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. 2017 Aug 1;6(8):1-6.
doi: 10.1093/gigascience/gix063.

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

Christopher M Austin  1   2   3 , Mun Hua Tan  1   2   3 , Katherine A Harrisson  4 , Yin Peng Lee  2   3 , Laurence J Croft  3   5 , Paul Sunnucks  4 , Alexandra Pavlova  4 , Han Ming Gan  1   2   3
Affiliations

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

Christopher M Austin et al. Gigascience. .

Abstract

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.

Keywords: Murray cod; genome; hybrid assembly; long reads; transcriptome.

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Figures

Figure 1:
Figure 1:
The iconic Murray cod. Photo: Paul Sunnucks.
Figure 2:
Figure 2:
Estimation of genome size, repeat content, and heterozygosity by GenomeScope, based on 21-mers in HiSeq sequence reads (max kmer coverage at 1000).
See this image and copyright information in PMC

References

    1. Pavlova A, Gan HM, Lee YP et al. Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish. Heredity 2017;118:466–76. - PMC - PubMed
    1. Harrisson K, Pavlova A, Gan HM et al. Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species. Heredity 2016;116(6):506–15. - PMC - PubMed
    1. Cole TL, Hammer MP, Unmack PJ et al. Range-wide fragmentation in a threatened fish associated with post-European settlement modification in the Murray–Darling Basin, Australia. Conserv Genet 2016;17(6):1377–91.
    1. Unmack PJ, Sandoval-Castillo J, Hammer MP et al. Genome-wide SNPs resolve a key conflict between sequence and allozyme data to confirm another threatened candidate species of river blackfishes (Teleostei: Percichthyidae: Gadopsis). Mol Phylogenet Evol 2017;109:415–20. - PubMed
    1. Austin CM, Tan MH, Lee YP et al. The complete mitogenome of the Murray cod, Maccullochella peelii (Mitchell, 1838) (Teleostei: Percichthyidae). Mitochondrial DNA 2016;27(1):729–30. - PubMed

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