Andrey Marakhonov1, Tatyana Vasilyeva2, Vitaly Kadyshev3, Rena Zinchenko41Research Center for Medical Genetics, marakhonov@generesearch.ru2Research Center for Medical Genetics, valyeva_debrie@mail.ru3Research Center for Medical Genetics, vvh.kad@gmail.com4Research 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.
Read MorePoster (download) Guzel Davletshina1, Sergey Kliver2, Elena Interesova3, Dmitry Prokopov4, Vladimir Trifonov51IMCB SB RAS, Novosibirsk, Russia; ICG SB RAS, Novosibirsk, Russia, guzel@mcb.nsc.ru2IMCB SB RAS, Novosibirsk, Russia, skliver@mcb.nsc.ru3TSU, Tomsk, Russia, e.interesova@ngs.ru4ICG SB RAS, Novosibirsk, Russia, dprokopov@mcb.nsc.ru5IMCB 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.
Read MoreAndrew G. Matveenko1, Anton B. Matiiv2, Yury A. Barbitoff3, Evgenia M. Maksiutenko4, Svetlana E. Moskalenko5, Alexandra V. Beliavskaia6, Alexander V. Predeus7, Galina A. Zhouravleva81Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, a.matveenko@spbu.ru2Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, antonmatiiv@yandex.ru3Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia; Bioinformatics Institute, St. Petersburg, Russia, barbitoff@bk.ru4Vavilov Institute of General Genetics, St. Petersburg Branch, St. Petersburg, Russia; Dpt. of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia, jmrose@yandex.ru5Vavilov 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.ru6University of Liverpool, Liverpool, UK, alex.beliavskaia@gmail.com7University of Liverpool, Liverpool, UK; Bioinformatics Institute, St. Petersburg, Russia, predeus@bioinf.me8Dpt. 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.
Read MorePoster (download) Julia Bocharkina1, Olga Razumova2, Gennady Karlov31Laboratory 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.ru2Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia, razumovao@gmail.com3Laboratory 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.
Read MorePoster (download) Yermakovich (Makarevich) Anna1, Siniauskaya Maryna2, Liaudanski Aleh3, Halayenka Innesa4, Davydenko Oleg51Institute of Genetics and Cytology of NAS of Belarus, Laboratory of Cytoplasmic Inheritance, bio.makarevich@gmail.com2Institute of Genetics and Cytology of NAS of Belarus, Laboratory of Cytoplasmic Inheritance, m.sin@inbox.ru3Institute of Genetics and Cytology of NAS of Belarus, Laboratory of Cytoplasmic Inheritance, 666555@tut.by4Institute of Genetics and Cytology of NAS of Belarus, Laboratory of Cytoplasmic Inheritance, goloenkoi@tut.by5Institute 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.
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