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

Тип публикации: статья из журнала

Год издания: 2017

Идентификатор DOI: 10.1186/s12862-017-1103-z

Ключевые слова: DNA repair, Eschrichtius robustus, Genome, Gray whale, Hypoxia-response, Transcriptome

Аннотация: 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. © 2017 The Author(s).

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Издание

Журнал: BMC Evolutionary Biology

Выпуск журнала: Vol. 17

ISSN журнала: 14712148

Издатель: BioMed Central Ltd.

Авторы

  • Moskalev A.A. (Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation, Institute of Biology of Komi Science, Center of Ural Branch, RAS, Syktyvkar, Russian Federation)
  • Kudryavtseva A.V. (Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation)
  • Graphodatsky A.S. (Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation, Novosibirsk State University, Novosibirsk, Russian Federation)
  • Beklemisheva V.R. (Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation)
  • Serdyukova N.A. (Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russian Federation)
  • Krutovsky K.V. (Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, Germany, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation, Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, Russian Federation, Department of Ecosystem Science and Management, Texas A and M University, College Station, TX, United States)
  • Sharov V.V. (Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, Russian Federation, Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, Russian Federation)
  • Kulakovskiy I.V. (Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation, Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russian Federation)
  • Lando A.S. (Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation)
  • Kasianov A.S. (Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation, Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russian Federation)
  • Kuzmin D.A. (Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, Russian Federation, Department of High Performance Computing, Institute of Space and Information Technologies, Siberian Federal University, Krasnoyarsk, Russian Federation)
  • Putintseva Y.A. (Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, Russian Federation)
  • Feranchuk S.I. (Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, Russian Federation, Irkutsk National Research Technical University, Irkutsk, Russian Federation, Limnological Institute, Siberian Branch, Russian Academy of Sciences, Irkutsk, Russian Federation)
  • Shaposhnikov M.V. (Institute of Biology of Komi Science, Center of Ural Branch, RAS, Syktyvkar, Russian Federation)
  • Fraifeld V.E. (Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, Israel)
  • Toren D. (Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, Israel)
  • Snezhkina A.V. (Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation)
  • Sitnik V.V. (Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russian Federation)

Вхождение в базы данных

  • Scopus (цитирований 2)
  • eLIBRARY.RU (цитирований 1)
  • Web of Science

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