Research output: Contribution to journal › Article › peer-review
De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus. / Moskalev, Alexey A.; Kudryavtseva, Anna V.; Graphodatsky, Alexander S. et al.
In: BMC Evolutionary Biology, Vol. 17, No. Suppl 2, 258, 28.12.2017, p. 258.Research output: Contribution to journal › Article › peer-review
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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 -
ID: 10521999