State University Irkutsk, Russia, nadya.mandzyak@mail.ru
2Surgut State University Surgut, Russia, ludiko@list.ru
3Limnological institute SB RAS Irkutsk, Russia, irina@lin.irk.ru

The poor knowledge of the glossiphoniid fauna of Western Siberia is a consequence of the unresolved taxonomy of this group. An incomplete description of the species due to the phylogenetic ambiguity of external morphological characters and high intraspecific variability complicated the identification of these leeches. Using molecular genetic methods in combination with classical morphological analysis, we proved the presence of 7 species of the family Glossiphoniidae in Western Siberia, with interspecific genetic pairwise distances varying from 3.7 to 18.2%. In addition to Theromyzon tessulatum, Helobdella stagnalis and Hemiclepsis marginata, previously detected in the region, four potentially new species (Glossiphonia sp. 1, Glossiphonia sp. 2, Glossiphonia sp. 3, and Alboglossiphonia sp.) were found. The results obtained for the Western Siberian leeches once again confirm the advantage of the DNA barcoding application, as one of the molecular methods for species delimitation, used in an integrated approach to the study of taxonomic composition of a fauna.

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Genomics,  bioinformatics  and evolution symposiumDevelopment of a database on radioresistant microorganisms as a useful tool for biotechnology.

Development of a database on radioresistant microorganisms as a useful tool for biotechnology.

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Alina Ryabova1, Azat Kadirov2, Elena Shagimardanova3
1KFU, Kazan, Russia, urban-nomad@yandex.ru
2KFU, Kazan, Russia, bilinet@mail.ru
3KFU, Kazan, Russia; NSU, Novosibirsk, Russia, rjuka@mail.ru

Mechanisms of prokaryotic radioresistance are an essential subject in radiation biology. We designed a specialized database aimed at making a comprehensive repository of identified radioresistant microorganisms with experimentally confirmed data.

Genomics,  bioinformatics  and evolution symposiumMitogenomics and Phylogenetics of Vulnerable and Endangered Birds of Genera Aratinga and Psittacus

Mitogenomics and Phylogenetics of Vulnerable and Endangered Birds of Genera Aratinga and Psittacus

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Sofia Ochkalova1
1Applied Genomics Lab, SCAMT, ITMO University, Saint-Petersburg, Russia, ochkalova@scamt-itmo.ru

Abstract— Among parrots, there are more threatened and endangered species than in any other avian order. Exploration of these outstanding birds exhibiting advanced cognitive abilities is a relevant scientific problem. In this study, we de novo assembled 19 mitochondrial genomes from Illumina raw reads, integrated them with information obtained from related genomes, and did a phylogenetic reconstruction of species from Aratinga and Psittacus genera. Additionally, we created a Python pipeline for assembly mtDNA bearing tandemly repeated regions from whole genome sequencing data. Then we annotated genes and finally performed phylogenetic analysis to provide insights into the evolution and demographic history of the species.

Genomics,  bioinformatics  and evolution symposiumConservative mitotic localization and functions of the nucleolar RPF2/Non3 protein in human and Drosophila cells

Conservative mitotic localization and functions of the nucleolar RPF2/Non3 protein in human and Drosophila cells

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Svetlana V. Maltseva1, Evgenia S. Omelina2, Julia V. Popova3, Gera A. Pavlova4, Lybov A. Yarinich5, Alena V. Razuvaeva6, Anastasia A. Yushkova7, Anna A. Ogienko8, Alexey V. Pindyurin9, Evgenia N. Andreyeva10
1Institute of Molecular and Cellular Biology SB RAS, Novosibirsk State University Novosibirsk, Russian Federation, smaltseva@mcb.nsc.ru
2Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation, omelina@mcb.nsc.ru
3Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation, popova@mcb.nsc.ru
4Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation, gera.pavlova@mcb.nsc.ru
5Institute of Molecular and Cellular Biology SB RAS, Novosibirsk State University Novosibirsk, Russian Federation, l.yarinich@mcb.nsc.ru
6Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation, alena.razuvaeva@mcb.nsc.ru
7Institute of Molecular and Cellular Biology SB RAS, Novosibirsk State University Novosibirsk, Russian Federation, a.yushkova@g.nsu.ru
8Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation, ogienko.anna@mcb.nsc.ru
9Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation, a.pindyurin@mcb.nsc.ru
10Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation, andreeva@mcb.nsc.ru

The nucleolus is a non-membrane nuclear organelle playing a crucial role in ribosome biogenesis in eukaryotes. Its morphology and function are associated with cell growth and proliferation, as well as with cell cycle regulation. Besides that, a set of nucleolar proteins are also known to be directly involved in mitotic cell division, taking a part in the spindle assembly. Among them is the human RRS1 (Ribosome biogenesis regulator 1 homolog) protein that function in complex with RPF2 (Ribosome production factor 2 homolog) in the ribosome biogenesis pathway. Here, we report the characterization of the mitotic localization and function of the human RPF2 and its Drosophila ortholog, the Non3 (Novel nucleolar protein 3) protein. We demonstrated that depletion of RPF2 using siRNA specific to all its splicing variants leads to abnormal mitotic chromosome segregation in HeLa S3 cells. Similarly, the RNAi-mediated depletion of Non3 in Drosophila S2 cells also resulted in mitotic spindle defects including those in sister chromatid separation and segregation. Thereby, it will be possible to investigate mitotic functions of the RPF2 protein in Drosophila model system.

Genomics,  bioinformatics  and evolution symposiumPlastid genome evolution in the genus Allium

Plastid genome evolution in the genus Allium

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Victoria Scobeyeva1
1Lomonosov Moscow State University, skobei-khanum@yandex.ru

Chloroplast genomes are highly conservative and plastomes of Alium specia are not an exception. We assembled and annotated plastomes of 12 specia from genus Allium. The only species with big inversion is A.paradoxa. В We identified some regions of Allium plastomes that can possibly be under selection and some genes in these regions. The ycf1 gene is evolving at the highest rate.

 

Genomics,  bioinformatics  and evolution symposiumEVALUATION OF Sinorhizobium meliloti GENOMIC ISLANDS INSERTED INTO THE tRNA-Thr

EVALUATION OF Sinorhizobium meliloti GENOMIC ISLANDS INSERTED INTO THE tRNA-Thr

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/502.pdf”]
Mariia Vladimirova1, Alexey Afonin2, Viktoria Muntyan3, Boris Simarov4, Marina Roumiantseva5
1ARRIAM, Saint Petersburg, Russia, mariiavladimirova@mail.ru
2ARRIAM, Saint Petersburg, Russia, afoninalexeym@gmail.com
3ARRIAM, Saint Petersburg, Russia, vucovar@yandex.ru
4ARRIAM, Saint Petersburg, Russia, genet@yandex.ru
5ARRIAM, Saint Petersburg, Russia, mroumiantseva@yandex.ru

Transfer RNAs (tRNA) widely abundant in genomes are extremely conservative molecules with well-defined role in protein synthesis. The central role of tRNA in the evolution of the genetic code and theirs novel undiscovered functions were recently predicted: these sequences could be a hotspots for the integration of foreign genomic DNA, like phage related genomic islands (GIs). In this work the 17th GIs site-specifically integrated into isoacceptors tRNAs-Thr (iso-tRNA-Thr) out of 84th GIs detected in genomes of Sinorhizobium meliloti strains were evaluated. It was shown that the homology of entire sequences of GIs inserted into a particular tRNA isoacceptor in genetically related strains is more than 80%, whereas homology of similar types of GIs in native strains from one population or from geographically remote areas could be distinct up to 70%. For the first time CRISPRs sequences were revealed in some GIs of S. meliloti. The phylogenetic analysis done for integrase encoding sequences of distinct GIs inserted in iso-tRNAs-Thr showed their homology with the corresponding sequences of phages from Podovirida, Myoviridae and Siphoviridae families. Proceeded data allowed concluding that the insertion of GIs into precise tRNA-Tre isoaceptor occurred due to the att-homologous recombination mechanism and that GIs of S. meliloti could be involved in improving adaptive immunity of rhizobia.

Genomics,  bioinformatics  and evolution symposiumNovel archaeal metagenome assembled genomes from acidophilic microbial community of Parys Mountain copper mine (UK)

Novel archaeal metagenome assembled genomes from acidophilic microbial community of Parys Mountain copper mine (UK)

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Aleksei Korzhenkov1, Stepan V. Toshchakov2, Ilya V. Kublanov3, Peter N. Golyshin4, Olga V. Golyshina5
1NRC Kurchatov Institute, oscypek@ya.ru
2FRC \”Biotechnology\” RAS, stepan.toshchakov@gmail.com
3FRC \”Biotechnology\” RAS, kublanov.ilya@gmail.com
4Bangor University, p.golyshin@bangor.ac.uk
5Bangor University, o.golyshina@bangor.ac.uk

Metagenomic analysis is a powerful tool for discovery of novel microbial taxa. Here we report reconstruction of several archaeal metagenome assembled genomes (arMAGs) belonging to uncultivated lineages of Euryarchaeota and DPANN superphylum.

Genomics,  bioinformatics  and evolution symposiumBioinformatic basis for species formation in the bacterial genera Pectobacterium and Dickeya

Bioinformatic basis for species formation in the bacterial genera Pectobacterium and Dickeya

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/469.pdf”]
Peter Evseev1, Alexander Ignatov2, Konstantin Miroshnikov3
1IBCh RAS, Moscow, Russia, petevseev@gmail.com
2Research Center “PhytoEngineering” Ltd., Rogachevo, Moscow region, and RUDN, Moscow, Russia, an.ignatov@gmail.com
3IBCh RAS, Moscow, Russia, kmi@bk.ru

Soft rot Pectobacteria (SRP) that cause soft rot and black leg of potato and vegetable crops are worldwide-spread phytopathogens posing serious economic threat to agriculture and food industry. We studied phylogenetic relations within genera Pectobacterium and Dickeya applying complete-genome comparisons of previously sequenced and obtained de novo genomes of the members of these genera. Phylogenetic studies with several different sets of conservative genes were done by several algorithms. Unique taxon-specific regions were found in the investigated genomes. We traced the relationships between species and detected several examples of lateral gene lateral transfer including conservative (core) genes exchange.

Genomics,  bioinformatics  and evolution symposiumPhylostratigraphic approach in evolutionary analysis: comparison of methods

Phylostratigraphic approach in evolutionary analysis: comparison of methods

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/459.pdf”]
Tatiana Martusheva1, Zakhar Mustafin2, Sergey Lashin3
1Novosibirsk State University, NSU, Novosibirsk, Russia, t.maryanovskaya@g.nsu.ru
2Kurchatov Genomics Center, ICG SB RAS, Novosibirsk, Russia, mustafinzs@bionet.nsc.ru
3Kurchatov Genomics Center, ICG SB RAS, Novosibirsk, Russia NSU, Novosibirsk, Russia, lashin@bionet.nsc.ru

Phylostratigraphic analysis allows us to determine the \”age of the gene\” – evolutionary time of its origin. There are different methods to calculate this age, each of which has its own issues. In this work, we compare several studies on phylostrastigraphic analysis. The correlation coefficient of the results of two research with different phylostratigraphic trees but the same method to count phylostratigraphic age (BLAST-based) was found to be 0.76. Comparison of the results of calculating the phylostratigraphic age by Orthoscape application (used KEGG as data source) and the myTAI package (used BLAST as data source) showed a lower corellation coefficient – only 0.27. It is planned to continue the studying of differences in the results of different methods and their reasons.

Genomics,  bioinformatics  and evolution symposiumDynamics and hypotheses of gene order shifts in mitochondrial genomes of Baikalian amphipods

Dynamics and hypotheses of gene order shifts in mitochondrial genomes of Baikalian amphipods

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/443.pdf”]
Elena V. Romanova1, Dmitry Yu. Sherbakov2
1Lab of gene systematics LIN SB RAS Irkutsk, Russia, elena_romanova@lin.irk.ru
2Lab of gene systematics LIN SB RAS Irkutsk, Russia, dysh007@gmail.com

In our study we describe the viabilities in mitochondrial gene order of amphipod species. Using phylogenetic inference and the methods of gene order rearrangement counting we identify species with mostly rearranged mitochondrial genomes and try to explain the reasons for such variability.В  В