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 |
[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
|