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High-continuity genome assembly of the jellyfish Chrysaora quinquecirrha

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

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

大西洋海刺水母高连接度的基因组组装

doi: 10.24272/j.issn.2095-8137.2020.258

High-continuity genome assembly of the jellyfish Chrysaora quinquecirrha

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
  • 摘要: 大西洋海刺水母(Chrysaora quinquecirrha)具有非常重要的生态价值和进化地位。然而,由于使用有限的测序技术和水母本身复杂的基因组等原因,导致之前组装出的大西洋海刺水母基因组序列片段化严重。因此,在本研究中我们使用当前先进的高通量染色体构象捕获(Hi-C)技术来获得高覆盖度的大西洋海刺水母基因组测序数据。然后,我们将得到的Hi-C数据回帖到前期发表的大西洋海刺水母contig水平的基因组上来提高其序列的连接度。最终,我们成功构建出了一个N50长度为3.83Mb的高连接度的大西洋海刺水母基因组序列(包含了1882个scaffold序列),此基因组版本的N50长度是之前所公布contig水平基因组长度的5.23倍。而且,进一步的多种评估分析结果表明该基因组版本具有较高的连接度和准确性。获取大西洋海刺水母高连接度的基因组序列,不仅为我们利用比较基因组学的手段研究水母的进化提供了基础,而且为我们研究水母的生长发育等基本问题提供了重要的资源。
    #Authors contributed equally to this work
  • Figure  1.  Statistics and evaluation of Hi-C-based genome assembly

    A: Cumulative assembly length of sequences from two genome assemblies of C. quinquecirrha. Two versions, including previously published contig version (Xia et al., 2020) and Hi-C version from this study, were used in statistical analysis. Dots above and below each line indicate L50 and L90 values, respectively. B: Scaffold-level genome assembly of C. quinquecirrha. Assembly results are shown in Circos diagram, with outer to inner rings showing distribution of protein-coding genes, tandem repeats (TRP), long tandem repeats (LTR), short interspersed repetitive elements (SINE), long interspersed repetitive elements (LINE), DNA elements, and GC content, respectively. C: Distribution of contigs and coding genes in each scaffold. Plot shows gene density distribution, contig number, and coding gene number in each scaffold, from left to right. D: Synteny of genomes between scaffold-level C. quinquecirrha and A. aurita. Syntenic blocks are linked between two genomes with a Circos plot.

    Table  1.   Statistics of two genome versions

    Statistical item Length (bp) Number Length (bp) Number
    Version Contig-version (Xia et al., 2020) Hi-C version (this study)
    N90 66 354 666 227 000 195
    N80 205 342 365 582 500 109
    N70 395 469 249 873 000 62
    N60 555 468 178 2 312 428 36
    N50 733 647 125 3 825 607 24
    Average length (bp) 134 943 179 287
    Max length (bp) 4 015 784 15 257 941
    Total length (bp) 336 819 409 337 419 359
    Total number 2 496 1 882
    Number ≥1 000 (bp) 2 496 1 880
    下载: 导出CSV
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  • ZR-2020-258 Supplementary Tables and Figures.pdf
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出版历程
  • 收稿日期:  2020-09-07
  • 录用日期:  2020-12-24
  • 网络出版日期:  2020-12-28
  • 刊出日期:  2021-01-18

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