Volume 42 Issue 1
Jan.  2021
Turn off MathJax
Article Contents
Wang-Xiao Xia, Hao-Rong Li, Jing-Hao Ge, Yao-Wu Liu, Hong-Hui Li, Yan-Hua Su, Hai-Zhen Wang, Hui-Fang Guo, Yu-Xuan Dai, Yao-Wen Liu, Xing-Chun Gou. High-continuity genome assembly of the jellyfish Chrysaora quinquecirrha. Zoological Research, 2021, 42(1): 130-134. doi: 10.24272/j.issn.2095-8137.2020.258
Citation: Wang-Xiao Xia, Hao-Rong Li, Jing-Hao Ge, Yao-Wu Liu, Hong-Hui Li, Yan-Hua Su, Hai-Zhen Wang, Hui-Fang Guo, Yu-Xuan Dai, Yao-Wen Liu, Xing-Chun Gou. High-continuity genome assembly of the jellyfish Chrysaora quinquecirrha. Zoological Research, 2021, 42(1): 130-134. doi: 10.24272/j.issn.2095-8137.2020.258

High-continuity genome assembly of the jellyfish Chrysaora quinquecirrha

doi: 10.24272/j.issn.2095-8137.2020.258
#Authors contributed equally to this work
Funds:  This work was supported by the Province of China (202011840014) Shaanxi College Students’ Innovation and Entrepreneurship Training Program (S202011840014), Xi’an Medical University College Students’ Innovation and Entrepreneurship Training Program (121520014), National Natural Science Foundation of China (31760671), Joint Special Project of Agricultural Basic Research in Yunnan Province (2018FG001-041), Yunnan Provincial Department of Education Research Fund (2020J0251), Scientific Research Fund of Shaanxi Provincial Education Department (20JS143), and Natural Science Basic Research Plan in Shaanxi Province of China (2020JQ-876)
More Information
  • The Atlantic sea nettle (Chrysaora quinquecirrha) has an important evolutionary position due to its high ecological value. However, due to limited sequencing technologies and complex jellyfish genomic sequences, the current C. quinquecirrha genome assembly is highly fragmented. Here, we used the most advanced high-throughput chromosome conformation capture (Hi-C) technology to obtain high-coverage sequencing data of the C. quinquecirrha genome. We then anchored these data to the previously published contig-level assembly to improve the genome. Finally, a high-continuity genome sequence of C. quinquecirrha was successfully assembled, which contained 1 882 scaffolds with a N50 length of 3.83 Mb. The N50 length of the genome assembly was 5.23 times longer than the previously released one, and additional analysis revealed that it had a high degree of genomic continuity and accuracy. Acquisition of the high-continuity genome sequence of C. quinquecirrha not only provides a basis for the study of jellyfish evolution through comparative genomics but also provides an important resource for studies on jellyfish growth and development.
  • #Authors contributed equally to this work
  • loading
  • [1]
    Burge C, Karlin S. 1997. Prediction of complete gene structures in human genomic DNA. Journal of Molecular Biology, 268(1): 78−94. doi: 10.1006/jmbi.1997.0951
    [2]
    Cali DS, Kim JS, Ghose S, Alkan C, Mutlu O. 2019. Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. Briefings in Bioinformatics, 20(4): 1542−1559. doi: 10.1093/bib/bby017
    [3]
    Chen MS, Niu LJ, Zhao ML, Xu CJ, Pan BZ, Fu QT, et al. 2020. De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas. GigaScience, 9(2): giaa009. doi: 10.1093/gigascience/giaa009
    [4]
    Decker MB, Brown CW, Hood RR, Purcell JE, Gross TF, Matanoski JC, et al. 2007. Predicting the distribution of the scyphomedusa Chrysaora quinquecirrha in Chesapeake Bay. Marine Ecology Progress Series, 329: 99−113. doi: 10.3354/meps329099
    [5]
    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
    [6]
    Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, et al. 2016a. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Systems, 3(1): 99−101. doi: 10.1016/j.cels.2015.07.012
    [7]
    Durand NC, Shamim MS, Machol I, Rao SSP, Huntley MH, Lander ES, et al. 2016b. 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
    [8]
    Finenko GA, Abolmasova GI, Romanova ZA, Datsyk NA, Anninskii BE. 2013. Population dynamics of the ctenophore Mnemiopsis leidyi and its impact on the zooplankton in the coastal regions of the black sea of the Crimean coast in 2004-2008. Oceanology, 53(1): 80−88. doi: 10.1134/S0001437012050074
    [9]
    Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, et al. 2019. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. PLoS Computational Biology, 15(8): e1007273. doi: 10.1371/journal.pcbi.1007273
    [10]
    Goin OB, Goin CJ, Bachmann K. 1968. DNA and amphibian life history. Copeia, 1968(3): 532−540. doi: 10.2307/1442021
    [11]
    Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, et al. 2010. The genome of the western clawed frog Xenopus tropicalis. Science, 328(5978): 633−636. doi: 10.1126/science.1183670
    [12]
    Jiang JB, Quattrini AM, Francis WR, Ryan JF, Rodríguez E, McFadden CS. 2019. A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome. GigaScience, 8(4): giz026.
    [13]
    Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. 2011. Adaptive seeds tame genomic sequence comparison. Genome Research, 21(3): 487−493. doi: 10.1101/gr.113985.110
    [14]
    Korf I. 2004. Gene finding in novel genomes. BMC Bioinformatics, 5: 59. doi: 10.1186/1471-2105-5-59
    [15]
    Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. 2009. Circos: an information aesthetic for comparative genomics. Genome Research, 19(9): 1639−1645. doi: 10.1101/gr.092759.109
    [16]
    Leclère L, Horin C, Chevalier S, Lapébie P, Dru P, Peron S, et al. 2019. The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle. Nature Ecology & Evolution, 3(5): 801−810.
    [17]
    Majoros WH, Pertea M, Salzberg SL. 2004. TigrScan and glimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics, 20(16): 2878−2879. doi: 10.1093/bioinformatics/bth315
    [18]
    Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, et al. 2018. The axolotl genome and the evolution of key tissue formation regulators. Nature, 554(7690): 50−55. doi: 10.1038/nature25458
    [19]
    Oguz T, Salihoglu B, Moncheva S, Abaza V. 2012. Regional peculiarities of community-wide trophic cascades in strongly degraded black sea food web. Journal of Plankton Research, 34(4): 338−343. doi: 10.1093/plankt/fbs002
    [20]
    Olesen NJ, Purcell JE, Stoecker DK. 1996. Feeding and growth by ephyrae of scyphomedusae Chrysaora quinquecirrha. Marine Ecology Progress Series, 137(1-3): 149−159.
    [21]
    Olmo E, Morescalchi A. 2005. Genome and cell sizes in frogs: a comparison with salamanders. Experientia, 34: 44−46.
    [22]
    Pal K, Forcato M, Ferrari F. 2019. Hi-C analysis: from data generation to integration. Biophysical Reviews, 11(1): 67−68. doi: 10.1007/s12551-018-0489-1
    [23]
    Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, et al. 2016. Genome evolution in the allotetraploid frog Xenopus laevis. Nature, 538(7625): 336−343. doi: 10.1038/nature19840
    [24]
    Sun YB, Xiong ZJ, Xiang XY, Liu SP, Zhou WW, Tu XL, et al. 2015. Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes. Proceedings of the National Academy of Sciences of the United States of America, 112(11): E1257−E1262. doi: 10.1073/pnas.1501764112
    [25]
    Xia WX, Li HR, Cheng WM, Li HH, Mi YJ, Gou XC, et al. 2020. High-quality genome assembly of Chrysaora quinquecirrha provides insights into the adaptive evolution of jellyfish. Frontiers in Genetics, 11: 535. doi: 10.3389/fgene.2020.00535
  • 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(1)  / Tables(1)

    Article Metrics

    Article views (159) PDF downloads(31) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return