复杂基因组测序技术研究进展
收稿日期: 2018-09-10
修回日期: 2018-10-29
网络出版日期: 2018-11-07
Advances of sequencing and assembling technologies for complex genomes
Received date: 2018-09-10
Revised date: 2018-10-29
Online published: 2018-11-07
高胜寒,禹海英,吴双阳,王森,耿佳宁,骆迎峰,胡松年 . 复杂基因组测序技术研究进展[J]. 遗传, 2018 , 40(11) : 944 -963 . DOI: 10.16288/j.yczz.18-255
Complex genomes are noted to be extremely difficult to sequence or assemble by using ordinary methods. Complex genomes are typically characterized as being highly repetitive, highly heterozygous, extremely GC biased, or naturally contaminated, i.e., contaminations which cannot be removed before sequencing. To solve these problems with sequencing and assembling complex genomes, three major techniques include: (1) DNA extraction experiments, (2) Sequencing technologies and platforms, and (3) Algorithms and strategies for assembling. In this review, we summarize these state-of-the-art technologies and strategies used in these directions. We also review the representative projects of complex genome sequencing and address the development of these technologies and strategies for solving the challenges when sequencing or assembling complex genomes.
Key words： complex genome; genome assembly; genome sequencing technologies
| [1] | Jiao WB, Schneeberger K . The impact of third generation genomic technologies on plant genome assembly. Curr Opin Plant Biol, 2017,36:64-70. |
| [2] | Tang C, Yang M, Fang Y, Luo Y, Gao S, Xiao X, An Z, Zhou B, Zhang B, Tan X, Yeang HY, Qin Y, Yang J, Lin Q, Mei H, Montoro P, Long X, Qi J, Hua Y, He Z, Sun M, Li W, Zeng X, Cheng H, Liu Y, Yang J, Tian W, Zhuang N, Zeng R, Li D, He P, Li Z, Zou Z, Li S, Li C, Wang J, Wei D, Lai CQ, Luo W, Yu J, Hu S, Huang H . The rubber tree genome reveals new insights into rubber production and species adaptation. Nat Plants, 2016,2(6):16073. |
| [3] | Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M, Tanaka EM, Myers EW . The axolotl genome and the evolution of key tissue formation regulators. Nature, 2018,554(7690):50-55. |
| [4] | Wei C, Yang H, Wang S, Zhao J, Liu C, Gao L, Xia E, Lu Y, Tai Y, She G, Sun J, Cao H, Tong W, Gao Q, Li Y, Deng W, Jiang X, Wang W, Chen Q, Zhang S, Li H, Wu J, Wang P, Li P, Shi C, Zheng F, Jian J, Huang B, Shan D, Shi M, Fang C, Yue Y, Li F, Li D, Wei S, Han B, Jiang C, Yin Y, Xia T, Zhang Z, Bennetzen JL, Zhao S, Wan X . Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. Proc Natl Acad Sci USA, 2018,115(18):E4151-E4158. |
| [5] | Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, Yabana M, Harada M, Nagayasu E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T . Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res, 2014,24(8):1384-1395. |
| [6] | Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J, Liang X, Huang G, Percy RG, Liu K, Yang W, Chen W, Du X, Shi C, Yuan Y, Ye W, Liu X, Zhang X, Liu W, Wei H, Wei S, Huang G, Zhang X, Zhu S, Zhang H, Sun F, Wang X, Liang J, Wang J, He Q, Huang L, Wang J, Cui J, Song G, Wang K, Xu X, Yu JZ, Zhu Y, Yu S . Genome sequence of cultivated upland cotton ( Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol, 2015,33(5):524-530. |
| [7] | Sun F, Fan G, Hu Q, Zhou Y, Guan M, Tong C, Li J, Du D, Qi C, Jiang L, Liu W, Huang S, Chen W, Yu J, Mei D, Meng J, Zeng P, Shi J, Liu K, Wang X, Wang X, Long Y, Liang X, Hu Z, Huang G, Dong C, Zhang H, Li J, Zhang Y, Li L, Shi C, Wang J, Lee SM, Guan C, Xu X, Liu S, Liu X, Chalhoub B, Hua W, Wang H . The high-quality genome of Brassica napus cultivar ‘ZS11’ reveals the introgression history in semi-winter morphotype. Plant J, 2017,92(3):452-468. |
| [8] | Chen YC, Liu T, Yu CH, Chiang TY, Hwang CC . Effects of GC bias in next-generation-sequencing data on de novo genome assembly. PLoS One, 2013,8(4):e62856. |
| [9] | Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ . Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods, 2009,6(4):291-295. |