De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus

BMC Evolutionary Biology

Research

Vasily V. Sitnik¹  Konstantin V. Krutovsky²  Anastasia V. Snezhkina³  Anna V. Kudryavtseva³  Alexey А. Moskalev⁴  Ivan V. Kulakovskiy⁵  Yuliya A. Putintseva⁶  Vadim V. Sharov⁷  Dmitry A. Kuzmin⁷  Sergey I. Feranchuk⁸  Mikhail V. Shaposhnikov⁹  Violetta R. Beklemisheva^1,10  Natalya A. Serdyukova^1,10  Alexander S. Graphodatsky^1,11  Dmitri Toren^1,12  Vadim E. Fraifeld^1,12  Andrey S. Lando^1,13  Artem S. Kasianov^1,14 

[1] Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, 143026, Moscow, Russia;Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077, Göttingen, Germany;Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russian Federation;Genome Research and Education Center, Siberian Federal University, 660036, Krasnoyarsk, Russian Federation;Department of Ecosystem Science and Management, Texas A&M University, 77843-2138, College Station, TX, USA;Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russian Federation;Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russian Federation;Institute of Biology of Komi Science Center of Ural Branch of RAS, 167982, Syktyvkar, Russian Federation;Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russian Federation;Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russian Federation;Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, 143026, Moscow, Russia;Genome Research and Education Center, Siberian Federal University, 660036, Krasnoyarsk, Russian Federation;Genome Research and Education Center, Siberian Federal University, 660036, Krasnoyarsk, Russian Federation;Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, 660074, Krasnoyarsk, Russian Federation;Genome Research and Education Center, Siberian Federal University, 660036, Krasnoyarsk, Russian Federation;Irkutsk National Research Technical University, 664074, Irkutsk, Russian Federation;Limnological Institute, Siberian Branch of Russian Academy of Sciences, 664033, Irkutsk, Russian Federation;Institute of Biology of Komi Science Center of Ural Branch of RAS, 167982, Syktyvkar, Russian Federation;Institute of Molecular and Cellular Biology SB RAS, 630090, Novosibirsk, Russian Federation;Institute of Molecular and Cellular Biology SB RAS, 630090, Novosibirsk, Russian Federation;Novosibirsk State University, 630090, Novosibirsk, Russian Federation;The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel;Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russian Federation;Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russian Federation;Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, 143026, Moscow, Russia;

关键词: Gray whale;    Eschrichtius robustus;    Genome;    Transcriptome;    DNA repair;    Hypoxia-response;   

DOI  :  10.1186/s12862-017-1103-z

来源: Springer

【 摘 要 】

BackgroundGray 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.ResultsIn 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.ConclusionsThis 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.

【 授权许可】

CC BY   
© The Author(s). 2017