Supporting data for "Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti"
The Antarctic bathydraconid dragonfish, Parachaenichthys charcoti, is an Antarctic notothenioid teleost endemic to the Southern Ocean. The Southern Ocean has cooled to ?1.8C over the past 30 million years, and the seawater had retained cold temperature and isolated oceanic environment by Antarctic C...
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ftdatacite:10.5524/100321 2023-05-15T14:05:20+02:00 Supporting data for "Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti" Do-Hwan Ahn Shin, Seung Chul Bo-Mi Kim Seunghyun Kang Jin-Hyoung Kim Inhye Ahn Joonho Park Park, Hyun 2017 https://dx.doi.org/10.5524/100321 http://gigadb.org/dataset/100321 en eng GigaScience Database CC0 1.0 Universal http://creativecommons.org/publicdomain/zero/1.0 CC0 Genomic Parachaenichthys charcoti Antarctic dragonfish Notothenioid De novo genome assembly Genome annotation dataset Dataset GigaDB Dataset 2017 ftdatacite https://doi.org/10.5524/100321 2021-11-05T12:55:41Z The Antarctic bathydraconid dragonfish, Parachaenichthys charcoti, is an Antarctic notothenioid teleost endemic to the Southern Ocean. The Southern Ocean has cooled to ?1.8C over the past 30 million years, and the seawater had retained cold temperature and isolated oceanic environment by Antarctic Circumpolar Current (ACC). Notothenioids dominate Antarctic fish, making up 90% biomass and all notothenioids have undergone molecular and ecological diversification to survive in this cold environment. Therefore, they are considered an attractive Antarctic fish model for evolutionary and ancestral genomic studies. Bathydraconidae is a speciose family of the Notothenioidei, the dominant taxonomic component of Antarctic teleosts. To understand the process of evolution of Antarctic fish, we select a typical Antarctic bathydraconid dragonfish, P. charcoti. Here, we have sequenced, de novo assembled and annotated a comprehensive genome from P. charcoti. The draft genome of P. charcoti is 709 Mb in size. The N50 contig length is 6,145 bp and its N50 scaffold length 178,362 kb. The genome of P. charcoti is predicted to contain 32,712 genes, 18,455 of which have been assigned preliminary functions. A total of 8,951 orthologous groups common to seven species fish were identified, while 333 genes were identified in P. charcoti only; 2,519 orthologous group were also identified in both P. charcoti and N. coriiceps, another Antarctic fish. Four gene ontology (GO) terms were statistically overrepresented among the 333 genes unique to P. charcoti, according to GO enrichment analysis. The draft P. charcoti genome will broaden our understanding of the evolution of Antarctic fish in their extreme environment. It will provide a basis for further investigating the unusual characteristics of Antarctic fishes. Dataset Antarc* Antarctic Southern Ocean DataCite Metadata Store (German National Library of Science and Technology) Antarctic Southern Ocean The Antarctic |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
Genomic Parachaenichthys charcoti Antarctic dragonfish Notothenioid De novo genome assembly Genome annotation |
spellingShingle |
Genomic Parachaenichthys charcoti Antarctic dragonfish Notothenioid De novo genome assembly Genome annotation Do-Hwan Ahn Shin, Seung Chul Bo-Mi Kim Seunghyun Kang Jin-Hyoung Kim Inhye Ahn Joonho Park Park, Hyun Supporting data for "Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti" |
topic_facet |
Genomic Parachaenichthys charcoti Antarctic dragonfish Notothenioid De novo genome assembly Genome annotation |
description |
The Antarctic bathydraconid dragonfish, Parachaenichthys charcoti, is an Antarctic notothenioid teleost endemic to the Southern Ocean. The Southern Ocean has cooled to ?1.8C over the past 30 million years, and the seawater had retained cold temperature and isolated oceanic environment by Antarctic Circumpolar Current (ACC). Notothenioids dominate Antarctic fish, making up 90% biomass and all notothenioids have undergone molecular and ecological diversification to survive in this cold environment. Therefore, they are considered an attractive Antarctic fish model for evolutionary and ancestral genomic studies. Bathydraconidae is a speciose family of the Notothenioidei, the dominant taxonomic component of Antarctic teleosts. To understand the process of evolution of Antarctic fish, we select a typical Antarctic bathydraconid dragonfish, P. charcoti. Here, we have sequenced, de novo assembled and annotated a comprehensive genome from P. charcoti. The draft genome of P. charcoti is 709 Mb in size. The N50 contig length is 6,145 bp and its N50 scaffold length 178,362 kb. The genome of P. charcoti is predicted to contain 32,712 genes, 18,455 of which have been assigned preliminary functions. A total of 8,951 orthologous groups common to seven species fish were identified, while 333 genes were identified in P. charcoti only; 2,519 orthologous group were also identified in both P. charcoti and N. coriiceps, another Antarctic fish. Four gene ontology (GO) terms were statistically overrepresented among the 333 genes unique to P. charcoti, according to GO enrichment analysis. The draft P. charcoti genome will broaden our understanding of the evolution of Antarctic fish in their extreme environment. It will provide a basis for further investigating the unusual characteristics of Antarctic fishes. |
format |
Dataset |
author |
Do-Hwan Ahn Shin, Seung Chul Bo-Mi Kim Seunghyun Kang Jin-Hyoung Kim Inhye Ahn Joonho Park Park, Hyun |
author_facet |
Do-Hwan Ahn Shin, Seung Chul Bo-Mi Kim Seunghyun Kang Jin-Hyoung Kim Inhye Ahn Joonho Park Park, Hyun |
author_sort |
Do-Hwan Ahn |
title |
Supporting data for "Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti" |
title_short |
Supporting data for "Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti" |
title_full |
Supporting data for "Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti" |
title_fullStr |
Supporting data for "Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti" |
title_full_unstemmed |
Supporting data for "Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti" |
title_sort |
supporting data for "draft genome of the antarctic dragonfish, parachaenichthys charcoti" |
publisher |
GigaScience Database |
publishDate |
2017 |
url |
https://dx.doi.org/10.5524/100321 http://gigadb.org/dataset/100321 |
geographic |
Antarctic Southern Ocean The Antarctic |
geographic_facet |
Antarctic Southern Ocean The Antarctic |
genre |
Antarc* Antarctic Southern Ocean |
genre_facet |
Antarc* Antarctic Southern Ocean |
op_rights |
CC0 1.0 Universal http://creativecommons.org/publicdomain/zero/1.0 |
op_rightsnorm |
CC0 |
op_doi |
https://doi.org/10.5524/100321 |
_version_ |
1766277156514562048 |