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
Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.
Institute of the Biological Problems of the North of the Far-Eastern Branch of the Russian Academy of Sciences, Magadan, Russia.
Vavilovskii Zhurnal Genet Selektsii. 2022 Feb;26(1):109-116. doi: 10.18699/VJGB-22-07.
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.
西伯利亚林蛙（Rana amurensis Boulenger，1886）是最耐缺氧的两栖动物。它能在几乎完全缺氧的环境中存活数月。对于这种非凡恢复力的机制我们知之甚少，部分原因是两栖动物基因组规模庞大，阻碍了相关研究。为了使西伯利亚林蛙更便于进行遗传分析，我们对处于缺氧和常氧状态下的黑龙江林蛙脑部以及常氧状态下的心脏进行了转录组测序和从头组装。为了构建黑龙江林蛙的从头转录组组装，我们利用了在常氧和缺氧条件下从脑部以及常氧状态下从心脏获得的125碱基对的双末端 reads。在由约1亿条 reads 组装而成的转录组中，81.5%的转录本被注释为完整，5.3%为片段化，13.2%为缺失。我们检测到59,078个已知转录本，它们聚集成22,251个基因；其中11,482个被分配到特定的基因本体（GO）类别。在这些基因中，我们发现6696个基因参与蛋白质结合，3531个基因参与催化活性，576个基因与转运活性相关。对可能参与缺氧反应的最重要神经递质受体编码基因的搜索，得到了一组表达的多巴胺、5-羟色胺、γ-氨基丁酸、谷氨酸、乙酰胆碱和去甲肾上腺素受体。出乎意料的是，未发现组胺受体的转录本。本研究获得的数据为研究西伯利亚林蛙的缺氧耐受机制以及一般两栖动物研究创造了宝贵资源。
