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. 2019 Nov;19(6):1461-1469.
doi: 10.1111/1755-0998.13064. Epub 2019 Aug 14.

De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C

Hui Ge  1   2 , Kebing Lin  1 , Mi Shen  3 , Shuiqing Wu  1 , Yilei Wang  2 , Ziping Zhang  4 , Zhiyong Wang  2 , Yong Zhang  5 , Zhen Huang  6 , Chen Zhou  1 , Qi Lin  1 , Jianshao Wu  1 , Lei Liu  3 , Jiang Hu  3 , Zhongchi Huang  1 , Leyun Zheng  1
Affiliations

De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C

Hui Ge et al. Mol Ecol Resour. 2019 Nov.

Abstract

The red-spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and South-East Asia and is a threatened species. The species is also considered a good model for studies of sex inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of E. akaara by taking advantage of long-read single-molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi-C. A red-spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96-fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudochromosomes covering approximately 95.55% of the genome assembly with Hi-C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 noncoding RNAs. Furthermore, combined with several RNA-seq data sets, 23,808 (99.5%) genes were functionally annotated from a total of 23,923 predicted protein-coding sequences. The high-quality chromosome-level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red-spotted grouper in the future.

Keywords: Hi-C; Nanopore sequencing; RNA-seq; genome assembly; red-spotted grouper.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
The red‐spotted grouper (Epinephelus akaara) [Colour figure can be viewed at http://wileyonlinelibrary.com]
Figure 2
Figure 2
Red‐spotted grouper genome contig contact matrix using Hi‐C data. The colour bar illuminates the contact density from red (high) to white (low) [Colour figure can be viewed at http://wileyonlinelibrary.com]
See this image and copyright information in PMC

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References

    1. Austin, C. M. , Tan, M. H. , Harrisson, K. A. , Lee, Y. P. , Croft, L. J. , Sunnucks, P. , … Gan, H. M. (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, 6(8), 1 10.1093/gigascience/gix063 - DOI - PMC - PubMed
    1. Benson, G. (1999). Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Research, 27(2), 573–580. 10.1093/nar/27.2.573 - DOI - PMC - PubMed
    1. Camacho, C. , Coulouris, G. , Avagyan, V. , Ma, N. , Papadopoulos, J. , Bealer, K. , & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10(1), 421 10.1186/1471-2105-10-421 - DOI - PMC - PubMed
    1. Chen, S. , Zhang, G. , Shao, C. , Huang, Q. , Liu, G. , Zhang, P. , … Wang, J. (2014). Whole‐genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. Nature Genetics, 46(3), 253–260. 10.1038/ng.2890 - DOI - PubMed
    1. Conte, M. A. , Gammerdinger, W. J. , Bartie, K. L. , Penman, D. J. , & Kocher, T. D. (2017). A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions. BMC Genomics, 18(1), 341 10.1186/s12864-017-3723-5 - DOI - PMC - PubMed

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