vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJGB-22-07vavilov-3261Research ArticleАКТУАЛЬНЫЕ ТЕХНОЛОГИИMAINSTREAM TECHNOLOGIESDe novo сборка и анализ транскриптома сибирской лягушки Rana amurensisDe novo assembly and analysis of the transcriptome of the Siberian wood frog Rana amurensishttps://orcid.org/0000-0002-9842-8181СмирновД. Н.SmirnovD. N.

Беэр-Шева; Москва

Moscow; Beer Sheva

https://orcid.org/0000-0001-5604-5601ШеховцовС. В.ShekhovtsovS. V.

 Магадан; Новосибирск

Magadan; Novosibirsk

shekhovtsov@bionet.nsc.ruhttps://orcid.org/0000-0001-7167-4481ШиповаА. А.ShipovaA. A.

Новосибирск

Novosibirsk

https://orcid.org/0000-0003-4978-8495ГазизоваГ. Р.GazizovaG. R.

Казань

 Kazan

https://orcid.org/0000-0003-2339-261XШагимардановаЕ. И.ShagimardanovaE. I.

Казань

 Kazan

https://orcid.org/0000-0002-3000-6476БулаховаН. А.BulakhovaN. A.

Магадан

Magadan

https://orcid.org/0000-0001-8089-4734МещеряковаЕ. Н.MeshcheryakovaE. N.

Магадан

Magadan

https://orcid.org/0000-0002-5652-0553ПолубояроваТ. В.PoluboyarovaT. V.

Новосибирск

Novosibirsk

https://orcid.org/0000-0001-6188-9139ХрамееваЕ. Е.KhrameevaE. E.

Москва

Moscow

https://orcid.org/0000-0002-3524-0456ПельтекС. Е.PeltekS. E.

 Новосибирск

Novosibirsk

https://orcid.org/0000-0002-2137-1324БерманД. И.BermanD. I.

Магадан

Magadan

Центр наук о жизни Сколковского института науки и технологий; Университет им. Давида Бен-Гуриона в Негеве, Отделение наук о жизниИзраильCenter of Life Sciences, Skolkovo Institute of Science and Technology; Ben-Gurion University of the Negev, Department of Life SciencesIsraelИнститут биологических проблем Севера Дальневосточного отделения Российской академии наук; Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesRussian FederationИнститут фундаментальной медицины и биологии Казанского федерального университетаРоссияInstitute of Fundamental Medicine and Biology, Kazan Federal UniversityRussian FederationИнститут биологических проблем Севера Дальневосточного отделения Российской академии наукРоссияInstitute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of SciencesRussian FederationЦентр наук о жизни Сколковского института науки и технологийРоссияCenter of Life Sciences, Skolkovo Institute of Science and TechnologyRussian Federation202202032022261109116Copyright © Смирнов Д.Н., Шеховцов С.В., Шипова А.А., Газизова Г.Р., Шагимарданова Е.И., Булахова Н.А., Мещерякова Е.Н., Полубоярова Т.В., Храмеева Е.Е., Пельтек С.Е., Берман Д.И., 20222022Смирнов Д.Н., Шеховцов С.В., Шипова А.А., Газизова Г.Р., Шагимарданова Е.И., Булахова Н.А., Мещерякова Е.Н., Полубоярова Т.В., Храмеева Е.Е., Пельтек С.Е., Берман Д.И.Smirnov D.N., Shekhovtsov S.V., Shipova A.A., Gazizova G.R., Shagimardanova E.I., Bulakhova N.A., Meshcheryakova E.N., Poluboyarova T.V., Khrameeva E.E., Peltek S.E., Berman D.I.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/3261

Сибирская лягушка Rana amurensis Boulenger, 1886 – наиболее устойчивый к гипоксии вид амфибий. Она может прожить несколько месяцев при почти полном отсутствии кислорода. О механизмах этой замечательной устойчивости мало что известно, отчасти потому, что исследования геномов амфибий затруднены из-за их большого размера. Чтобы сделать сибирскую лягушку более доступной для генетического анализа, мы провели секвенирование и сборку de novo транскриптома мозга R. amurensis в условиях гипоксии и нормоксии, а также для сердца – в нормоксии. Для сборки транскриптома de novo использовали парные прочтения длиной 125 п.н., полученные для мозга сибирской лягушки в нормоксии и гипоксии, а также для сердца контрольных особей. В транскриптоме, собранном из примерно 100 млн ридов, 81.5 % транскриптов были аннотированы как полные, 5.3 – как фрагментированные и 13.2 % – как отсутствующие. Мы обнаружили 59 078 известных транскриптов, которые были сгруппированы в 22251 ген, 11482 из них были отнесены к определенным категориям Gene Ontology. Среди них – 6696 генов, участвующих в белок-белковом взаимодействии, 3531 ген, кодирующий белок с каталитической функцией, и 576 генов, связанных с транспортной активностью. Для большинства транскриптов были установлены тканеспецифичные различия в экспрессии. Известно, что нейротрансмиттеры играют важную роль в ответе на гипоксию различных организмов, устойчивых к недостатку кислорода. Поиск генов, кодирующих рецепторы важнейших нейромедиаторов, которые могут участвовать в реакции на гипоксию, выявил набор экспрессируемых рецепторов дофамина, серотонина, гамма-аминомасляной кислоты (ГАМК), глутамата, ацетилхолина и норадреналина. При этом не обнаружено транскриптов для рецепторов гистамина. Данные, полученные в нашей работе, представляют собой ценный ресурс для исследования механизмов толерантности к гипоксии у сибирской лягушки, а также для изучения амфибий в целом

The Siberian wood frog Rana amurensis Boulenger, 1886 is the most hypoxia-tolerant amphibian. It can survive for several months in an almost complete absence of oxygen. Little is known about the mechanisms of this remarkable resilience, in part because studies of amphibian genomes are impeded by their large size. To make the Siberian wood frog more amenable for genetic analysis, we performed transcriptome sequencing and de novo assembly for the R. amurensis brain under hypoxia and normoxia, as well as for the normoxic heart. In order to build a de novo transcriptome assembly of R. amurensis, we utilized 125-bp paired-end reads obtained from the brain under normoxia and hypoxia conditions, and from the heart under normoxia. In the transcriptome assembled from about 100,000,000 reads, 81.5 % of transcripts were annotated as complete, 5.3 % as fragmented, and 13.2 % as missing. We detected 59,078 known transcripts that clustered into 22,251 genes; 11,482 of them were assigned to specific GO categories. Among them, we found 6696 genes involved in protein binding, 3531 genes involved in catalytic activity, and 576 genes associated with transporter activity. A search for genes encoding receptors of the most important neurotransmitters, which may participate in the response to hypoxia, resulted in a set of expressed receptors of dopamine, serotonin, GABA, glutamate, acetylcholine, and norepinephrine. Unexpectedly, no transcripts for histamine receptors were found. The data obtained in this study create a valuable resource for studying the mechanisms of hypoxia tolerance in the Siberian wood frog, as well as for amphibian studies in general.

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The authors declare that there are no conflicts of interest present.