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

ABSTRACT: 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.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.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.

SUBMITTER: Moskalev A?

PROVIDER: S-EPMC5751776 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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

Moskalev Alexey А AА Kudryavtseva Anna V AV Graphodatsky Alexander S AS Beklemisheva Violetta R VR Serdyukova Natalya A NA Krutovsky Konstantin V KV Sharov Vadim V VV Kulakovskiy Ivan V IV Lando Andrey S AS Kasianov Artem S AS Kuzmin Dmitry A DA Putintseva Yuliya A YA Feranchuk Sergey I SI Shaposhnikov Mikhail V MV Fraifeld Vadim E VE Toren Dmitri D Snezhkina Anastasia V AV Sitnik Vasily V VV

BMC evolutionary biology 20171228 Suppl 2

<h4>Background</h4>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.<h4>Results</h4 ...[more]

PMID: 29297306

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Project description:Beginning in December 2018, increased numbers of gray whale (Eschrichtius robustus) strandings were reported along the west coast of Mexico, the United States, and Canada, prompting declaration of a gray whale Unusual Mortality Event (UME) by the United States National Marine Fisheries Service. Although strandings declined in 2020 and 2021 from a peak in 2019, the UME is still ongoing as of fall 2023. Between 17 December 2018 and 31 December 2021, 503 animals stranded along the west coast of North America, with 226 strandings in Mexico, 71 in California, 12 in Oregon, 56 in Washington, 21 in British Columbia, and 117 in Alaska. These included 187 males, 167 females, and 149 whales of undetermined sex; and 193 adults, 194 subadults, 40 calves, 1 fetus, and 75 whales of undetermined age class. We report on 61 of the 503 carcasses (12%) that had external and internal gross necropsy and/or histopathology data: of these 61 whales, findings that contributed to death were identified in 33 (54%) whales. Sixteen of the 61 (26%) were severely emaciated. Gross lesions of blunt force trauma consistent with vessel strike were identified in 11 of the 61 animals (18%), only two of which were emaciated. Two whales (3%) were entangled at time of death, and one died from entrapment. Signs of killer whale (Orcinus orca) interaction were documented in 19 of the 61 animals; five were deemed from recent interactions and three (5%) likely contributed to mortality. A specific cause of death could not be identified in 28 of 61 whales (46%). Additionally, logistical challenges and the advanced state of decomposition of most examined carcasses precluded detection of potential infectious or toxic causes of morbidity or mortality. Up to 2016, the eastern North Pacific population of gray whale population had generally been increasing since the cessation of historic whaling and a prior UME in 1999-2000. However, recent abundance and calf production estimates have declined, a trend that overlaps the current UME. The relative contributions of carrying capacity, environmental change, prey shifts, and infectious, toxic, and other processes to the increased gray whale mortalities have not yet been resolved. Nevertheless, the marked temporal increase in strandings, including findings of malnutrition in some of the whales, along with low calf production, likely represent consequences of complex and dynamic ecological interactions in the ocean impacting the population.

Dataset Information

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

Publications

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

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