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 symposiumThe prospects for the study of the avirulence genes characteristic for the West Siberian population of wheat stem rust Puccinia graminis f. sp. tritici

The prospects for the study of the avirulence genes characteristic for the West Siberian population of wheat stem rust Puccinia graminis f. sp. tritici

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/195.pdf”]
Vasiliy Kelbin1, Ekaterina Sergeeva2, Ekaterina Skolotneva3, Elena Salina4
1IC&G SB RAS, kelbin@bionet.nsc.ru
2IC&G SB RAS, sergeeva@bionet.nsc.ru
3IC&G SB RAS, skolotnevaes@bionet.nsc.ru
4IC&G SB RAS, salina@bionet.nsc.ru

Wheat stem rust is a plant disease caused by pathogenic fungus Puccinia graminis f. sp. tritici which leads to significant damage of the crop. During the last decade the disease affected the crops in West Siberia. The plant response to infection is determined by the correspondence of host resistance (Sr) and fungus avirulence/virulence (Avr/vr) genes. We first characterized the West Siberian population of wheat stem rust: the probable sources of infection were traced, the race composition and main avirulence genes were defined. Four fungal lines with contrasting patterns of Avr genes were selected for whole genomic sequencing.

Bioinformatics and systems biology of plants symposiumGenome-wide analysis of highly expressed plant retrotransposons

Genome-wide analysis of highly expressed plant retrotransposons

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Murad Omarov1, Pavel Merkulov2, Sofia Gvaramia3, Liza Kolganova4, Ilya Kirov5
1All-Russia Research Institute of Agriculture biotechnology, muradok98@gmail.com
2All-Russia Research Institute of Agriculture biotechnology, paulmerkulov97@gmail.com
3All-Russia Research Institute of Agriculture biotechnology, sofia.gvaramia@gmail.com
4All-Russia Research Institute of Agriculture biotechnology, liza.colg@gmail.com
5All-Russia Research Institute of Agriculture biotechnology, kirovez@gmail.com

Retrotransposons (TEs) are mobile genomic elements capable of transposition via reverse transcription of RNA intermediate. Transcription and mobility of TEs in a cell are under strong epigenetic silencing being partially recovered during stress and some development stages. But recent studies cast doubt on this axiomatic statement, revealing many transcripts of TEs (retrotranscriptome) in somatic organs under non-stressed conditions. The composition and structure of plant retrotranscriptome are still not clear. Here, we developed a pipeline for transcribed TEs identification and applied it to 7 plant species using RNA-seq data from different organs and under different conditions. Our results showed that TEs transcription under non-stressed conditions is the widespread phenomenon in plants and expressed TEs possess some distinctive genomic features

Bioinformatics and systems biology of plants symposiumFlowering patterns of herbaceous multi-flowered monocarpic shoots of Campanula sarmatica

Flowering patterns of herbaceous multi-flowered monocarpic shoots of Campanula sarmatica

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Eduard Fomin1
1Federal Research Center Institute of Cytology and Genetics SB RAS, fomin@bionet.nsc.ru

Flowering analysis of Campanula sarmatica, Campanulaceae family at the level of individual shoots was performed. It has been established that the flowering curves of C. sarmatica shoots are bimodal. The first peak corresponds to the flowering of the main axis, and the second to the lateral axes of the inflorescence. Flowering curves have noticeable individual differences in the heights of the main peaks, due to the difference in the number of flowers on the main axis and lateral axes on different shoots. The found mechanism of the formation of the curves makes it possible to extract the type of inflorescence (botryoid or panicle) and estimate the number of lateral axes directly from the flowering curve for any observed shoot.

Bioinformatics and systems biology of plants symposiumMolecular genetic analysis of alloplasmic recombinant lines (Triticum dicoccum) -Triticum aestivum

Molecular genetic analysis of alloplasmic recombinant lines (Triticum dicoccum) -Triticum aestivum

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/133.pdf”]
Shcherban A.B.1, Perfil’ev R.N2, Salina E.A.3
1Institute of Cytology and Genetics SB RAS, atos@bionet.nsc.ru
2Novosibirsk State Agrarian University, pervf.1999@gmail.com
3Institute of Cytology and Genetics SB RAS, sunday01@mail.ru

Molecular markers were used to analyze the mitochondrial genome of the alloplasmic lines of wheat containing the nuclear genome of the hexaploid wheat T. aestivum against the background of the cytoplasm of tetraploid wheat T.dicoccum. Eight lines showed patterns of PCR and CAPS markers corresponding to the species T. aestivum, indicating the substitution of the mitochondrial genome of T. dicoccum during backcrossing with hexaploid wheat. In the D-N-05 line, the rps19 and orf256 gene markers corresponded to the parental species T.dicoccum. This line is promising in terms of studying the mechanisms of fertility restoration in hybrids with CMS. Also, using molecular marker, the nuclear gene Dreb-1, which is a regulator of drought tolerance, was analyzed and it was shown that В line D-41-05 had an introgression of this gene from the B genome of T. dicoccum, which may lead to the previously established increased drought tolerance of this line.

Bioinformatics and systems biology of plants symposiumGenome-wide Prediction of Transcription Start Site in Four Conifer Species

Genome-wide Prediction of Transcription Start Site in Four Conifer Species

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/104.pdf”]
Eugeniia I. Bondar1, Dmitry A. Kuzmin2, Konstantin V. Krutovsky3, Vadim V. Sharov4, Tatiana V. Tatarinova5
1Laboratory of Forest Genomics, Siberian Federal University; Laboratory of Genomeic Research and Biotechnology, FRC KSC SB RAS, Krasnoyarsk, Russia, bondar.ev@ksc.krasn.ru
2Laboratory of Forest Genomics Siberian Federal University; Department of High Performance Computing, Siberian Federal University, Krasnoyarsk, Russia, dm.kuzmin@gmail.com
3Laboratory of Forest Genomics, Siberian Federal University, Krasnoyarsk, Russia; Department of Forest Genetics and Forest Tree Breeding, Georg-August of Göttingen, Göttingen, Germany; Laboratory of Population Genetics, Vavilov Institute of General Genetics, Moscow, Russia; Department of Ecosystem Science and Management Texas A&M University College Station, TX, USA, konstantin.krutovsky@forst.uni-goettingen.de
4Laboratory of Genomeic Research and Biotechnology, FRC KSC SB RAS; Laboratory of Forest Genomics, Siberian Federal University; Department of High Performance Computing, Siberian Federal University, Krasnoyarsk, Russia, sharvadim07@ya.ru
5Department of Biology, University of La Verne, La Verne, USA; Functional Genomics Group, Vavilov Institute for General Genetics, Moscow, Russia; Siberian Federal University, Krasnoyarsk, Russia; Bioinformatics Center of IITP RAS, Moscow, Russia, ttatarinova@laverne.edu

Current draft annotations for sequenced conifer genomes are preliminary and limited, but provide opportunities for further structural and functional analysis. We attempted to improve the existing genome annotations by marking 5’-UTRs in the four conifer species Pinus taeda, Picea glauca, Picea abies and Larix sibirica. Prediction of transcription start sites (TSS) was performed on the promoter sequences of genes with RNA or protein support using TSS prediction program TSSPlant. The distribution of 5’-UTR lengths from the annotations of several model plants was used to select the best prediction per gene. Frequency of TATA(A/T)A(A/T) motif in the predicted TSS-centered promoter regions showed a pronounced peak around 60 bp upstream of TSS.

Bioinformatics and systems biology of plants symposiumThe characteristics of interaction of miRNA with mRNA of C2H2, ERF and GRAS transcription factors of arabidopsis, rice and maize

The characteristics of interaction of miRNA with mRNA of C2H2, ERF and GRAS transcription factors of arabidopsis, rice and maize

No Comment on The characteristics of interaction of miRNA with mRNA of C2H2, ERF and GRAS transcription factors of arabidopsis, rice and maize

Rakhmetullina Aizhan1, Turasheva Svetlana2, Pyrkova Anna3
1SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, zhanullina1994@gmail.com
2SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, svetlana.turasheva@kaznu.kz
3SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, anna.pyrkova@kaznu.kz

The miRNA binding sites with mRNA of genes encoding C2H2, ERF, GRAS transcription factors (TFs) were identified for Arabidopsis thaliana, Oryza sativa and Zea mays. The free energy (ΔG) of interaction of miRNA with mRNA target genes, the maximum of free energy (ΔGm), the ratio ΔG/ΔGm, and location of the potential binding sites were calculated using MirTarget program. In mRNA of C2H2, ERF, GRAS genes of all studied plants, miRNA binding sites were located in the protein-coding part (CDS) and 5’-untranslated region (5’UTR). The ath-miR5658-5p, ath-miR5021-5p, osa-miR2102-5p, osa-miR5075-3p had binding sites in mRNA of three studied families, with the value of ΔG/ΔGm from 91% to 98%. The miR171a-3p had binding sites in mRNA GRAS transcription factors family of all studied plants, with the value of ΔG/ΔGm equal 100%. The nucleotide sequences of ath-miR171a-3p, osa-miR171a-3p, and zma-miR171a-3p were similar, and their quantitative characteristics of interaction with mRNA of LOC_Os02g44360.1, GRMZM2G037792_P01, and AT2G45160.1 genes, were also similar. The obtained results indicate the dependence of expression TF of C2H2, ERF, GRAS families on miRNA.  

Bioinformatics and systems biology of plants symposiumWheat and maize miRNAs are potential regulators of human genes expression

Wheat and maize miRNAs are potential regulators of human genes expression

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Rakhmetullina Aizhan1, Ivashchenko Anatoliy2, Pyrkova Anna3
1SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, zhanullina1994@gmail.com
2SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, a.iavashchenko@gmail.com
3SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, anna.pyrkova@kaznu.kz

With food, a huge variety of biological material gets into the human digestive tract, which the body uses for life support. The variety of food material entering the gastrointestinal tract, especially at the molecular level, cannot be distinguished from endogenous metabolites and these exogenous compounds can significantly alter the body\’s metabolism. Such compounds include plant miRNAs, which are indistinguishable from endogenous human miRNAs in physicochemical properties. It is necessary to clarify the degree of influence of exogenous plant miRNAs on the expression of human genes, since it is not known in advance what consequences can occur when plant miRNAs enters the human body. A huge amount of research does not allow experiments with all human genes and all plant miRNAs, so we have studied the effect of wheat and maize miRNAs on human genes using computer methods. As a result of studying the binding of 125 tae-miRNAs and 325 zma-miRNAs to mRNAs of 17508 human genes it was revealed that 158 genes were targets for 52 tae-miRNAs and 51 genes for 11 zma-miRNAs. Binding sites in the mRNA of human genes were located in 5\’UTR, CDS, 3\’UTR.