TY - JOUR

T1 - De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus

AU - Moskalev, Alexey A.

AU - Kudryavtseva, Anna V.

AU - Graphodatsky, Alexander S.

AU - Beklemisheva, Violetta R.

AU - Serdyukova, Natalya A.

AU - Krutovsky, Konstantin V.

AU - Sharov, Vadim V.

AU - Kulakovskiy, Ivan V.

AU - Lando, Andrey S.

AU - Kasianov, Artem S.

AU - Kuzmin, Dmitry A.

AU - Putintseva, Yuliya A.

AU - Feranchuk, Sergey I.

AU - Shaposhnikov, Mikhail V.

AU - Fraifeld, Vadim E.

AU - Toren, Dmitri

AU - Snezhkina, Anastasia V.

AU - Sitnik, Vasily V.

N1 - Publisher Copyright: © 2017 The Author(s).

PY - 2017/12/28

Y1 - 2017/12/28

N2 - 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.

AB - 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.

KW - DNA repair

KW - Eschrichtius robustus

KW - Genome

KW - Gray whale

KW - Hypoxia-response

KW - Transcriptome

KW - Gene Library

KW - Molecular Sequence Annotation

KW - Gene Expression Regulation

KW - Phylogeny

KW - Whales/genetics

KW - Transcriptome/genetics

KW - Animals

KW - PHYLOGENIES

KW - ANNOTATIONS

KW - MARINE MAMMALS

KW - EVOLUTION

KW - DATABASE

KW - FAMILIES

KW - SEQUENCE ALIGNMENTS

KW - KIDNEY

KW - BLAST

KW - PROGRAM

UR - http://www.scopus.com/inward/record.url?scp=85039740129&partnerID=8YFLogxK

U2 - 10.1186/s12862-017-1103-z

DO - 10.1186/s12862-017-1103-z

M3 - Article

C2 - 29297306

AN - SCOPUS:85039740129

VL - 17

SP - 258

JO - BMC Evolutionary Biology

JF - BMC Evolutionary Biology

SN - 1471-2148

IS - Suppl 2

M1 - 258

ER -