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De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read

Austin, Christopher M., Tan, Mun Hua, Harrisson, Katherine A., Lee, Yin Peng, Croft, Laurence J., Sunnucks, Paul, Pavlova, Alexandra and Gan, Han Ming 2017, De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read, GigaScience, vol. 6, no. 8, pp. 1-6, doi: 10.1093/gigascience/gix063.

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Title De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read
Formatted title De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read
Author(s) Austin, Christopher M.ORCID iD for Austin, Christopher M. orcid.org/0000-0003-1848-6267
Tan, Mun Hua
Harrisson, Katherine A.
Lee, Yin Peng
Croft, Laurence J.
Sunnucks, Paul
Pavlova, Alexandra
Gan, Han Ming
Journal name GigaScience
Volume number 6
Issue number 8
Start page 1
End page 6
Total pages 6
Publisher Oxford University Publishing
Place of publication Oxford, Eng.
Publication date 2017-08
ISSN 2047-217X
Keyword(s) Murray cod
genome
hybrid assembly
long reads
transcriptome
Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
EVOLUTION
DATABASE
EFFICIENT
ALIGNMENT
FAMILIES
RANGE
Summary 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 to age ≥48 years. The Murray cod is of a conservation concern as a result of strong population contractions, but it 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 research, as well as to better understand 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 2 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 generated 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 the Percichthydae family.
Language eng
DOI 10.1093/gigascience/gix063
Field of Research 060408 Genomics
070405 Fish Physiology and Genetics
070401 Aquaculture
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2017, The Authors
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30103153

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Created: Thu, 04 Jan 2018, 09:47:19 EST

Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.