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Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)

BACKGROUND: The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking. FINDINGS: He...

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Autores principales: Tang, Boping, Zhang, Daizhen, Li, Haorong, Jiang, Senhao, Zhang, Huabin, Xuan, Fujun, Ge, Baoming, Wang, Zhengfei, Liu, Yu, Sha, Zhongli, Cheng, Yongxu, Jiang, Wei, Jiang, Hui, Wang, Zhongkai, Wang, Kun, Li, Chaofeng, Sun, Yue, She, Shusheng, Qiu, Qiang, Wang, Wen, Li, Xinzheng, Li, Yongxin, Liu, Qiuning, Ren, Yandong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944217/
https://www.ncbi.nlm.nih.gov/pubmed/31904811
http://dx.doi.org/10.1093/gigascience/giz161
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author Tang, Boping
Zhang, Daizhen
Li, Haorong
Jiang, Senhao
Zhang, Huabin
Xuan, Fujun
Ge, Baoming
Wang, Zhengfei
Liu, Yu
Sha, Zhongli
Cheng, Yongxu
Jiang, Wei
Jiang, Hui
Wang, Zhongkai
Wang, Kun
Li, Chaofeng
Sun, Yue
She, Shusheng
Qiu, Qiang
Wang, Wen
Li, Xinzheng
Li, Yongxin
Liu, Qiuning
Ren, Yandong
author_facet Tang, Boping
Zhang, Daizhen
Li, Haorong
Jiang, Senhao
Zhang, Huabin
Xuan, Fujun
Ge, Baoming
Wang, Zhengfei
Liu, Yu
Sha, Zhongli
Cheng, Yongxu
Jiang, Wei
Jiang, Hui
Wang, Zhongkai
Wang, Kun
Li, Chaofeng
Sun, Yue
She, Shusheng
Qiu, Qiang
Wang, Wen
Li, Xinzheng
Li, Yongxin
Liu, Qiuning
Ren, Yandong
author_sort Tang, Boping
collection PubMed
description BACKGROUND: The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking. FINDINGS: Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with an N50 length of 21.80 Mb by Hi-C technology. CONCLUSIONS: We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction.
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spelling pubmed-69442172020-01-08 Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus) Tang, Boping Zhang, Daizhen Li, Haorong Jiang, Senhao Zhang, Huabin Xuan, Fujun Ge, Baoming Wang, Zhengfei Liu, Yu Sha, Zhongli Cheng, Yongxu Jiang, Wei Jiang, Hui Wang, Zhongkai Wang, Kun Li, Chaofeng Sun, Yue She, Shusheng Qiu, Qiang Wang, Wen Li, Xinzheng Li, Yongxin Liu, Qiuning Ren, Yandong Gigascience Data Note BACKGROUND: The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking. FINDINGS: Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with an N50 length of 21.80 Mb by Hi-C technology. CONCLUSIONS: We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction. Oxford University Press 2020-01-06 /pmc/articles/PMC6944217/ /pubmed/31904811 http://dx.doi.org/10.1093/gigascience/giz161 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Tang, Boping
Zhang, Daizhen
Li, Haorong
Jiang, Senhao
Zhang, Huabin
Xuan, Fujun
Ge, Baoming
Wang, Zhengfei
Liu, Yu
Sha, Zhongli
Cheng, Yongxu
Jiang, Wei
Jiang, Hui
Wang, Zhongkai
Wang, Kun
Li, Chaofeng
Sun, Yue
She, Shusheng
Qiu, Qiang
Wang, Wen
Li, Xinzheng
Li, Yongxin
Liu, Qiuning
Ren, Yandong
Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)
title Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)
title_full Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)
title_fullStr Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)
title_full_unstemmed Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)
title_short Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)
title_sort chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (portunus trituberculatus)
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944217/
https://www.ncbi.nlm.nih.gov/pubmed/31904811
http://dx.doi.org/10.1093/gigascience/giz161
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