Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti
The crocodile icefish, Chionobathyscus dewitti , belonging to the family Channichthyidae, is an endemic species of the Southern Ocean. The study of its biological features and genetics is challenging as the fish inhabits the deep sea around Antarctic waters. The icefish, the sole cryopelagic species...
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ftdoajarticles:oai:doaj.org/article:5f7f3298ad8946ff9c5995a2f99de62a 2023-05-15T13:38:40+02:00 Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti Jinmu Kim Seung-Jae Lee Euna Jo Eunkyung Choi Minjoo Cho Soyun Choi Jeong-Hoon Kim Hyun Park 2022-09-01T00:00:00Z https://doi.org/10.3390/ani12192598 https://doaj.org/article/5f7f3298ad8946ff9c5995a2f99de62a EN eng MDPI AG https://www.mdpi.com/2076-2615/12/19/2598 https://doaj.org/toc/2076-2615 doi:10.3390/ani12192598 2076-2615 https://doaj.org/article/5f7f3298ad8946ff9c5995a2f99de62a Animals, Vol 12, Iss 2598, p 2598 (2022) Chionobathyscus dewitti crocodile icefish Illumina Novaseq 6000 Jellyfish GenomeScope K-value Veterinary medicine SF600-1100 Zoology QL1-991 article 2022 ftdoajarticles https://doi.org/10.3390/ani12192598 2022-12-30T23:12:05Z The crocodile icefish, Chionobathyscus dewitti , belonging to the family Channichthyidae, is an endemic species of the Southern Ocean. The study of its biological features and genetics is challenging as the fish inhabits the deep sea around Antarctic waters. The icefish, the sole cryopelagic species, shows unique physiological and genetic features, unlike other teleosts. It lacks hemoglobin and has evolved antifreeze proteins. Here, we report the genome sequencing data of crocodile icefish produced using the Illumina Novaseq 6000 platform. The estimated genome size was 0.88 Gb with a K-value of 19, and the unique sequence, heterozygosity, error, and duplication rates were 57.4%, 0.421%, 0.317%, and 0.738%, respectively. A genome assembly of 880.69 Mb, with an N50 scaffold length of 2401 bp, was conducted. We identified 2,252,265 microsatellite motifs from the genome assembly data, and dinucleotide repeats (1,920,127; 85.25%) had the highest rate. We selected 84 primer pairs from the genome survey assembly and randomly selected 30 primer pairs for validation. As a result, 15 primer pairs were validated as microsatellite markers. Article in Journal/Newspaper Antarc* Antarctic Icefish Southern Ocean Directory of Open Access Journals: DOAJ Articles Antarctic Southern Ocean Animals 12 19 2598 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Chionobathyscus dewitti crocodile icefish Illumina Novaseq 6000 Jellyfish GenomeScope K-value Veterinary medicine SF600-1100 Zoology QL1-991 |
spellingShingle |
Chionobathyscus dewitti crocodile icefish Illumina Novaseq 6000 Jellyfish GenomeScope K-value Veterinary medicine SF600-1100 Zoology QL1-991 Jinmu Kim Seung-Jae Lee Euna Jo Eunkyung Choi Minjoo Cho Soyun Choi Jeong-Hoon Kim Hyun Park Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti |
topic_facet |
Chionobathyscus dewitti crocodile icefish Illumina Novaseq 6000 Jellyfish GenomeScope K-value Veterinary medicine SF600-1100 Zoology QL1-991 |
description |
The crocodile icefish, Chionobathyscus dewitti , belonging to the family Channichthyidae, is an endemic species of the Southern Ocean. The study of its biological features and genetics is challenging as the fish inhabits the deep sea around Antarctic waters. The icefish, the sole cryopelagic species, shows unique physiological and genetic features, unlike other teleosts. It lacks hemoglobin and has evolved antifreeze proteins. Here, we report the genome sequencing data of crocodile icefish produced using the Illumina Novaseq 6000 platform. The estimated genome size was 0.88 Gb with a K-value of 19, and the unique sequence, heterozygosity, error, and duplication rates were 57.4%, 0.421%, 0.317%, and 0.738%, respectively. A genome assembly of 880.69 Mb, with an N50 scaffold length of 2401 bp, was conducted. We identified 2,252,265 microsatellite motifs from the genome assembly data, and dinucleotide repeats (1,920,127; 85.25%) had the highest rate. We selected 84 primer pairs from the genome survey assembly and randomly selected 30 primer pairs for validation. As a result, 15 primer pairs were validated as microsatellite markers. |
format |
Article in Journal/Newspaper |
author |
Jinmu Kim Seung-Jae Lee Euna Jo Eunkyung Choi Minjoo Cho Soyun Choi Jeong-Hoon Kim Hyun Park |
author_facet |
Jinmu Kim Seung-Jae Lee Euna Jo Eunkyung Choi Minjoo Cho Soyun Choi Jeong-Hoon Kim Hyun Park |
author_sort |
Jinmu Kim |
title |
Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti |
title_short |
Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti |
title_full |
Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti |
title_fullStr |
Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti |
title_full_unstemmed |
Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti |
title_sort |
whole-genome survey and microsatellite marker detection of antarctic crocodile icefish, chionobathyscus dewitti |
publisher |
MDPI AG |
publishDate |
2022 |
url |
https://doi.org/10.3390/ani12192598 https://doaj.org/article/5f7f3298ad8946ff9c5995a2f99de62a |
geographic |
Antarctic Southern Ocean |
geographic_facet |
Antarctic Southern Ocean |
genre |
Antarc* Antarctic Icefish Southern Ocean |
genre_facet |
Antarc* Antarctic Icefish Southern Ocean |
op_source |
Animals, Vol 12, Iss 2598, p 2598 (2022) |
op_relation |
https://www.mdpi.com/2076-2615/12/19/2598 https://doaj.org/toc/2076-2615 doi:10.3390/ani12192598 2076-2615 https://doaj.org/article/5f7f3298ad8946ff9c5995a2f99de62a |
op_doi |
https://doi.org/10.3390/ani12192598 |
container_title |
Animals |
container_volume |
12 |
container_issue |
19 |
container_start_page |
2598 |
_version_ |
1766109244647538688 |