灰鲸（Eschrichtius robustus）基因组和转录组的从头组装与初步分析。
De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus.
作者信息
Moskalev Alexey А, Kudryavtseva Anna V, Graphodatsky Alexander S, Beklemisheva Violetta R, Serdyukova Natalya A, Krutovsky Konstantin V, Sharov Vadim V, Kulakovskiy Ivan V, Lando Andrey S, Kasianov Artem S, Kuzmin Dmitry A, Putintseva Yuliya A, Feranchuk Sergey I, Shaposhnikov Mikhail V, Fraifeld Vadim E, Toren Dmitri, Snezhkina Anastasia V, Sitnik Vasily V
机构信息
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation.
Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, 167982, Russian Federation.
出版信息
BMC Evol Biol. 2017 Dec 28;17(Suppl 2):258. doi: 10.1186/s12862-017-1103-z.
BACKGROUND
Gray whale, Eschrichtius robustus (E. robustus), is a single member of the family Eschrichtiidae, which is considered to be the most primitive in the class Cetacea. Gray whale is often described as a "living fossil". It is adapted to extreme marine conditions and has a high life expectancy (77 years). The assembly of a gray whale genome and transcriptome will allow to carry out further studies of whale evolution, longevity, and resistance to extreme environment.
RESULTS
In this work, we report the first de novo assembly and primary analysis of the E. robustus genome and transcriptome based on kidney and liver samples. The presented draft genome assembly is complete by 55% in terms of a total genome length, but only by 24% in terms of the BUSCO complete gene groups, although 10,895 genes were identified. Transcriptome annotation and comparison with other whale species revealed robust expression of DNA repair and hypoxia-response genes, which is expected for whales.
CONCLUSIONS
This preliminary study of the gray whale genome and transcriptome provides new data to better understand the whale evolution and the mechanisms of their adaptation to the hypoxic conditions.
背景
灰鲸（Eschrichtius robustus，E. robustus）是灰鲸科的唯一成员，被认为是鲸目动物中最原始的。灰鲸常被描述为“活化石”。它适应极端的海洋环境，寿命较长（77岁）。灰鲸基因组和转录组的组装将有助于进一步开展关于鲸鱼进化、寿命以及对极端环境抵抗力的研究。
结果
在这项工作中，我们报告了基于肾脏和肝脏样本对E. robustus基因组和转录组进行的首次从头组装及初步分析。所呈现的基因组组装草图在总基因组长度方面完成了55%，但在BUSCO完整基因组方面仅完成了24%，不过已鉴定出10,895个基因。转录组注释以及与其他鲸鱼物种的比较揭示了DNA修复和低氧反应基因的强烈表达，这在鲸鱼中是预期的。
结论
这项对灰鲸基因组和转录组的初步研究提供了新的数据，以更好地理解鲸鱼进化及其适应低氧条件的机制。
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