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Volume 13
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10.3390/d13120668
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Article

Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies

by
Euna Jo
1,†,
Seung Jae Lee
1,†,
Jeong-Hoon Kim
2,
Steven J. Parker
3,
Eunkyung Choi
1,
Jinmu Kim
1,
So-Ra Han
4,
Tae-Jin Oh
4,* and
Hyun Park
1,*
1
Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
2
Division of Polar Life Science, Korea Polar Research Institute, Incheon 21990, Korea
3
National Institute of Water & Atmospheric Research Ltd. (NIWA), 217 Akersten Street Port Nelson, Nelson 7001, New Zealand
4
Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, Asan 31460, Korea
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Diversity 2021, 13(12), 668; https://doi.org/10.3390/d13120668
Submission received: 8 November 2021 / Revised: 7 December 2021 / Accepted: 12 December 2021 / Published: 14 December 2021
(This article belongs to the Special Issue Biodiversity of the Ross Sea Region Marine Protected Area (Antarctica))
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Abstract

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.
Keywords: Antarctic fish; notothenioids; long-read sequencing; Hi-C; chromosomal-level assembly Antarctic fish; notothenioids; long-read sequencing; Hi-C; chromosomal-level assembly
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MDPI and ACS Style

Jo, E.; Lee, S.J.; Kim, J.-H.; Parker, S.J.; Choi, E.; Kim, J.; Han, S.-R.; Oh, T.-J.; Park, H. Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies. Diversity 2021, 13, 668. https://doi.org/10.3390/d13120668

AMA Style

Jo E, Lee SJ, Kim J-H, Parker SJ, Choi E, Kim J, Han S-R, Oh T-J, Park H. Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies. Diversity. 2021; 13(12):668. https://doi.org/10.3390/d13120668

Chicago/Turabian Style

Jo, Euna, Seung Jae Lee, Jeong-Hoon Kim, Steven J. Parker, Eunkyung Choi, Jinmu Kim, So-Ra Han, Tae-Jin Oh, and Hyun Park. 2021. "Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies" Diversity 13, no. 12: 668. https://doi.org/10.3390/d13120668

APA Style

Jo, E., Lee, S. J., Kim, J.-H., Parker, S. J., Choi, E., Kim, J., Han, S.-R., Oh, T.-J., & Park, H. (2021). Chromosomal-Level Assembly of Antarctic Scaly Rockcod, Trematomus loennbergii Genome Using Long-Read Sequencing and Chromosome Conformation Capture (Hi-C) Technologies. Diversity, 13(12), 668. https://doi.org/10.3390/d13120668

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