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

Tag

NGS

5 RESULTS
Systems Biology and Biomedicine symposiumThe role of NGS in diagnosis of hereditary ophthalmic pathology

The role of NGS in diagnosis of hereditary ophthalmic pathology

No Comment on The role of NGS in diagnosis of hereditary ophthalmic pathology

Andrey Marakhonov1, Tatyana Vasilyeva2, Vitaly Kadyshev3, Rena Zinchenko4
1Research Center for Medical Genetics, marakhonov@generesearch.ru
2Research Center for Medical Genetics, valyeva_debrie@mail.ru
3Research Center for Medical Genetics, vvh.kad@gmail.com
4Research Center for Medical Genetics, renazinchenko@mail.ru

Here we discuss the requirements, efficiency, place as well as performance of next generation methods in DNA diagnosis of hereditary ophthalmic diseases.

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.

Genomics, transcriptomics, bioinformatics symposiumWhole genome sequencing and assembly of Saccharomyces cerevisiae genomes using Oxford Nanopore data

Whole genome sequencing and assembly of Saccharomyces cerevisiae genomes using Oxford Nanopore data

No Comment on Whole genome sequencing and assembly of Saccharomyces cerevisiae genomes using Oxford Nanopore data

Andrew G. Matveenko1, Anton B. Matiiv2, Yury A. Barbitoff3, Evgenia M. Maksiutenko4, Svetlana E. Moskalenko5, Alexandra V. Beliavskaia6, Alexander V. Predeus7, Galina A. Zhouravleva8
1Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, a.matveenko@spbu.ru
2Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, antonmatiiv@yandex.ru
3Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia; Bioinformatics Institute, St. Petersburg, Russia, barbitoff@bk.ru
4Vavilov Institute of General Genetics, St. Petersburg Branch, St. Petersburg, Russia; Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, jmrose@yandex.ru
5Vavilov Institute of General Genetics, St. Petersburg Branch, St. Petersburg, Russia; Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, s.moskalenko@spbu.ru
6University of Liverpool, Liverpool, UK, alex.beliavskaia@gmail.com
7University of Liverpool, Liverpool, UK; Bioinformatics Institute, St. Petersburg, Russia, predeus@bioinf.me
8Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, g.zhuravleva@spbu.ru

The Peterhof genetic collection (PGC) of yeastВ SaccharomycesВ cerevisiae is one of the rareВ examplesВ of a large genetic collection established independently of reference S288C strain. We assembled genomes of two widely used PGC strains, 1A-D1628 and 74-D694, using Oxford Nanopore MinION sequencing data. Subsequent analysis of structural variations showed a number of differences between PGC strains and S288C.

Bioinformatics and systems biology of plants symposiumAnalysis of repeatomes in Cannabaceae family

Analysis of repeatomes in Cannabaceae family

No Comment on Analysis of repeatomes in Cannabaceae family

Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/362.pdf”]
Julia Bocharkina1, Olga Razumova2, Gennady Karlov3
1Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia; Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia, julia.bocharkina@skoltech.ru
2Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia, razumovao@gmail.com
3Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia, karlovg@gmail.com

Analysis of repeatomes in the Cannabaceae family was done. There were found family-specific, species-specific and sex-specific clusters. Primers were created and checked.

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

No Comment on Complete sequencing of barley organellar genomes: new data for intraspecific differentiation

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.