Minke whale genome and aquatic adaptation in cetaceans

Hyung Soon Yim; Yun Sung Cho; Xuanmin Guang; Sung Gyun Kang; Jae Yeon Jeong; Sun Shin Cha; Hyun Myung Oh; Jae Hak Lee; Eun Chan Yang; Kae Kyoung Kwon; Yun Jae Kim; Tae Wan Kim; Wonduck Kim; Jeong Ho Jeon; Sang Jin Kim; Dong Han Choi; Sungwoong Jho; Hak Min Kim; Junsu Ko; Hyunmin Kim; Young Ah Shin; Hyun Ju Jung; Yuan Zheng; Zhuo Wang; Yan Chen; Ming Chen; Awei Jiang; Erli Li; Shu Zhang; Haolong Hou; Tae Hyung Kim; Lili Yu; Sha Liu; Kung Ahn; Jesse Cooper; Sin Gi Park; Chang Pyo Hong; Wook Jin; Heui Soo Kim; Chankyu Park; Kyooyeol Lee; Sung Chun; Phillip A. Morin; Stephen J. O'Brien; Hang Lee; Jumpei Kimura; Dae Yeon Moon; Andrea Manica; Jeremy Edwards; Byung Chul Kim; Sangsoo Kim; Jun Wang; Jong Bhak; Hyun Sook Lee; Jung Hyun Lee

doi:10.1038/ng.2835

Minke whale genome and aquatic adaptation in cetaceans

Hyung Soon Yim, Yun Sung Cho, Xuanmin Guang, Sung Gyun Kang, Jae Yeon Jeong, Sun Shin Cha, Hyun Myung Oh, Jae Hak Lee, Eun Chan Yang, Kae Kyoung Kwon, Yun Jae Kim, Tae Wan Kim, Wonduck Kim, Jeong Ho Jeon, Sang Jin Kim, Dong Han Choi, Sungwoong Jho, Hak Min Kim, Junsu Ko, Hyunmin KimYoung Ah Shin, Hyun Ju Jung, Yuan Zheng, Zhuo Wang, Yan Chen, Ming Chen, Awei Jiang, Erli Li, Shu Zhang, Haolong Hou, Tae Hyung Kim, Lili Yu, Sha Liu, Kung Ahn, Jesse Cooper, Sin Gi Park, Chang Pyo Hong, Wook Jin, Heui Soo Kim, Chankyu Park, Kyooyeol Lee, Sung Chun, Phillip A. Morin, Stephen J. O'Brien, Hang Lee, Jumpei Kimura, Dae Yeon Moon, Andrea Manica, Jeremy Edwards, Byung Chul Kim, Sangsoo Kim, Jun Wang, Jong Bhak, Hyun Sook Lee, Jung Hyun Lee

Chemistry & Nanoscience

Research output: Contribution to journal › Article › peer-review

182 Scopus citations

Abstract

The shift from terrestrial to aquatic life by whales was a substantial evolutionary event. Here we report the whole-genome sequencing and de novo assembly of the minke whale genome, as well as the whole-genome sequences of three minke whales, a fin whale, a bottlenose dolphin and a finless porpoise. Our comparative genomic analysis identified an expansion in the whale lineage of gene families associated with stress-responsive proteins and anaerobic metabolism, whereas gene families related to body hair and sensory receptors were contracted. Our analysis also identified whale-specific mutations in genes encoding antioxidants and enzymes controlling blood pressure and salt concentration. Overall the whale-genome sequences exhibited distinct features that are associated with the physiological and morphological changes needed for life in an aquatic environment, marked by resistance to physiological stresses caused by a lack of oxygen, increased amounts of reactive oxygen species and high salt levels.

Original language	English
Pages (from-to)	88-92
Number of pages	5
Journal	Nature Genetics
Volume	46
Issue number	1
DOIs	https://doi.org/10.1038/ng.2835
State	Published - Jan 2014

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@article{eb131069b1504494a7ac76eec3e36b72,

title = "Minke whale genome and aquatic adaptation in cetaceans",

abstract = "The shift from terrestrial to aquatic life by whales was a substantial evolutionary event. Here we report the whole-genome sequencing and de novo assembly of the minke whale genome, as well as the whole-genome sequences of three minke whales, a fin whale, a bottlenose dolphin and a finless porpoise. Our comparative genomic analysis identified an expansion in the whale lineage of gene families associated with stress-responsive proteins and anaerobic metabolism, whereas gene families related to body hair and sensory receptors were contracted. Our analysis also identified whale-specific mutations in genes encoding antioxidants and enzymes controlling blood pressure and salt concentration. Overall the whale-genome sequences exhibited distinct features that are associated with the physiological and morphological changes needed for life in an aquatic environment, marked by resistance to physiological stresses caused by a lack of oxygen, increased amounts of reactive oxygen species and high salt levels.",

author = "Yim, {Hyung Soon} and Cho, {Yun Sung} and Xuanmin Guang and Kang, {Sung Gyun} and Jeong, {Jae Yeon} and Cha, {Sun Shin} and Oh, {Hyun Myung} and Lee, {Jae Hak} and Yang, {Eun Chan} and Kwon, {Kae Kyoung} and Kim, {Yun Jae} and Kim, {Tae Wan} and Wonduck Kim and Jeon, {Jeong Ho} and Kim, {Sang Jin} and Choi, {Dong Han} and Sungwoong Jho and Kim, {Hak Min} and Junsu Ko and Hyunmin Kim and Shin, {Young Ah} and Jung, {Hyun Ju} and Yuan Zheng and Zhuo Wang and Yan Chen and Ming Chen and Awei Jiang and Erli Li and Shu Zhang and Haolong Hou and Kim, {Tae Hyung} and Lili Yu and Sha Liu and Kung Ahn and Jesse Cooper and Park, {Sin Gi} and Hong, {Chang Pyo} and Wook Jin and Kim, {Heui Soo} and Chankyu Park and Kyooyeol Lee and Sung Chun and Morin, {Phillip A.} and O'Brien, {Stephen J.} and Hang Lee and Jumpei Kimura and Moon, {Dae Yeon} and Andrea Manica and Jeremy Edwards and Kim, {Byung Chul} and Sangsoo Kim and Jun Wang and Jong Bhak and Lee, {Hyun Sook} and Lee, {Jung Hyun}",

note = "Funding Information: No animals were killed or captured as a result of these studies. Samples of four minke whales and a finless porpoise for sequencing were acquired from the east coast of Korea after they were accidently killed and investigated by the maritime police. The sample from a bottlenose dolphin was obtained from Marine Park in Jeju Island, Korea. The fin whale sample was collected from a dead stranded fin whale by the Southwest Fisheries Science Center (SWFSC 134239) under US Marine Mammal Permit 14097-01, and the sample was transported internationally under a Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) permit. We thank C.-W. Kim (Marine Park Co., Ltd.) and Y.-R. An (Cetacean Research Institute) for the bottlenose dolphin and minke whale samples, respectively. We also thank M. Bhak for editing. We thank many people not listed as authors who provided feedback, samples and encouragement, especially the Cetacean Research Institute in Ulsan, Korea. This work was supported by the Korea Institute of Ocean Science and Technology (KIOST) in-house program (PE98993), the Marine and Extreme Genome Research Center program of the Ministry of Oceans and Fisheries, Korea. This work was also supported by the Industrial Strategic Technology Development Program 10040231,",

year = "2014",

month = jan,

doi = "10.1038/ng.2835",

language = "English",

volume = "46",

pages = "88--92",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

number = "1",

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Yim, HS, Cho, YS, Guang, X, Kang, SG, Jeong, JY, Cha, SS, Oh, HM, Lee, JH, Yang, EC, Kwon, KK, Kim, YJ, Kim, TW, Kim, W, Jeon, JH, Kim, SJ, Choi, DH, Jho, S, Kim, HM, Ko, J, Kim, H, Shin, YA, Jung, HJ, Zheng, Y, Wang, Z, Chen, Y, Chen, M, Jiang, A, Li, E, Zhang, S, Hou, H, Kim, TH, Yu, L, Liu, S, Ahn, K, Cooper, J, Park, SG, Hong, CP, Jin, W, Kim, HS, Park, C, Lee, K, Chun, S, Morin, PA, O'Brien, SJ, Lee, H, Kimura, J, Moon, DY, Manica, A, Edwards, J, Kim, BC, Kim, S, Wang, J, Bhak, J, Lee, HS & Lee, JH 2014, 'Minke whale genome and aquatic adaptation in cetaceans', Nature Genetics, vol. 46, no. 1, pp. 88-92. https://doi.org/10.1038/ng.2835

TY - JOUR

T1 - Minke whale genome and aquatic adaptation in cetaceans

AU - Yim, Hyung Soon

AU - Cho, Yun Sung

AU - Guang, Xuanmin

AU - Kang, Sung Gyun

AU - Jeong, Jae Yeon

AU - Cha, Sun Shin

AU - Oh, Hyun Myung

AU - Lee, Jae Hak

AU - Yang, Eun Chan

AU - Kwon, Kae Kyoung

AU - Kim, Yun Jae

AU - Kim, Tae Wan

AU - Kim, Wonduck

AU - Jeon, Jeong Ho

AU - Kim, Sang Jin

AU - Choi, Dong Han

AU - Jho, Sungwoong

AU - Kim, Hak Min

AU - Ko, Junsu

AU - Kim, Hyunmin

AU - Shin, Young Ah

AU - Jung, Hyun Ju

AU - Zheng, Yuan

AU - Wang, Zhuo

AU - Chen, Yan

AU - Chen, Ming

AU - Jiang, Awei

AU - Li, Erli

AU - Zhang, Shu

AU - Hou, Haolong

AU - Kim, Tae Hyung

AU - Yu, Lili

AU - Liu, Sha

AU - Ahn, Kung

AU - Cooper, Jesse

AU - Park, Sin Gi

AU - Hong, Chang Pyo

AU - Jin, Wook

AU - Kim, Heui Soo

AU - Park, Chankyu

AU - Lee, Kyooyeol

AU - Chun, Sung

AU - Morin, Phillip A.

AU - O'Brien, Stephen J.

AU - Lee, Hang

AU - Kimura, Jumpei

AU - Moon, Dae Yeon

AU - Manica, Andrea

AU - Edwards, Jeremy

AU - Kim, Byung Chul

AU - Kim, Sangsoo

AU - Wang, Jun

AU - Bhak, Jong

AU - Lee, Hyun Sook

AU - Lee, Jung Hyun

N1 - Funding Information: No animals were killed or captured as a result of these studies. Samples of four minke whales and a finless porpoise for sequencing were acquired from the east coast of Korea after they were accidently killed and investigated by the maritime police. The sample from a bottlenose dolphin was obtained from Marine Park in Jeju Island, Korea. The fin whale sample was collected from a dead stranded fin whale by the Southwest Fisheries Science Center (SWFSC 134239) under US Marine Mammal Permit 14097-01, and the sample was transported internationally under a Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) permit. We thank C.-W. Kim (Marine Park Co., Ltd.) and Y.-R. An (Cetacean Research Institute) for the bottlenose dolphin and minke whale samples, respectively. We also thank M. Bhak for editing. We thank many people not listed as authors who provided feedback, samples and encouragement, especially the Cetacean Research Institute in Ulsan, Korea. This work was supported by the Korea Institute of Ocean Science and Technology (KIOST) in-house program (PE98993), the Marine and Extreme Genome Research Center program of the Ministry of Oceans and Fisheries, Korea. This work was also supported by the Industrial Strategic Technology Development Program 10040231,

PY - 2014/1

Y1 - 2014/1

N2 - The shift from terrestrial to aquatic life by whales was a substantial evolutionary event. Here we report the whole-genome sequencing and de novo assembly of the minke whale genome, as well as the whole-genome sequences of three minke whales, a fin whale, a bottlenose dolphin and a finless porpoise. Our comparative genomic analysis identified an expansion in the whale lineage of gene families associated with stress-responsive proteins and anaerobic metabolism, whereas gene families related to body hair and sensory receptors were contracted. Our analysis also identified whale-specific mutations in genes encoding antioxidants and enzymes controlling blood pressure and salt concentration. Overall the whale-genome sequences exhibited distinct features that are associated with the physiological and morphological changes needed for life in an aquatic environment, marked by resistance to physiological stresses caused by a lack of oxygen, increased amounts of reactive oxygen species and high salt levels.

AB - The shift from terrestrial to aquatic life by whales was a substantial evolutionary event. Here we report the whole-genome sequencing and de novo assembly of the minke whale genome, as well as the whole-genome sequences of three minke whales, a fin whale, a bottlenose dolphin and a finless porpoise. Our comparative genomic analysis identified an expansion in the whale lineage of gene families associated with stress-responsive proteins and anaerobic metabolism, whereas gene families related to body hair and sensory receptors were contracted. Our analysis also identified whale-specific mutations in genes encoding antioxidants and enzymes controlling blood pressure and salt concentration. Overall the whale-genome sequences exhibited distinct features that are associated with the physiological and morphological changes needed for life in an aquatic environment, marked by resistance to physiological stresses caused by a lack of oxygen, increased amounts of reactive oxygen species and high salt levels.

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Minke whale genome and aquatic adaptation in cetaceans

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