African lungfish genome sheds light on the vertebrate water-to-land transition

Kun Wang; Jun Wang; Chenglong Zhu; Liandong Yang; Yandong Ren; Jue Ruan; Guangyi Fan; Jiang Hu; Wenjie Xu; Xupeng Bi; Youan Zhu; Yue Song; Huatao Chen; Tiantian Ma; Ruoping Zhao; Haifeng Jiang; Bin Zhang; Chenguang Feng; Yuan Yuan; Xiaoni Gan; Yongxin Li; Honghui Zeng; Qun Liu; Yaolei Zhang; Feng Shao; Shijie Hao; He Zhang; Xun Xu; Xin Liu; Depeng Wang; Min Zhu; Guojie Zhang; Wenming Zhao; Qiang Qiu; Shunping He; Wen Wang

doi:10.1016/j.cell.2021.01.047

African lungfish genome sheds light on the vertebrate water-to-land transition

Kun Wang, Jun Wang, Chenglong Zhu, Liandong Yang, Yandong Ren, Jue Ruan, Guangyi Fan, Jiang Hu, Wenjie Xu, Xupeng Bi, Youan Zhu, Yue Song, Huatao Chen, Tiantian Ma, Ruoping Zhao, Haifeng Jiang, Bin Zhang, Chenguang Feng, Yuan Yuan, Xiaoni GanYongxin Li, Honghui Zeng, Qun Liu, Yaolei Zhang, Feng Shao, Shijie Hao, He Zhang, Xun Xu, Xin Liu, Depeng Wang, Min Zhu, Guojie Zhang, Wenming Zhao, Qiang Qiu, Shunping He, Wen Wang

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

126 Scopus citations

Abstract

Lungfishes are the closest extant relatives of tetrapods and preserve ancestral traits linked with the water-to-land transition. However, their huge genome sizes have hindered understanding of this key transition in evolution. Here, we report a 40-Gb chromosome-level assembly of the African lungfish (Protopterus annectens) genome, which is the largest genome assembly ever reported and has a contig and chromosome N50 of 1.60 Mb and 2.81 Gb, respectively. The large size of the lungfish genome is due mainly to retrotransposons. Genes with ultra-long length show similar expression levels to other genes, indicating that lungfishes have evolved high transcription efficacy to keep gene expression balanced. Together with transcriptome and experimental data, we identified potential genes and regulatory elements related to such terrestrial adaptation traits as pulmonary surfactant, anxiolytic ability, pentadactyl limbs, and pharyngeal remodeling. Our results provide insights and key resources for understanding the evolutionary pathway leading from fishes to humans.

Original language	English
Pages (from-to)	1362-1376.e18
Journal	Cell
Volume	184
Issue number	5
DOIs	https://doi.org/10.1016/j.cell.2021.01.047
State	Published - 4 Mar 2021
Externally published	Yes

Keywords

aestivation
ancestral karyotype
anxiolytic ability
huge genome size
lungfishes
pentadactyl limbs
pharyngeal remodeling
pulmonary surfactant
water-to-land transition

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10.1016/j.cell.2021.01.047

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@article{3b94d59ceea9446da85a241ec29841fd,

title = "African lungfish genome sheds light on the vertebrate water-to-land transition",

abstract = "Lungfishes are the closest extant relatives of tetrapods and preserve ancestral traits linked with the water-to-land transition. However, their huge genome sizes have hindered understanding of this key transition in evolution. Here, we report a 40-Gb chromosome-level assembly of the African lungfish (Protopterus annectens) genome, which is the largest genome assembly ever reported and has a contig and chromosome N50 of 1.60 Mb and 2.81 Gb, respectively. The large size of the lungfish genome is due mainly to retrotransposons. Genes with ultra-long length show similar expression levels to other genes, indicating that lungfishes have evolved high transcription efficacy to keep gene expression balanced. Together with transcriptome and experimental data, we identified potential genes and regulatory elements related to such terrestrial adaptation traits as pulmonary surfactant, anxiolytic ability, pentadactyl limbs, and pharyngeal remodeling. Our results provide insights and key resources for understanding the evolutionary pathway leading from fishes to humans.",

keywords = "aestivation, ancestral karyotype, anxiolytic ability, huge genome size, lungfishes, pentadactyl limbs, pharyngeal remodeling, pulmonary surfactant, water-to-land transition",

author = "Kun Wang and Jun Wang and Chenglong Zhu and Liandong Yang and Yandong Ren and Jue Ruan and Guangyi Fan and Jiang Hu and Wenjie Xu and Xupeng Bi and Youan Zhu and Yue Song and Huatao Chen and Tiantian Ma and Ruoping Zhao and Haifeng Jiang and Bin Zhang and Chenguang Feng and Yuan Yuan and Xiaoni Gan and Yongxin Li and Honghui Zeng and Qun Liu and Yaolei Zhang and Feng Shao and Shijie Hao and He Zhang and Xun Xu and Xin Liu and Depeng Wang and Min Zhu and Guojie Zhang and Wenming Zhao and Qiang Qiu and Shunping He and Wen Wang",

note = "Publisher Copyright: {\textcopyright} 2021 Elsevier Inc.",

year = "2021",

month = mar,

day = "4",

doi = "10.1016/j.cell.2021.01.047",

language = "英语",

volume = "184",

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Wang, K, Wang, J, Zhu, C, Yang, L, Ren, Y, Ruan, J, Fan, G, Hu, J, Xu, W, Bi, X, Zhu, Y, Song, Y, Chen, H, Ma, T, Zhao, R, Jiang, H, Zhang, B, Feng, C, Yuan, Y, Gan, X, Li, Y, Zeng, H, Liu, Q, Zhang, Y, Shao, F, Hao, S, Zhang, H, Xu, X, Liu, X, Wang, D, Zhu, M, Zhang, G, Zhao, W, Qiu, Q, He, S & Wang, W 2021, 'African lungfish genome sheds light on the vertebrate water-to-land transition', Cell, vol. 184, no. 5, pp. 1362-1376.e18. https://doi.org/10.1016/j.cell.2021.01.047

TY - JOUR

T1 - African lungfish genome sheds light on the vertebrate water-to-land transition

AU - Wang, Kun

AU - Wang, Jun

AU - Zhu, Chenglong

AU - Yang, Liandong

AU - Ren, Yandong

AU - Ruan, Jue

AU - Fan, Guangyi

AU - Hu, Jiang

AU - Xu, Wenjie

AU - Bi, Xupeng

AU - Zhu, Youan

AU - Song, Yue

AU - Chen, Huatao

AU - Ma, Tiantian

AU - Zhao, Ruoping

AU - Jiang, Haifeng

AU - Zhang, Bin

AU - Feng, Chenguang

AU - Yuan, Yuan

AU - Gan, Xiaoni

AU - Li, Yongxin

AU - Zeng, Honghui

AU - Liu, Qun

AU - Zhang, Yaolei

AU - Shao, Feng

AU - Hao, Shijie

AU - Zhang, He

AU - Xu, Xun

AU - Liu, Xin

AU - Wang, Depeng

AU - Zhu, Min

AU - Zhang, Guojie

AU - Zhao, Wenming

AU - Qiu, Qiang

AU - He, Shunping

AU - Wang, Wen

PY - 2021/3/4

Y1 - 2021/3/4

N2 - Lungfishes are the closest extant relatives of tetrapods and preserve ancestral traits linked with the water-to-land transition. However, their huge genome sizes have hindered understanding of this key transition in evolution. Here, we report a 40-Gb chromosome-level assembly of the African lungfish (Protopterus annectens) genome, which is the largest genome assembly ever reported and has a contig and chromosome N50 of 1.60 Mb and 2.81 Gb, respectively. The large size of the lungfish genome is due mainly to retrotransposons. Genes with ultra-long length show similar expression levels to other genes, indicating that lungfishes have evolved high transcription efficacy to keep gene expression balanced. Together with transcriptome and experimental data, we identified potential genes and regulatory elements related to such terrestrial adaptation traits as pulmonary surfactant, anxiolytic ability, pentadactyl limbs, and pharyngeal remodeling. Our results provide insights and key resources for understanding the evolutionary pathway leading from fishes to humans.

AB - Lungfishes are the closest extant relatives of tetrapods and preserve ancestral traits linked with the water-to-land transition. However, their huge genome sizes have hindered understanding of this key transition in evolution. Here, we report a 40-Gb chromosome-level assembly of the African lungfish (Protopterus annectens) genome, which is the largest genome assembly ever reported and has a contig and chromosome N50 of 1.60 Mb and 2.81 Gb, respectively. The large size of the lungfish genome is due mainly to retrotransposons. Genes with ultra-long length show similar expression levels to other genes, indicating that lungfishes have evolved high transcription efficacy to keep gene expression balanced. Together with transcriptome and experimental data, we identified potential genes and regulatory elements related to such terrestrial adaptation traits as pulmonary surfactant, anxiolytic ability, pentadactyl limbs, and pharyngeal remodeling. Our results provide insights and key resources for understanding the evolutionary pathway leading from fishes to humans.

KW - aestivation

KW - ancestral karyotype

KW - anxiolytic ability

KW - huge genome size

KW - lungfishes

KW - pentadactyl limbs

KW - pharyngeal remodeling

KW - pulmonary surfactant

KW - water-to-land transition

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U2 - 10.1016/j.cell.2021.01.047

DO - 10.1016/j.cell.2021.01.047

M3 - 文章

C2 - 33545087

AN - SCOPUS:85100403772

SN - 0092-8674

VL - 184

SP - 1362-1376.e18

JO - Cell

JF - Cell

IS - 5

ER -

African lungfish genome sheds light on the vertebrate water-to-land transition

Abstract

Keywords

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