Comparative genomics of heat shock proteins system in extremophile nonbiting midges

Poster (download) Olga Kozlova1, Guzel Gazizova2, Elena Shagimardanova3, Oleg Gusev41Kazan Federal University, olga-sphinx@yandex.ru2Kazan Federal University, grgazizova@gmail.com3Kazan Federal University, rjuka@mail.ru4Kazan Federal University, gaijin.ru@gmail.com Here we compare the number and expression profiles of HSP-coding genes in larvae of Chironomidae family (Diptera), who are known for their ability to successfully combat abiotic stresses using wide range of behavioral, morphological and biochemical features. In order to perform comparative studies we sequenced and assembled genomes of 4 chironomids from different habitats and also sequenced whole-genome RNA of their larvae in control and stressed conditions. It was shown that compact genome sizes (up to 200 Mb) are typical for Chironomidae, while changes in size of a genome are mediated by elongation and shortening of introns length, as well as by changes in quantity and content of dispersed repeats. For all extremophile species under consideration species-specific gene expansion accompanied by formation of compact clusters in a genome was detected. The most amplitudinous reaction towards abiotic stress (desiccation) was shown by anhydrobiotic species Polypedilum vanderplanki (Africa). As for HSP-coding genes, it was noticed that genes of HSP20 and HSP70 show the most dramatic and universal up-regulation of expression in response to abiotic stress, while genes of chaperonins (HSP60) tend to be up-regulated in response to desiccation, but not to heat shock. But the most surprising notion was linked to acid-tolerant species Polipedilum cf. tamanigrum (Japan), because none of HSP-coding genes in this species showed statistically significant up-regulation, what may be explained by absence of special regulatory sequence – heat shock element (HSE) in their promotor regions.

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Automatic Annotation of Operons Responsible for O-antigen Synthesis

Danil Zilov1, Polina Chesnokova2, Alexey Komissarov31Laboratory of Applied Genomics, SCAMT, ITMO University, St. Petersburg, Russia, zilov@scamt-itmo.ru2Laboratory of Applied Genomics, SCAMT, ITMO University, St. Petersburg, Russia, chesnokova@scamt-itmo.ru3Laboratory of Applied Genomics, SCAMT, ITMO University, St. Petersburg, Russia, komissarov@scamt-itmo.ru Unfortunately, the most ready-made tools for serotype determination are limited to genome E. Coli only. However, there is a problem due to the low accuracy of Рћ-antigen cluster identification in the genome. Pipeline, which was created due the work, solves this problem and can be used to find and annotate a cluster of genes in genome of the most gram-negative bacteria.

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Comparative analysis of flax (Linum usitatissimum L.) genomes and transcriptomes

Poster (download) Elena Pushkova1, George Krasnov2, Roman Novakovskiy3, Liubov Povkhova4, Artemy Beniaminov5, Nadezhda Bolsheva6, Tatiana Rozhmina7, Alexey Dmitriev8, Nataliya Melnikova91Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, pushkova18@gmail.com2Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, gskrasnov@mail.ru3Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, 0legovich46@mail.ru4Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, Russia, povhova.lv@phystech.edu5Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, abeniaminov@mail.ru6Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, nlbolsheva@mail.ru7Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia; Federal Research Center for Bast Fiber Crops, Torzhok, Russia, tatyana_rozhmina@mail.ru8Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, alex_245@mail.ru9Engelhardt Institute of Molecular Biology, RAS, Moscow, Russia, mnv-4529264@yandex.ru Flax (Linum usitatissimum L.) is an agriculturally important plant that has a wide range of applications in industry, and the direction of cultivar application is determined by its genetic characteristics. The present work aimed to obtain high-quality sequences of flax genomes and transcriptomes for genetically diverse cultivars and lines, which have breeding value and different direction of use. Six cultivars/lines (LM98, #3896, Diplomat, Atlant, Universal, Alizee) were selected for the present work. We have developed an optimal method for the extraction of pure high-molecular-weight DNA from flax plants and performed genome and transcriptome sequencing. From 6 to 10 Gb was obtained for each of the studied flax cultivars/lines on the Oxford Nanopore platform and 20-25 million reads on the Illumina platform. Transcriptome sequencing of different flax tissues was also performed. Genome assembly using Flye resulted in the N50 value from 200 kb to 1 Mb depending on the genotype. Genome annotation was then performed. The obtained genome assemblies are the basis for molecular genetic studies in flax and allow assessment of the differences in L. usitatissimum cultivars/lines at the genome-wide level.

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Genome Assembly and Annotation of Nothobranchius rachovii killifish

Zulfiia Guvatova1, George Krasnov2, Anastasiya Snezhkina3, Artemy Tokarev4, Maria Fedorova5, Anna Kudryavtseva61Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, guvatova.zulfiya@mail.ru2Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, gskrasnov@mail.ru3Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, leftger@rambler.ru4Artemy Tokarev Veterinary biology faculty MSAVM&B – MVA named after K.I. Skryabin Moscow, Russia, artemiy.tokarev@mail.ru5Laboratory of Postgenomic Research Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, fedorowams@yandex.ru6Center for Precision Genome Editing and Genetic Technologies for Biomedicine Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia, rhizamoeba@mail.ru Nothobranchius rachovii is a species of freshwater annual killifish native to Africa. This organism is an attractive model in aging studies because of short lifetime and rapid maturation. In this study, we present draft genome assembly of this organism based on Nanopore reads and polished with Illumina reads. We tested four popular Nanopore reads assemblers (Flye, MaSuRCA, Shasta, wtdbg2) and two polishers (Pilon and MaSuRCA-polish tool). We selected the best combination of these tools in terms of contig length and assembly completeness.

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