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 symposiumBtr1 genes and the evolution of wheat and Aegilops species

Btr1 genes and the evolution of wheat and Aegilops species

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/258.pdf”]
Valeriya Vavilova1, Irina Konopatskaia2, Alexandr Blinov3, Nikolay P. Goncharov4
1ICG SB RAS, valeriya-vavilova@bionet.nsc.ru
2ICG SB RAS, sormacheva@bionet.nsc.ru
3ICG SB RAS, blinov@bionet.nsc.ru
4ICG SB RAS, gonch@bionet.nsc.ru

Non-brittle rachis 1 (Btr1) gene involves in regulation of the brittle/ non-brittle spike trait, which is one of the key domestication traits in Triticum species. In this study genetic variability of Btr1 genes from di- and tetraploid wheat species and Aegilops speltoides, which is donor of B-genome for polyploid wheat species, were investigated.

Bioinformatics and systems biology of plants symposiumConstruction of a Barley Gene Regulatory Network for Phenolic Metabolism Using Mutants and Near-Isogenic Lines

Construction of a Barley Gene Regulatory Network for Phenolic Metabolism Using Mutants and Near-Isogenic Lines

No Comment on Construction of a Barley Gene Regulatory Network for Phenolic Metabolism Using Mutants and Near-Isogenic Lines

Olesya Shoeva1, Ksenia Strygina2, Anastasiia Glagoleva3, Tatjana Kukoeva4, Elena Gordeeva5, Shakhira Zakhrabekova6, Mats Hansson7, Elena Khlestkina8
1ICG SB RAS, Novosibirsk, Russia, olesya_ter@bionet.nsc.ru
2VIR, St. Petersburg, Russia, k.strygina@vir.nw.ru
3ICG SB RAS, Novosibirsk, Russia, glagoleva@bionet.nsc.ru
4ICG SB RAS, Novosibirsk, Russia, kukoeva@bionet.nsc.ru
5ICG SB RAS, Novosibirsk, Russia, elgordeeva@bionet.nsc.ru
6Lund University, Lund, Sweden, shakhira.zakhrabekova@biol.lu.se
7Lund University, Lund, Sweden, mats.hansson@biol.lu.se
8ICG SB RAS, Novosibirsk, Russia; VIR, St. Petersburg, Russia, khlest@bionet.nsc.ru

In the present study, the components of the gene regulatory network governing the anthocyanin and proanthocyanidin biosynthesis in barely grain and leaf sheath were identified based on comparative mapping and transcription analysis approaches. The regulatory relationships between the genes were established using unique barley anthocyanin/proanthocyanidin mutants and near-isogenic lines.

Bioinformatics and systems biology of plants symposiumTranscriptomic response of pea (Pisum sativum L.) plants to inoculation with nodule bacteria, arbuscular-mycorrhizal fungi and PGPB

Transcriptomic response of pea (Pisum sativum L.) plants to inoculation with nodule bacteria, arbuscular-mycorrhizal fungi and PGPB

No Comment on Transcriptomic response of pea (Pisum sativum L.) plants to inoculation with nodule bacteria, arbuscular-mycorrhizal fungi and PGPB

Vladimir Zhukov1, Alexey Afonin2, Gulnar Akhtemova3, Andrei Bovin4, Aleksandra Dolgikh5, Artemii Gorshkov6, Emma Gribchenko7, Kira Ivanova8, Anna Kirienko9, Anna Kitaeva10, Marina Kliukova11, Olga Kulaeva12, Pyotr Kusakin13, Irina Leppyanen14, Olga Pavlova15, Daria Romanyuk16, Tatiana Serova17, Oksana Shtark18, Anton Sulima19, Anna Tsyganova20, Ekaterina Vasileva21, Aleksandr Zhernakov22, Evgeny Zorin23, Elena Dolgikh24, Viktor Tsyganov25, Igor Tikhonovich26
1ARRIAM, Saint-Petersburg, Russia, vzhukov@arriam.ru
2ARRIAM, Saint-Petersburg, Russia, afoninalexeym@gmail.com
3ARRIAM, Saint-Petersburg, Russia, ahgulya@yandex.ru
4ARRIAM, Saint-Petersburg, Russia, andy-piter2007@mail.ru
5ARRIAM, Saint-Petersburg, Russia, sqshadol@gmail.com
6ARRIAM, Saint-Petersburg, Russia, artemius1993@yandex.ru
7ARRIAM, Saint-Petersburg, Russia, gribemma@gmail.com
8ARRIAM, Saint-Petersburg, Russia, kirakosmonavt_24@mail.ru
9ARRIAM, Saint-Petersburg, Russia, kirienkoann@yandex.ru
10ARRIAM, Saint-Petersburg, Russia, anykitaeva@gmail.com
11ARRIAM, Saint-Petersburg, Russia, marina.kliukova@gmail.com
12ARRIAM, Saint-Petersburg, Russia, okulaeva@arriam.ru
13ARRIAM, Saint-Petersburg, Russia, kussakin@gmail.com
14ARRIAM, Saint-Petersburg, Russia, leppyanen_irina@rambler.ru
15ARRIAM, Saint-Petersburg, Russia, dobbi85@list.ru
16ARRIAM, Saint-Petersburg, Russia, daria-rom@yandex.ru
17ARRIAM, Saint-Petersburg, Russia, t_serova@rambler.ru
18ARRIAM, Saint-Petersburg, Russia, oshtark@yandex.ru
19ARRIAM, Saint-Petersburg, Russia, sulan555@mail.ru
20ARRIAM, Saint-Petersburg, Russia, isaakij@mail.ru
21ARRIAM, Saint-Petersburg, Russia, evasilieva@arriam.ru
22ARRIAM, Saint-Petersburg, Russia, azhernakov@gmail.com
23ARRIAM, Saint-Petersburg, Russia, kjokkjok8@gmail.com
24ARRIAM, Saint-Petersburg, Russia, dol2helen@yahoo.com
25ARRIAM, Saint-Petersburg, Russia, tsyganov@arriam.spb.ru
26ARRIAM, Saint-Petersburg, Russia; Saint-Petersburg State University, Saint-Petersburg, Russia, arriam2008@yandex.ru

Mutualistic symbioses formed by garden pea have been studied with use of transcriptomics in order to gain a new understanding of molecular mechanisms of beneficial effect that microsymbionts have on seed yield and quality.

Bioinformatics and systems biology of plants symposiumNew insight on diversity of the Nikita Botanical Gardens plant collections from advanced NGS

New insight on diversity of the Nikita Botanical Gardens plant collections from advanced NGS

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Irina Mitrifanova1, Olga Krivenko2, Olga Kuleshova3, Svetlana Chelombit4, Valentina Brailko5, Olga Mitrofanova6
1NBG-NSC RAS, Yalta, Russia, irimitrofanova@yandex.ru
2NBG-NSC RAS, Yalta, Russia, olkrivenko@gmail.com
3NBG-NSC RAS, Yalta, Russia, v_olgo4ka@inbox.ru
4NBG-NSC RAS, Yalta, Russia, chelombit@inbox.ru
5NBG-NSC RAS, Yalta, Russia, labgennbs@yandex.ru
6NBG-NSC RAS, Yalta, Russia, invitro_plant@yandex.ru

New scientific program of genomic screening of the Nikita Botanical Gardens plant collections targeted at comprehensive description of their molecular diversity in close connection with morphological, physiological and others phenotype features has started. Strategic goal is to develop and implement advanced molecular approaches for plant biotechnology, breeding, propagation, and conservation routine works. Two whole-genome sequencing projects to produce a high quality assembly of the reference genomes of the common fig Ficus carica L. (Moraceae) and Crimean endemic species Heracleum ligusticifolium M. Bieb. (Apiaceae) are in progress. Several hybrid assembly approaches using combined data sets with long and short reads obtained by Oxford Nanopore MinION and Illumina NextSeq550 instruments are tested to create accurate and well-resolved reference genome. The first versions of the reference genomes of F. carica cultivar ‘Sabrutsiya Rozovaya’ and H. ligusticifolium were made, and their annotations are performing. Subsequent improvement and development of the primary genome assemblies up to \”pan-genome\” rank will be carried out using advanced bioinformation approaches and computational tools by assimilation of new sequenced genomes and transcriptomes of the model species taken from the NBS-NSC collections and from nature biotopes as well. Such integrative reference genome construction will provide an important resource both for advanced molecular breeding and fundamental researches in plant biology and ecology based on genomic approaches using F. carica and H. ligusticifolium as model species.

Bioinformatics and systems biology of plants symposiumIdentification of genetic factors responsible for symbiotic effectiveness in pea (Pisum sativum L.)

Identification of genetic factors responsible for symbiotic effectiveness in pea (Pisum sativum L.)

No Comment on Identification of genetic factors responsible for symbiotic effectiveness in pea (Pisum sativum L.)

Aleksandr Zhernakov1, Oksana Shtark2, Olga Kulaeva3, Igor Tikhonovich4, Vladimir Zhukov5
1All-Russia Research Institute for Agricultural Microbiology, azhernakov@arriam.ru
2All-Russia Research Institute for Agricultural Microbiology, oshtark@yandex.ru
3All-Russia Research Institute for Agricultural Microbiology, okulaeva@arriam.ru
4All-Russia Research Institute for Agricultural Microbiology; Saint-Petersburg State University, Saint-Petersburg, Russia, arriam2008@yandex.ru
5All-Russia Research Institute for Agricultural Microbiology, vzhukov@arriam.ru

Legumes (Leguminosae, syn. Fabaceae) develop two highly integrated mutually beneficial endosymbioses, namely nitrogen-fixing root nodules with rhizobia bacteria and arbuscular mycorrhiza that makes them a key component of modern technologies for crop production. We applied the comparative transcriptome analysis for identification of pea genes essential for effective symbiosis with beneficial soil microbes. The allelic forms of the two identified genes most likely have a significant effect on the effectiveness of symbiosis pea with rhizobia bacteria and arbuscular mycorrhiza.

Bioinformatics and systems biology of plants symposiumDetection and investigation of genes with circadian expression pattern in common wheat

Detection and investigation of genes with circadian expression pattern in common wheat

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Antonina Kiseleva1, Maria Bragina2, Elena Salina3
1ICG SB RAS, Novosibirsk, Russia, antkiseleva@bionet.nsc.ru
2ICG SB RAS, Novosibirsk, Russia, koltunova@bionet.nsc.ru
3ICG SB RAS, Novosibirsk, Russia, salina@bionet.nsc.ru

The study of daily oscillations of the wheat transcriptome, the identification of both the core circadian genes and the genes of metabolic pathways under the influence of daily rhythms is the main topic of this work.

Bioinformatics and systems biology of plants symposiumApplication of neural networks to image recognition of wheat rust diseases

Application of neural networks to image recognition of wheat rust diseases

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/416.pdf”]
Mikhail Genaev1
1Mikhail Genaev ICG SB RAS, Kurchatov Genomic Center, Novosibirsk, Russia NSU, Novosibirsk, Russia, mag@bionet.nsc.ru

Rust diseases of cereals are caused by pathogenic fungi and can significantly reduce plant productivity. Many cultures are subject to them. The disease is difficult to control on a large scale, so one of the most relevant approaches is crop monitoring, which helps to identify the disease at an early stage and make efforts to prevent its spread. One of the most effective methods of control is the identification of the disease from digital images that obtained by a smartphone camera. In this paper, we present a deep learning algorithm that uses a digital image of wheat plants to determine whether they are affected by a disease and, if so, what type: leaf rust or stem rust. The algorithm based on the convolution neural network of the densenet architecture. The resulting model demonstrates high accuracy of classification: the measure of accuracy F1 on the validation sample is 0.9, the AUC averaged over 3 classes is 0.98.

Bioinformatics and systems biology of plants symposiumSeedCounter – mobile application for high throughput grain phenotyping

SeedCounter – mobile application for high throughput grain phenotyping

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Mikhail Genaev1
1ICG SB RAS, Kurchatov Genomic Center, Novosibirsk, Russia NSU, Novosibirsk, Russia, mag@bionet.nsc.ru

Grains morphometry is an important step in selecting new high-yielding plants. The manual assessment of parameters such as the number of grains per ear and their size is laborious. The solution to this problem is image-based analysis, which can be performed using a desktop PC. The effectiveness of this analysis in the field can be improved through the use of mobile devices. We propose a method for the automated evaluation of phenotypic parameters of grains using mobile devices running the Android operational system. The experimental results show that this approach is efficient and sufficiently accurate for the large-scale analysis of phenotypic characteristics in wheat grains.

 

Bioinformatics and systems biology of plants symposiumMolecular markers based on SNPs in FAD3 genes for determination of linolenic acid content in flax seed

Molecular markers based on SNPs in FAD3 genes for determination of linolenic acid content in flax seed

No Comment on Molecular markers based on SNPs in FAD3 genes for determination of linolenic acid content in flax seed

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/399.pdf”]
Liubov Povkhova1, Parfait Kezimana2, Tatiana Rozhmina3, Elena Pushkova4, Roman Novakovskiy5, George Krasnov6, Alexey Dmitriev7, Nataliya Melnikova8
1Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, Russia, povhova.lv@phystech.edu
2Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; RUDN University, Moscow, Russia, k1par@mail.ru
3Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Federal Research Center for Bast Fiber Crops, Torzhok, Russia, tatyana_rozhmina@mail.ru
4Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, pushkova18@gmail.com
5Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, 0legovich46@mail.ru
6Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, gskrasnov@mail.ru
7Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, alex_245@mail.ru
8Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, mnv-4529264@yandex.ru

Flax is grown for seeds in many countries. Depending on the ratio of fatty acids, seeds are used in pharmaceutical, food, feed, or polymer production. It is known that genes of FAD3 family responsible for the desaturation of linoleic (LIO) into linolenic (LIN) fatty acid and some alleles of these genes are associated with a certain composition of flax oil. However, the development of the marker-assisted selection of flax is complicated due to a lack of methods for the identification of these polymorphisms. In the present study, we used 84 flax cultivars/lines with diverse content of LIO and LIN to search for fatty acid associated SNPs and then developed HRM-based system for identification of these SNPs that can increase the efficiency of breeding by obtaining pure improved cultivars with the targeted LIO and LIN content.

Bioinformatics and systems biology of plants symposiumComplete sequencing of barley organellar genomes: new data for intraspecific differentiation

Complete sequencing of barley organellar genomes: new data for intraspecific differentiation

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/392.pdf”]
Yermakovich (Makarevich) Anna1, Siniauskaya Maryna2, Liaudanski Aleh3, Halayenka Innesa4, Davydenko Oleg5
1Institute of Genetics and Cytology of NAS of Belarus, Laboratory of Cytoplasmic Inheritance, bio.makarevich@gmail.com
2Institute of Genetics and Cytology of NAS of Belarus, Laboratory of Cytoplasmic Inheritance, m.sin@inbox.ru
3Institute of Genetics and Cytology of NAS of Belarus, Laboratory of Cytoplasmic Inheritance, 666555@tut.by
4Institute of Genetics and Cytology of NAS of Belarus, Laboratory of Cytoplasmic Inheritance, goloenkoi@tut.by
5Institute of Genetics and Cytology of NAS of Belarus, Laboratory of Cytoplasmic Inheritance, davydenko@tut.by

Organelle genomes are an important tool to investigate domestication, distribution and microevolution of plant species. However, they have found limited use in cereal intraspecific studies so far.

In the present study, organelle genomes of wild (Hordeum vulgare subsp. spontaneum) and cultivated (H. vulgare subsp. vulgare) barley forms were sequenced. We conducted theВ NGS of isolated chloroplast and mitochondrial DNA mixtures. This non-trivial approach allowed to obtain both genomes for each sample but required some specific steps in the data processing.

Comparative analysis of obtained sequences revealed more than 100 polymorphic sites in the chloroplast genome, including new intraspecific SSR-markers, and more than 20 polymorphisms in the mitochondrial genome.

We also carry out the phylogenetic analysis of these genomes. Chloroplast and mitochondrial DNA trees were consistent with each other, indicating the presence of two large clades containing both wild and cultivated forms.

Our results are conforming with a hypothesis of several domestication centres of barley. They also provide direct evidence of a higher rate of nucleotide substitutions in the chloroplast genomes as compared to that of mitochondria on a microevolution scale. The revealed high level of variability of chloroplast genomes makes it possible to use them for intraspecific barley differentiation.