Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies
Trematomus species (suborder Notothenioidei; family Nototheniidae) are widely distributed in the southern oceans near Antarctica. There are 11 recognized species in the genus Trematomus, and notothenioids are known to have high chromosomal diversity (2n = 24–58) because of relatively recent and rapi...
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ftdoajarticles:oai:doaj.org/article:154d2800086444628f738359d762ea6e 2023-05-15T13:40:50+02:00 Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies Euna Jo Seung Jae Lee Jeong-Hoon Kim Steven J. Parker Eunkyung Choi Jinmu Kim So-Ra Han Tae-Jin Oh Hyun Park 2021-12-01T00:00:00Z https://doi.org/10.3390/d13120668 https://doaj.org/article/154d2800086444628f738359d762ea6e EN eng MDPI AG https://www.mdpi.com/1424-2818/13/12/668 https://doaj.org/toc/1424-2818 doi:10.3390/d13120668 1424-2818 https://doaj.org/article/154d2800086444628f738359d762ea6e Diversity, Vol 13, Iss 668, p 668 (2021) Antarctic fish notothenioids long-read sequencing Hi-C chromosomal-level assembly Biology (General) QH301-705.5 article 2021 ftdoajarticles https://doi.org/10.3390/d13120668 2022-12-30T23:54:08Z Trematomus species (suborder Notothenioidei; family Nototheniidae) are widely distributed in the southern oceans near Antarctica. There are 11 recognized species in the genus Trematomus, and notothenioids are known to have high chromosomal diversity (2n = 24–58) because of relatively recent and rapid adaptive radiation. Herein, we report the chromosomal-level genome assembly of T. loennbergii, the first characterized genome representative of the genus Trematomus. The final genome assembly of T. loennbergii was obtained using a Pacific Biosciences long-read sequencing platform and high-throughput chromosome conformation capture technology. Twenty-three chromosomal-level scaffolds were assembled to 940 Mb in total size, with a longest contig size of 48.5 Mb and contig N50 length of 24.7 Mb. The genome contained 42.03% repeat sequences, and a total of 24,525 protein-coding genes were annotated. We produced a high-quality genome assembly of T. loennbergii. Our results provide a first reference genome for the genus Trematomus and will serve as a basis for studying the molecular taxonomy and evolution of Antarctic fish. Article in Journal/Newspaper Antarc* Antarctic Antarctica Directory of Open Access Journals: DOAJ Articles Antarctic Pacific Diversity 13 12 668 |
institution |
Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Antarctic fish notothenioids long-read sequencing Hi-C chromosomal-level assembly Biology (General) QH301-705.5 |
spellingShingle |
Antarctic fish notothenioids long-read sequencing Hi-C chromosomal-level assembly Biology (General) QH301-705.5 Euna Jo Seung Jae Lee Jeong-Hoon Kim Steven J. Parker Eunkyung Choi Jinmu Kim So-Ra Han Tae-Jin Oh Hyun Park Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies |
topic_facet |
Antarctic fish notothenioids long-read sequencing Hi-C chromosomal-level assembly Biology (General) QH301-705.5 |
description |
Trematomus species (suborder Notothenioidei; family Nototheniidae) are widely distributed in the southern oceans near Antarctica. There are 11 recognized species in the genus Trematomus, and notothenioids are known to have high chromosomal diversity (2n = 24–58) because of relatively recent and rapid adaptive radiation. Herein, we report the chromosomal-level genome assembly of T. loennbergii, the first characterized genome representative of the genus Trematomus. The final genome assembly of T. loennbergii was obtained using a Pacific Biosciences long-read sequencing platform and high-throughput chromosome conformation capture technology. Twenty-three chromosomal-level scaffolds were assembled to 940 Mb in total size, with a longest contig size of 48.5 Mb and contig N50 length of 24.7 Mb. The genome contained 42.03% repeat sequences, and a total of 24,525 protein-coding genes were annotated. We produced a high-quality genome assembly of T. loennbergii. Our results provide a first reference genome for the genus Trematomus and will serve as a basis for studying the molecular taxonomy and evolution of Antarctic fish. |
format |
Article in Journal/Newspaper |
author |
Euna Jo Seung Jae Lee Jeong-Hoon Kim Steven J. Parker Eunkyung Choi Jinmu Kim So-Ra Han Tae-Jin Oh Hyun Park |
author_facet |
Euna Jo Seung Jae Lee Jeong-Hoon Kim Steven J. Parker Eunkyung Choi Jinmu Kim So-Ra Han Tae-Jin Oh Hyun Park |
author_sort |
Euna Jo |
title |
Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies |
title_short |
Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies |
title_full |
Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies |
title_fullStr |
Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies |
title_full_unstemmed |
Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies |
title_sort |
chromosomal-level assembly of antarctic scaly rockcod, trematomus loennbergii genome using long-read sequencing and chromosome conformation capture (hi-c) technologies |
publisher |
MDPI AG |
publishDate |
2021 |
url |
https://doi.org/10.3390/d13120668 https://doaj.org/article/154d2800086444628f738359d762ea6e |
geographic |
Antarctic Pacific |
geographic_facet |
Antarctic Pacific |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_source |
Diversity, Vol 13, Iss 668, p 668 (2021) |
op_relation |
https://www.mdpi.com/1424-2818/13/12/668 https://doaj.org/toc/1424-2818 doi:10.3390/d13120668 1424-2818 https://doaj.org/article/154d2800086444628f738359d762ea6e |
op_doi |
https://doi.org/10.3390/d13120668 |
container_title |
Diversity |
container_volume |
13 |
container_issue |
12 |
container_start_page |
668 |
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1766141045783920640 |