Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

Xiaojun Zhang; Jianbo Yuan; Yamin Sun; Shihao Li; Yi Gao; Yang Yu; Chengzhang Liu; Quanchao Wang; Xinjia Lv; Xiaoxi Zhang; Ka Yan Ma; Xiaobo Wang; Wenchao Lin; Long Wang; Xueli Zhu; Chengsong Zhang; Jiquan Zhang; Songjun Jin; Kuijie Yu; Jie Kong; Peng Xu; Jack Chen; Hongbin Zhang; Patrick Sorgeloos; Amir Sagi; Acacia Alcivar-Warren; Zhanjiang Liu; Lei Wang; Jue Ruan; Ka Hou Chu; Bin Liu; Fuhua Li; Jianhai Xiang

doi:10.1038/s41467-018-08197-4

Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

Xiaojun Zhang, Jianbo Yuan, Yamin Sun, Shihao Li, Yi Gao, Yang Yu, Chengzhang Liu, Quanchao Wang, Xinjia Lv, Xiaoxi Zhang, Ka Yan Ma, Xiaobo Wang, Wenchao Lin, Long Wang, Xueli Zhu, Chengsong Zhang, Jiquan Zhang, Songjun Jin, Kuijie Yu, Jie KongPeng Xu, Jack Chen, Hongbin Zhang, Patrick Sorgeloos, Amir Sagi, Acacia Alcivar-Warren, Zhanjiang Liu, Lei Wang, Jue Ruan, Ka Hou Chu, Bin Liu, Fuhua Li, Jianhai Xiang

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

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Abstract

Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture.

Original language	English (US)
Article number	356
Journal	Nature Communications
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-08197-4
State	Published - Dec 1 2019
Externally published	Yes

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
General
Physics and Astronomy(all)

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Zhang, X, Yuan, J, Sun, Y, Li, S, Gao, Y, Yu, Y, Liu, C, Wang, Q, Lv, X, Zhang, X, Ma, KY, Wang, X, Lin, W, Wang, L, Zhu, X, Zhang, C, Zhang, J, Jin, S, Yu, K, Kong, J, Xu, P, Chen, J, Zhang, H, Sorgeloos, P, Sagi, A, Alcivar-Warren, A, Liu, Z, Wang, L, Ruan, J, Chu, KH, Liu, B, Li, F & Xiang, J 2019, 'Penaeid shrimp genome provides insights into benthic adaptation and frequent molting', Nature Communications, vol. 10, no. 1, 356. https://doi.org/10.1038/s41467-018-08197-4

@article{c12ec118c0cc4d0ab207d8b8f04cfcb2,

title = "Penaeid shrimp genome provides insights into benthic adaptation and frequent molting",

abstract = "Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture.",

author = "Xiaojun Zhang and Jianbo Yuan and Yamin Sun and Shihao Li and Yi Gao and Yang Yu and Chengzhang Liu and Quanchao Wang and Xinjia Lv and Xiaoxi Zhang and Ma, {Ka Yan} and Xiaobo Wang and Wenchao Lin and Long Wang and Xueli Zhu and Chengsong Zhang and Jiquan Zhang and Songjun Jin and Kuijie Yu and Jie Kong and Peng Xu and Jack Chen and Hongbin Zhang and Patrick Sorgeloos and Amir Sagi and Acacia Alcivar-Warren and Zhanjiang Liu and Lei Wang and Jue Ruan and Chu, {Ka Hou} and Bin Liu and Fuhua Li and Jianhai Xiang",

note = "Funding Information: We acknowledge financial support from the State 863 High Technology R&D Project of China (2012AA10A404 to J.X.), the National Natural Science Foundation of China (31830100 to F.L. and 41876167 to J.Y.), the grants from Qingdao National Laboratory for Marine Science and Technology (MS2017NO04 to F.L.), The Senior User Project of RV KEXUE (KEXUE2018G19 to F.L. and X.Z.), the China Agriculture Research system-48 (CARS-48 to F.L.) and the Hong Kong Collaborative Research Fund (CRF) project (No. C4042-14G to K.H.C). We acknowledge the support from High Performance Computing Center, Institute of Oceanology, CAS. We would like to express our gratitude to Prof. Jun Yu, Prof. Songnian Hu, Prof. Jingfa Xiao and Dr. Tongwu Zhang (Beijing Institute of Genomics, Chinese Academy of Sciences), Prof. Ximing Guo (Rutgers University), Dr. Ruiqiang Li, Dr. Zhi Jiang and Dr. Jinbo Zhang (Novogene Bioinformatics Institute), Dr. Junyi Wang and Dr. Dongliang Zhan (Hangzhou 1Gene Ltd), for their support of the shrimp genome project, genome sequencing and assembly. We appreciate Dr. Hao Huang (Hainan Guangtai Ocean Breeding Co., Ltd) for the help with shrimp materials and Dr. Yang Zhang and Dr. Han Cao (Bionano Genomics) help for the construction of optical map. We thank Cui Zhao, Jiankai Wei, Xiaoqing Sun, Jingwen Liu, Jiangli Du, Mingzhe Sun and Yan Zhang for help with DNA, RNA extraction, and data analysis. We are grateful to Prof. Li Sun, Prof. Linsheng Song, Prof. Jinsheng Sun, Prof. Zhaoxia Cui, Prof. Baozhong Liu and Dr. Pin Huan for helpful discussions. We thank other faculty and staff at the Institute of Oceanology, Chinese Academy of Science who contributed to the shrimp genome project. We thank Dr. Jing Qin for revisions of the manuscript. We appreciate Mr. Huawei Zhang for shrimp photography. Publisher Copyright: {\textcopyright} 2019, The Author(s).",

year = "2019",

month = dec,

day = "1",

doi = "10.1038/s41467-018-08197-4",

language = "English (US)",

volume = "10",

journal = "Nature Communications",

issn = "2041-1723",

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TY - JOUR

T1 - Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

AU - Zhang, Xiaojun

AU - Yuan, Jianbo

AU - Sun, Yamin

AU - Li, Shihao

AU - Gao, Yi

AU - Yu, Yang

AU - Liu, Chengzhang

AU - Wang, Quanchao

AU - Lv, Xinjia

AU - Zhang, Xiaoxi

AU - Ma, Ka Yan

AU - Wang, Xiaobo

AU - Lin, Wenchao

AU - Wang, Long

AU - Zhu, Xueli

AU - Zhang, Chengsong

AU - Zhang, Jiquan

AU - Jin, Songjun

AU - Yu, Kuijie

AU - Kong, Jie

AU - Xu, Peng

AU - Chen, Jack

AU - Zhang, Hongbin

AU - Sorgeloos, Patrick

AU - Sagi, Amir

AU - Alcivar-Warren, Acacia

AU - Liu, Zhanjiang

AU - Wang, Lei

AU - Ruan, Jue

AU - Chu, Ka Hou

AU - Liu, Bin

AU - Li, Fuhua

AU - Xiang, Jianhai

N1 - Funding Information: We acknowledge financial support from the State 863 High Technology R&D Project of China (2012AA10A404 to J.X.), the National Natural Science Foundation of China (31830100 to F.L. and 41876167 to J.Y.), the grants from Qingdao National Laboratory for Marine Science and Technology (MS2017NO04 to F.L.), The Senior User Project of RV KEXUE (KEXUE2018G19 to F.L. and X.Z.), the China Agriculture Research system-48 (CARS-48 to F.L.) and the Hong Kong Collaborative Research Fund (CRF) project (No. C4042-14G to K.H.C). We acknowledge the support from High Performance Computing Center, Institute of Oceanology, CAS. We would like to express our gratitude to Prof. Jun Yu, Prof. Songnian Hu, Prof. Jingfa Xiao and Dr. Tongwu Zhang (Beijing Institute of Genomics, Chinese Academy of Sciences), Prof. Ximing Guo (Rutgers University), Dr. Ruiqiang Li, Dr. Zhi Jiang and Dr. Jinbo Zhang (Novogene Bioinformatics Institute), Dr. Junyi Wang and Dr. Dongliang Zhan (Hangzhou 1Gene Ltd), for their support of the shrimp genome project, genome sequencing and assembly. We appreciate Dr. Hao Huang (Hainan Guangtai Ocean Breeding Co., Ltd) for the help with shrimp materials and Dr. Yang Zhang and Dr. Han Cao (Bionano Genomics) help for the construction of optical map. We thank Cui Zhao, Jiankai Wei, Xiaoqing Sun, Jingwen Liu, Jiangli Du, Mingzhe Sun and Yan Zhang for help with DNA, RNA extraction, and data analysis. We are grateful to Prof. Li Sun, Prof. Linsheng Song, Prof. Jinsheng Sun, Prof. Zhaoxia Cui, Prof. Baozhong Liu and Dr. Pin Huan for helpful discussions. We thank other faculty and staff at the Institute of Oceanology, Chinese Academy of Science who contributed to the shrimp genome project. We thank Dr. Jing Qin for revisions of the manuscript. We appreciate Mr. Huawei Zhang for shrimp photography. Publisher Copyright: © 2019, The Author(s).

PY - 2019/12/1

Y1 - 2019/12/1

N2 - Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture.

AB - Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering ~1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture.

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DO - 10.1038/s41467-018-08197-4

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VL - 10

JO - Nature Communications

JF - Nature Communications

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ER -

Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

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