动植物高质量基因组的获取及其主要应用
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摘要
自国际千人基因组计划实施以来,伴随着测序技术的发展和成本的下降,几乎所有重要的动植物都拥有了参考基因组以及全基因组重测序数据。针对二代和三代测序技术产生的海量数据,准确和高效的组装是获得高质量基因组的关键。对于重复序列较多、杂合性较高的复杂基因组的组装尤其具有挑战性,基因组从头组装算法不断被更新,联合组装策略正在发挥强大优势。高质量的基因组不仅能提高精细定位效率,还能提高全基因组关联分析的准确性和精度,为动植物复杂性状的遗传机制解析奠定基础。同时,高质量的基因组对于比较基因组以及泛基因组的研究都具有重要的推动作用。
Since the implementation of the International Thousand Human Genome Project, almost all important plants and animals have attained reference genomes and genome-wide resequencing data with the development of sequencing technology and the decrease in sequencing costs. Accurate and efficient assembly of the vast amounts of data generated by second-and third-generation sequencing technologies is the key to acquire high-quality genomes.The assembly of complex genomes with more repeats and higher heterozygosity rate is particularly challenging.The genome de novo assembly algorithm is constantly being updated, and the joint assembly strategy is showing strong advantages. High-quality genomes not only improve the efficiency of fine mapping, but also improve the accuracy and precision of genome-wide association analysis, thus laying the foundation for the genetic dissection of complex traits of plants and animals. Meanwhile, high-quality genomes would promote the study of comparative genomics and pan-genomics.
Since the implementation of the International Thousand Human Genome Project, almost all important plants and animals have attained reference genomes and genome-wide resequencing data with the development of sequencing technology and the decrease in sequencing costs. Accurate and efficient assembly of the vast amounts of data generated by second-and third-generation sequencing technologies is the key to acquire high-quality genomes.The assembly of complex genomes with more repeats and higher heterozygosity rate is particularly challenging.The genome de novo assembly algorithm is constantly being updated, and the joint assembly strategy is showing strong advantages. High-quality genomes not only improve the efficiency of fine mapping, but also improve the accuracy and precision of genome-wide association analysis, thus laying the foundation for the genetic dissection of complex traits of plants and animals. Meanwhile, high-quality genomes would promote the study of comparative genomics and pan-genomics.
引文
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[2]The International Wheat Genome Sequencing Consortium(IWGSC),Appels R,Eversole K,et al.Shifting the limits in wheat research and breeding using a fully annotated reference genome.Science,2018,361:eaar7191
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[4]Zerbino D,Birney E.Velvet:algorithms for de novo short read assembly using de Bruijn graphs.Genome Res,2008,18:821-9
[5]Li R,Zhu H,Ruan J,et al.De novo assembly of human genomes with massively parallel short read sequencing.Genome Res,2010,20:265-72
[6]Xie Y,Wu G,Tang J,et al.SOAPdenovo-Trans:de novo transcriptome assembly with short RNA-Seq reads.Bioinformatics,2014,30:1660-6
[7]Ye C,Ma ZS.Sparc:a sparsity-based consensus algorithm for long erroneous sequencing reads.Peer J,2016,4:e2016
[8]Kajitani R,Toshimoto K,Noguchi H,et al.Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.Genome Res,2014,24:1384-95
[9]Gnerre S,Maccallum I,Przybylski D,et al.High-quality draft assemblies of mammalian genomes from massively parallel sequence data.Proc Natl Acad Sci USA,2011,108:1513-8
[10]Chin CS,Alexander DH,Marks P,et al.Nonhybrid,finished microbial genome assemblies from long-read SMRT sequencing data.Nat Methods,2013,10:563-9
[11]Ye C,Hill CM,Wu S,et al.DBG2OLC:efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies.Sci Rep,2016,6:31900
[12]Wang M,Tu L,Yuan D,et al.Reference genome sequences of two cultivated allotetraploid cottons,Gossypium hirsutum and Gossypium barbadense.Nat Genet,2019,51:224-9
[13]Deng Y,Zhai K,Xie Z,et al.Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance.Science,2017,355:962-5
[14]Stein JC,Yu Y,Copetti D,et al.Publisher correction:genomes of 13 domesticated and wild rice relatives highlight genetic conservation,turnover and innovation across the genus Oryza.Nat Genet,2018,50:285-96
[15]Yang Q,Li Z,Li W,et al.CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize.Proc Natl Acad Sci USA,2013,110:16969-74
[16]Huang C,Sun H,Xu D,et al.ZmCCT9 enhances maize adaptation to higher latitudes.Proc Natl Acad Sci USA,2018,115:E334-41
[17]Zhang Z,Zhang B,Chen Z,et al.A PECTIN METHYLE-STERASE gene at the maize Ga1 locus confers male function in unilateral cross-incompatibility.Nat Commun,2018,9:3678
[18]Zhang H,Liu X,Zhang Y,et al.Genetic analysis and fine mapping of the Ga1-S gene region conferring crossincompatibility in maize.Theor Appl Genet,2012,124:459-65
[19]Lauter ANM,Muszynski MG,Huffman RD,et al.A pectin methylesterase ZmPme3 is expressed in gametophyte factor1-s(Ga1-s)silks and maps to that locus in maize(Zea mays L.).Front Plant Sci,2017,8:1926
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[21]Huyghe JR,Bien SA,Harrison TA,et al.Discovery of common and rare genetic risk variants for colorectal cancer.Nat Genet,2019,51:76-87
[22]Li H,Peng Z,Yang X,et al.Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels.Nat Genet,2013,45:43-50
[23]Xue Y,Warburton ML,Sawkins M,et al.Genome-wide association analysis for nine agronomic traits in maize under well-watered and water-stressed conditions.Theor Appl Genet,2013,126:2587-96
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[26]Fang L,Wang Q,Hu Y,et al.Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits.Nat Genet,2017,49:1089-98
[27]Liu R,Gong J,Xiao X,et al.GWAS analysis and QTLidentification of fiber quality traits and yield components in upland cotton using enriched high-density SNP markers.Front Plant Sci,2018,9:1067
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[29]Wang J,Zhao X,Wang W,et al.Genome-wide association study of inflorescence length of cultivated soybean based on the high-throughout single-nucleotide markers.Mol Genet Genomics,2019,294:607-20
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[42]Sun C,Hu Z,Zheng T,et al.RPAN:rice pan-genome browser for~3000 rice genomes.Nucleic Acids Res,2016,45:597-605
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[51]Shang Y,Ma Y,Zhou Y,et al.Plant science.Biosynthesis,regulation,and domestication of bitterness in cucumber.Science,2014,346:1084-8