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

被引：10

作者：

Moskalev, Alexey A. ^{[1
,2
]}

Kudryavtseva, Anna V. ^{[1
]}

Graphodatsky, Alexander S. ^{[3
,4
]}

Beklemisheva, Violetta R. ^{[3
]}

Serdyukova, Natalya A. ^{[3
]}

Krutovsky, Konstantin V. ^{[5
,6
,7
,8
]}

Sharov, Vadim V. ^{[7
,9
]}

Kulakovskiy, Ivan V. ^{[1
,6
,10
]}

Lando, Andrey S. ^{[6
]}

Kasianov, Artem S. ^{[6
,10
]}

Kuzmin, Dmitry A. ^{[7
,9
]}

Putintseva, Yuliya A. ^{[7
]}

Feranchuk, Sergey I. ^{[7
,11
,12
]}

Shaposhnikov, Mikhail V. ^{[2
]}

Fraifeld, Vadim E. ^{[13
]}

Toren, Dmitri ^{[13
]}

Snezhkina, Anastasia V. ^{[1
]}

Sitnik, Vasily V. ^{[10
]}

机构：

[1] Russian Acad Sci, Engelhardt Inst Mol Biol, Moscow 119991, Russia

[2] RAS, Inst Biol, Komi Sci Ctr, Ural Branch, Syktyvkar 167982, Russia

[3] RAS, SB, Inst Mol & Cellular Biol, Novosibirsk 630090, Russia

[4] Novosibirsk State Univ, Novosibirsk 630090, Russia

[5] Georg August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, D-37077 Gottingen, Germany

[6] Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia

[7] Siberian Fed Univ, Genome Res & Educ Ctr, Krasnoyarsk 660036, Russia

[8] Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USA

[9] Siberian Fed Univ, Dept High Performance Comp, Inst Space & Informat Technol, Krasnoyarsk 660074, Russia

[10] Skolkovo Inst Sci & Technol, Ctr Data Intens Biomed & Biotechnol, Moscow 143026, Russia

[11] Irkutsk Natl Res Tech Univ, Irkutsk 664074, Russia

[12] Russian Acad Sci, Limnol Inst, Siberian Branch, Irkutsk 664033, Russia

[13] Ben Gurion Univ Negev, Shraga Segal Dept Microbiol Immunol & Genet, Fac Hlth Sci, Ctr Multidisciplinary Res Aging, IL-8410501 Beer Sheva, Israel

来源：

BMC EVOLUTIONARY BIOLOGY | 2017年 / 17卷

基金：

俄罗斯科学基金会;

关键词：

Gray whale; Eschrichtius robustus; Genome; Transcriptome; DNA repair; Hypoxia-response; SEQUENCE; EVOLUTION; ALIGNMENT; DATABASE; ANNOTATION; KIDNEY; BLAST;

D O I：

10.1186/s12862-017-1103-z

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：9

共 56 条

[11] The role of the kidney in blood volume regulation: The kidney as a regulator of the hematocrit [J].

Dunn, A. ;

Donnelly, S. .

AMERICAN JOURNAL OF THE MEDICAL SCIENCES, 2007, 334 (01) :65-71

[12] InterPro in 2017-beyond protein family and domain annotations [J].

Finn, Robert D. ;

Attwood, Teresa K. ;

Babbitt, Patricia C. ;

Bateman, Alex ;

Bork, Peer ;

Bridge, Alan J. ;

Chang, Hsin-Yu ;

Dosztanyi, Zsuzsanna ;

El-Gebali, Sara ;

Fraser, Matthew ;

Gough, Julian ;

Haft, David ;

Holliday, Gemma L. ;

Huang, Hongzhan ;

Huang, Xiaosong ;

Letunic, Ivica ;

Lopez, Rodrigo ;

Lu, Shennan ;

Marchler-Bauer, Aron ;

Mi, Huaiyu ;

Mistry, Jaina ;

Natale, Darren A. ;

Necci, Marco ;

Nuka, Gift ;

Orengo, Christine A. ;

Park, Youngmi ;

Pesseat, Sebastien ;

Piovesan, Damiano ;

Potter, Simon C. ;

Rawlings, Neil D. ;

Redaschi, Nicole ;

Richardson, Lorna ;

Rivoire, Catherine ;

Sangrador-Vegas, Amaia ;

Sigrist, Christian ;

Sillitoe, Ian ;

Smithers, Ben ;

Squizzato, Silvano ;

Sutton, Granger ;

Thanki, Narmada ;

Thomas, Paul D. ;

Tosatto, Silvio C. E. ;

Wu, Cathy H. ;

Xenarios, Ioannis ;

Yeh, Lai-Su ;

Young, Siew-Yit ;

Mitchell, Alex L. .

NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) :D190-D199

[13] The Pfam protein families database: towards a more sustainable future [J].

Finn, Robert D. ;

Coggill, Penelope ;

Eberhardt, Ruth Y. ;

Eddy, Sean R. ;

Mistry, Jaina ;

Mitchell, Alex L. ;

Potter, Simon C. ;

Punta, Marco ;

Qureshi, Matloob ;

Sangrador-Vegas, Amaia ;

Salazar, Gustavo A. ;

Tate, John ;

Bateman, Alex .

NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) :D279-D285

[14] Convergent evolution of the genomes of marine mammals [J].

Foote, Andrew D. ;

Liu, Yue ;

Thomas, Gregg W. C. ;

Vinar, Tomas ;

Alfoeldi, Jessica ;

Deng, Jixin ;

Dugan, Shannon ;

van Elk, Cornelis E. ;

Hunter, Margaret E. ;

Joshi, Vandita ;

Khan, Ziad ;

Kovar, Christie ;

Lee, Sandra L. ;

Lindblad-Toh, Kerstin ;

Mancia, Annalaura ;

Nielsen, Rasmus ;

Qin, Xiang ;

Qu, Jiaxin ;

Raney, Brian J. ;

Vijay, Nagarjun ;

Wolf, Jochen B. W. ;

Hahn, Matthew W. ;

Muzny, Donna M. ;

Worley, Kim C. ;

Gilbert, M. Thomas P. ;

Gibbs, Richard A. .

NATURE GENETICS, 2015, 47 (03) :272-+

[15]

Gregory T.R., 2005, ANIMAL GENOME SIZE D

[16] Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments [J].

Haas, Brian J. ;

Salzberg, Steven L. ;

Zhu, Wei ;

Pertea, Mihaela ;

Allen, Jonathan E. ;

Orvis, Joshua ;

White, Owen ;

Buell, C. Robin ;

Wortman, Jennifer R. .

GENOME BIOLOGY, 2008, 9 (01)

[17] De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis [J].

Haas, Brian J. ;

Papanicolaou, Alexie ;

Yassour, Moran ;

Grabherr, Manfred ;

Blood, Philip D. ;

Bowden, Joshua ;

Couger, Matthew Brian ;

Eccles, David ;

Li, Bo ;

Lieber, Matthias ;

MacManes, Matthew D. ;

Ott, Michael ;

Orvis, Joshua ;

Pochet, Nathalie ;

Strozzi, Francesco ;

Weeks, Nathan ;

Westerman, Rick ;

William, Thomas ;

Dewey, Colin N. ;

Henschel, Robert ;

Leduc, Richard D. ;

Friedman, Nir ;

Regev, Aviv .

NATURE PROTOCOLS, 2013, 8 (08) :1494-1512

[18] The Dfam database of repetitive DNA families [J].

Hubley, Robert ;

Finn, Robert D. ;

Clements, Jody ;

Eddy, Sean R. ;

Jones, Thomas A. ;

Bao, Weidong ;

Smit, Arian F. A. ;

Wheelers, Travis J. .

NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) :D81-D89

[19] eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences [J].

Huerta-Cepas, Jaime ;

Szklarczyk, Damian ;

Forslund, Kristoffer ;

Cook, Helen ;

Heller, Davide ;

Walter, Mathias C. ;

Rattei, Thomas ;

Mende, Daniel R. ;

Sunagawa, Shinichi ;

Kuhn, Michael ;

Jensen, Lars Juhl ;

von Mering, Christian ;

Bork, Peer .

NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) :D286-D293

[20]

Jones M.Lou., 1984, The gray whale Eschrichtius robustus

← 1 2 3 4 5 6 →