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Data released on July 18, 2017

De novo genome assembly and annotation data for the Murray cod (Maccullochella peelii), Australia's largest freshwater fish

Austin, C, M; Croft, L, J; Gan, H, M; Harrisson, K, A; Lee, Y, P; Pavlova, A; Sunnucks, P; Tan, M, H (2017): De novo genome assembly and annotation data for the Murray cod (Maccullochella peelii), Australia's largest freshwater fish GigaScience Database. http://dx.doi.org/10.5524/100329 RIS BibTeX Text

One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell, 1838), a freshwater species that can grow to ~1.8 metres in length and live ≥ 48 years of age. The Murray cod is of conservation concern as a result of strong population contractions, but is also popular for recreational fishing and is of growing aquaculture interest. In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation and management-related research, as well as to understand better the evolutionary ecology and history of the species.
A draft Murray cod genome of 633 Mbp (N50=109,974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of two fish individuals with an identical maternal lineage. 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were from the second individual. The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome leading to the identification of 26,539 protein-coding genes.
We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic and phylogenetic studies of the Murray cod and more generally other fish species of Percichthydae family.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix063

Accessions (data included in GigaDB):

BioProject: PRJNA290988
BioProject: PRJNA383091

Keywords:

Murray Cod long reads genome transcriptome hybrid assembly 

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100329.jpg

Funding:

  • Funding body - Australian Research Council
  • Award ID - LP11020001
  • Awardee - Prof P Sunnucks

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN03938494135761 Murray codMaccullochella peelii Description:Sequencing of the Murray Cod genome
Analyte type:DNA
Alternative names:KMC200 or MCC0324
...
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SAMN06759032135761 Murray codMaccullochella peelii Description:Sequencing of the Murray Cod transcrip...
Analyte type:RNA
Alternative names:BrokenCreek1
...
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SAMN07329765135761 Murray codMaccullochella peelii Description:Sequencing of the Murray Cod genome
Analyte type:DNA
Isolation source:Fish Market in Melbourne, Victori...
...
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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 
SAMN03938494annotationGFF18.19 MB2017-07-05
SAMN03938494annotationGFF507.95 MB2017-07-05
SAMN03938494Coding SequenceFASTA17.42 MB2017-07-05
SAMN06759032Coding SequenceFASTA55.47 MB2017-07-05
SAMN03938494Genome sequenceFASTA161.76 MB2017-07-05
SAMN03938494Genome sequenceFASTA167.54 MB2017-07-05
SAMN03938494Genome sequenceFASTA175.51 MB2017-07-05
SAMN03938494otherTSV7.14 MB2017-07-05
SAMN03938494protein sequenceFASTA8.12 MB2017-07-05
ReadmeTEXT1.05 KB2017-07-05
Displaying 1-10 of 12 File(s).

History:

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