A chromosome-level genome assembly of the red drum, Sciaenops ocellatus
Sciaenops ocellatus, also known as red drum, is a valuable commercial fish that is widely cultured in China. In recent years, while the genetic research and molecular breeding on S. ocellatus has been widely performed, whole-genome resources are lacking. In our study, we assembled the S. ocellatus g...
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KeAi Communications Co., Ltd.
2021
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ftdoajarticles:oai:doaj.org/article:07f3d0668e97484389f511dd21333dbc 2023-05-15T18:05:59+02:00 A chromosome-level genome assembly of the red drum, Sciaenops ocellatus Tianjun Xu Ye Li Qing Chu Weiwei Zheng 2021-03-01T00:00:00Z https://doi.org/10.1016/j.aaf.2020.08.001 https://doaj.org/article/07f3d0668e97484389f511dd21333dbc EN eng KeAi Communications Co., Ltd. http://www.sciencedirect.com/science/article/pii/S2468550X20301143 https://doaj.org/toc/2468-550X 2468-550X doi:10.1016/j.aaf.2020.08.001 https://doaj.org/article/07f3d0668e97484389f511dd21333dbc Aquaculture and Fisheries, Vol 6, Iss 2, Pp 178-185 (2021) Red drum Whole-genome Chromosomal assembly Phylogenetic Genome evolution Aquaculture. Fisheries. Angling SH1-691 article 2021 ftdoajarticles https://doi.org/10.1016/j.aaf.2020.08.001 2022-12-31T05:47:21Z Sciaenops ocellatus, also known as red drum, is a valuable commercial fish that is widely cultured in China. In recent years, while the genetic research and molecular breeding on S. ocellatus has been widely performed, whole-genome resources are lacking. In our study, we assembled the S. ocellatus genome by high-quality genome sequencing, followed by complete annotation. The size of final genome was 686.62 Mb and N50 length of contig and scaffold is 99.71 Kb and 25.62 Mb, respectively. Using the Hi-C technology, we obtained 24 pseudochromosomes containing 87.82% of the total scaffolds. We annotated 20,053 protein-coding genes in S. ocellatus genome, of which 99.93% were homologous to proteins in different database. Totally, we detected 133.54 Mb repeat sequences, which accounts for 19.45% of the assembly. According to the phylogenetic analysis, S. ocellatus is most closed to L. croea with a divergence time about 30 million years ago. We assembled a high-quality genome that will be a valuable resource to further study the biology of S. ocellatus and will inform how to breed the red drum to enhance its economic traits. Article in Journal/Newspaper Red drum Sciaenops ocellatus Directory of Open Access Journals: DOAJ Articles Aquaculture and Fisheries 6 2 178 185 |
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Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Red drum Whole-genome Chromosomal assembly Phylogenetic Genome evolution Aquaculture. Fisheries. Angling SH1-691 |
spellingShingle |
Red drum Whole-genome Chromosomal assembly Phylogenetic Genome evolution Aquaculture. Fisheries. Angling SH1-691 Tianjun Xu Ye Li Qing Chu Weiwei Zheng A chromosome-level genome assembly of the red drum, Sciaenops ocellatus |
topic_facet |
Red drum Whole-genome Chromosomal assembly Phylogenetic Genome evolution Aquaculture. Fisheries. Angling SH1-691 |
description |
Sciaenops ocellatus, also known as red drum, is a valuable commercial fish that is widely cultured in China. In recent years, while the genetic research and molecular breeding on S. ocellatus has been widely performed, whole-genome resources are lacking. In our study, we assembled the S. ocellatus genome by high-quality genome sequencing, followed by complete annotation. The size of final genome was 686.62 Mb and N50 length of contig and scaffold is 99.71 Kb and 25.62 Mb, respectively. Using the Hi-C technology, we obtained 24 pseudochromosomes containing 87.82% of the total scaffolds. We annotated 20,053 protein-coding genes in S. ocellatus genome, of which 99.93% were homologous to proteins in different database. Totally, we detected 133.54 Mb repeat sequences, which accounts for 19.45% of the assembly. According to the phylogenetic analysis, S. ocellatus is most closed to L. croea with a divergence time about 30 million years ago. We assembled a high-quality genome that will be a valuable resource to further study the biology of S. ocellatus and will inform how to breed the red drum to enhance its economic traits. |
format |
Article in Journal/Newspaper |
author |
Tianjun Xu Ye Li Qing Chu Weiwei Zheng |
author_facet |
Tianjun Xu Ye Li Qing Chu Weiwei Zheng |
author_sort |
Tianjun Xu |
title |
A chromosome-level genome assembly of the red drum, Sciaenops ocellatus |
title_short |
A chromosome-level genome assembly of the red drum, Sciaenops ocellatus |
title_full |
A chromosome-level genome assembly of the red drum, Sciaenops ocellatus |
title_fullStr |
A chromosome-level genome assembly of the red drum, Sciaenops ocellatus |
title_full_unstemmed |
A chromosome-level genome assembly of the red drum, Sciaenops ocellatus |
title_sort |
chromosome-level genome assembly of the red drum, sciaenops ocellatus |
publisher |
KeAi Communications Co., Ltd. |
publishDate |
2021 |
url |
https://doi.org/10.1016/j.aaf.2020.08.001 https://doaj.org/article/07f3d0668e97484389f511dd21333dbc |
genre |
Red drum Sciaenops ocellatus |
genre_facet |
Red drum Sciaenops ocellatus |
op_source |
Aquaculture and Fisheries, Vol 6, Iss 2, Pp 178-185 (2021) |
op_relation |
http://www.sciencedirect.com/science/article/pii/S2468550X20301143 https://doaj.org/toc/2468-550X 2468-550X doi:10.1016/j.aaf.2020.08.001 https://doaj.org/article/07f3d0668e97484389f511dd21333dbc |
op_doi |
https://doi.org/10.1016/j.aaf.2020.08.001 |
container_title |
Aquaculture and Fisheries |
container_volume |
6 |
container_issue |
2 |
container_start_page |
178 |
op_container_end_page |
185 |
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1766177543477526528 |