Volume 42 Issue 1
Jan.  2021
Turn off MathJax
Article Contents
Seung Jae Lee, Jeong-Hoon Kim, Euna Jo, Eunkyung Choi, Jinmu Kim, Seok-Gwan Choi, Sangdeok Chung, Hyun-Woo Kim, Hyun Park. Chromosomal assembly of the Antarctic toothfish (Dissostichus mawsoni) genome using third-generation DNA sequencing and Hi-C technology. Zoological Research, 2021, 42(1): 124-129. doi: 10.24272/j.issn.2095-8137.2020.264
Citation: Seung Jae Lee, Jeong-Hoon Kim, Euna Jo, Eunkyung Choi, Jinmu Kim, Seok-Gwan Choi, Sangdeok Chung, Hyun-Woo Kim, Hyun Park. Chromosomal assembly of the Antarctic toothfish (Dissostichus mawsoni) genome using third-generation DNA sequencing and Hi-C technology. Zoological Research, 2021, 42(1): 124-129. doi: 10.24272/j.issn.2095-8137.2020.264

Chromosomal assembly of the Antarctic toothfish (Dissostichus mawsoni) genome using third-generation DNA sequencing and Hi-C technology

doi: 10.24272/j.issn.2095-8137.2020.264
#Authors contributed equally to this work
Funds:  This study was supported by a grant from the National Institute of Fisheries Science (NIFS) of the Republic of Korea (R2019021) and “Ecosystem Structure and Function of Marine Protected Area (MPA) in Antarctica” project (PM19060) funded by the Ministry of Oceans and Fisheries (20170336), Korea
More Information
  • Corresponding author: E-mail: kimhw@pknu.ac.krhpark@korea.ac.kr
  • Received Date: 2020-09-14
  • Accepted Date: 2020-11-30
  • Available Online: 2020-12-01
  • Publish Date: 2021-01-18
  • The Antarctic toothfish, Dissostichus mawsoni, belongs to the Nototheniidae family and is distributed in sub-zero temperatures below S60° latitude in the Southern Ocean. Therefore, it is an attractive model species to study the stenothermal cold-adapted character state. In this study, we successfully generated highly contiguous genome sequences of D. mawsoni, which contained 1 062 scaffolds with a N50 length of 36.98 Mb and longest scaffold length of 46.82 Mb. Repetitive elements accounted for 40.87% of the genome. We also inferred 32 914 protein-coding genes using in silico gene prediction and transcriptome sequencing and detected splicing variants using Isoform-Sequencing (Iso-Seq), which will be invaluable resource for further exploration of the adaptation mechanisms of Antarctic toothfish. This new high-quality reference genome of D. mawsoni provides a fundamental resource for a deeper understanding of cold adaptation and conservation of species.
  • #Authors contributed equally to this work
  • loading
  • [1]
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215(3): 403−410. doi: 10.1016/S0022-2836(05)80360-2
    [2]
    Bao ZR, Eddy SR. 2002. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Research, 12(8): 1269−1276. doi: 10.1101/gr.88502
    [3]
    Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. 2012. Hi–C: a comprehensive technique to capture the conformation of genomes. Methods, 58(3): 268−276. doi: 10.1016/j.ymeth.2012.05.001
    [4]
    Benson DA, Boguski MS, Lipman DJ, Ostell J, Ouellette BFF, Rapp BA, et al. 1999. GenBank. Nucleic Acids Research, 27(1): 12−17. doi: 10.1093/nar/27.1.12
    [5]
    Benson GJ. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27(2): 573−580. doi: 10.1093/nar/27.2.573
    [6]
    Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, et al. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research, 31(1): 365−370. doi: 10.1093/nar/gkg095
    [7]
    Chalopin D, Naville M, Plard F, Galiana D, Volff JN. 2015. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biology and Evolution, 7(2): 567−580. doi: 10.1093/gbe/evv005
    [8]
    Chen LB, Lu Y, Li WH, Ren YD, Yu MC, Jiang SW, et al. 2019. The genomic basis for colonizing the freezing Southern Ocean revealed by Antarctic toothfish and Patagonian robalo genomes. GigaScience, 8(4): giz016.
    [9]
    Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods, 10(6): 563−569. doi: 10.1038/nmeth.2474
    [10]
    Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18): 3674−3676. doi: 10.1093/bioinformatics/bti610
    [11]
    Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, et al. 2012. The UniProt-GO annotation database in 2011. Nucleic Acids Research, 40(D1): D565−D570. doi: 10.1093/nar/gkr1048
    [12]
    Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, et al. 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 356(6333): 92−95. doi: 10.1126/science.aal3327
    [13]
    Durand NC, Shamim MS, Machol I, Rao SSP, Huntley MH, Lander ES, et al. 2016. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Systems, 3(1): 95−98. doi: 10.1016/j.cels.2016.07.002
    [14]
    Eastman JT. 2005. The nature of the diversity of Antarctic fishes. Polar Biology, 28(2): 93−107. doi: 10.1007/s00300-004-0667-4
    [15]
    Eastman JT, DeVries AL. 1981. Buoyancy adaptations in a swim-bladderless Antarctic fish. Journal of Morphology, 167(1): 91−102. doi: 10.1002/jmor.1051670108
    [16]
    Eastman JT, DeVries AL. 1982. Buoyancy studies of notothenioid fishes in McMurdo Sound, Antarctica. Copeia, 1982(2): 385−393. doi: 10.2307/1444619
    [17]
    Ghigliotti L, Mazzei F, Ozouf-Costaz C, Bonillo C, Williams R, Cheng CHC, et al. 2007. The two giant sister species of the Southern Ocean, Dissostichus eleginoides and Dissostichus mawsoni, differ in karyotype and chromosomal pattern of ribosomal RNA genes. Polar Biology, 30(5): 625−634. doi: 10.1007/s00300-006-0222-6
    [18]
    Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. 2005. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Research, 33(S1): D121−D124.
    [19]
    Hedges SB, Dudley J, Kumar S. 2006. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics, 22(23): 2971−2972. doi: 10.1093/bioinformatics/btl505
    [20]
    Holt C, Yandell M. 2011. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics, 12(1): 491. doi: 10.1186/1471-2105-12-491
    [21]
    Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 28(1): 27−30. doi: 10.1093/nar/28.1.27
    [22]
    Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2): 111−120. doi: 10.1007/BF01731581
    [23]
    Korf I. 2004. Gene finding in novel genomes. BMC Bioinformatics, 5(1): 59. doi: 10.1186/1471-2105-5-59
    [24]
    Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18): 3094−3100. doi: 10.1093/bioinformatics/bty191
    [25]
    Li L, Stoeckert CJ Jr, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research, 13(9): 2178−2189. doi: 10.1101/gr.1224503
    [26]
    Livermore R, Nankivell A, Eagles G, Morris P. 2005. Paleogene opening of Drake passage. Earth and Planetary Science Letters, 236(1-2): 459−470. doi: 10.1016/j.jpgl.2005.03.027
    [27]
    Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25(5): 955−964. doi: 10.1093/nar/25.5.955
    [28]
    Löytynoja A, Goldman N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences of the United States of America, 102(30): 10557−10562. doi: 10.1073/pnas.0409137102
    [29]
    Maschette D, Wotherspoon S, Ziegler P. 2019. Exploration of CPUE Standardisation Variances in the Ross Sea (Subareas 88.1 and 88.2A South of 70°s) Antarctic Toothfish (Dissostichus mawsoni) Exploratory Longline Fishery. Hobart, Tasmania: CCAMLR.
    [30]
    Nawrocki EP, Eddy SR. 2013. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29(22): 2933−2935. doi: 10.1093/bioinformatics/btt509
    [31]
    Price AL, Jones NC, Pevzner PA. 2005. De novo identification of repeat families in large genomes. Bioinformatics, 21(S1): i351−i358.
    [32]
    Simão FA, Waterhouse RM, Ioannidis P, Kriventseva E, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31(19): 3210−3212. doi: 10.1093/bioinformatics/btv351
    [33]
    Tardaguila M, De La Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, et al. 2018. SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Research, 28(3): 396−411. doi: 10.1101/gr.222976.117
    [34]
    Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, et al. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Research, 29(1): 22−28. doi: 10.1093/nar/29.1.22
    [35]
    Tseng E. 2017(2020-10-16). Cupcake ToFU: supporting scripts for Iso-Seq after clustering step. https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step.
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(2)

    Article Metrics

    Article views (345) PDF downloads(73) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return