Help Login Create account

Data released on July 07, 2017

Supporting data for "Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti"

Ahn, D; Ahn, I; Kang, S; Kim, B; Kim, J; Park, H; Park, J; Shin, S, C (2017): Supporting data for "Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti" GigaScience Database. http://dx.doi.org/10.5524/100321 RIS BibTeX Text

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.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix060

Accessions (data included in GigaDB):

BioProject: PRJNA330735

Keywords:

Parachaenichthys charcoti Antarctic dragonfish Notothenioid De novo genome assembly Genome annotation 

Genomic

http://gigadb.org/images/data/cropped/100321.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SRS157960536187  Parachaenichthys charcoti Description:Genomic DNA extracted from the mucle t...
Molecular data type:DNA
Alternative accession-BioSample:SAMN05421612
...
+
SRS157961436187  Parachaenichthys charcoti Description:Genomic DNA extracted from liver sampl...
Molecular data type:DNA
Alternative accession-BioSample:SAMN05421683
...
+
SRS192312336187  Parachaenichthys charcoti Description:Transcribed RNA extracted from the liv...
Molecular data type:RNA
Alternative accession-BioSample:SAMN06232533
...
+
Displaying 1-3 of 3 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
ReadmeTEXT-0 KB2017-06-19
Phylogenetic treeUNKNOWN0.16 KB2017-06-19
TextTEXT0.47 KB2017-06-19
TextTEXT1.09 MB2017-06-19
TextTEXT1.31 MB2017-06-19
tabular dataUNKNOWN5.78 MB2017-06-19
protein sequenceFASTA14.22 MB2017-06-19
Mixed archivearchive27.34 MB2017-06-19
Coding sequenceFASTA38.78 MB2017-06-19
Coding sequenceFASTA45.92 MB2017-06-19
Displaying 1-10 of 14 File(s).

History:

+

Other datasets you might like: