园艺作物基因组测序研究进展
摘要
回顾了园艺作物全基因组测序的发展历程,介绍3代测序技术的特点和应用现状。总结了葡萄、番木瓜、草莓等果树,黄瓜、白菜、番茄等蔬菜以及莲、康乃馨等花卉在内的25种园艺作物基因组测序简况。重点介绍了全基因组测序在基因注释、比较基因组学研究、重测序、全基因组关联分析、转录组学、SNP芯片开发等方面的应用。最后讨论了全基因测序研究的难点和今后的研究方向。
引文
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[2]Collins F S,Morgan M,Patrinos A.The human genome project:lessons from large-scale biology[J].Science,2003,300(5617):286-290.
[3]Arabidopsis Genome Initiative.Analysis of the genome sequence of the flowering plant Arabidopsis thaliana[J].Nature,2000,408(6814):796-815.
[4]Schloss J A.How to get genomes at one ten-thousandth the cost[J].Nature Biotechnology,2008,26(10):1113-1115.
[5]Margulies M,Egholm M,Altman W E,et al.Genome sequencing in microfabricated high-density picolitre reactors[J].Nature,2005,437(757):376-380.
[6]Velasco R,Zharkikh A,Affourtit J,et al.The genome of the domesticated apple(Malus×domestica Borkh.)[J].Nature Genetics,2010,42(10):833-839.
[7]Argout X,Salse J,Aury J M,et al.The genome of Theobroma cacao[J].Nature Genetics,2011,43(2):101-108.
[8]Rodríguez-Moreno L,González V M,Benjak A,et al.Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin[J].BMC Genomics,2011,12:424.
[9]Huang S,Li R,Zhang Z,et al.The genome of the cucumber,Cucumis sativus L.[J].Nature Genetics,2009,41(12):1275-1281.
[10]Shulaev V,Sargent D J,Crowhurst R N,et al.The genome of woodland strawberry(Fragaria vesca)[J].Nature Genetics,2011,43(2):109-116.
[11]Wang X,Wang H,Wang J,et al.The genome of the mesopolyploid crop species Brassica rapa[J].Nature Genetics,2011,43(10):1035-1039.
[12]Potato Genome Sequencing Consortium,Xu X,Pan S,et al.Genome sequence and analysis of the tuber crop potato[J].Nature,2011,475(7355):189-195.
[13]D'hont A,Denoeud F,Aury J M,et al.The banana(Musa acuminata)genome and the evolution of monocotyledonous plants[J].Nature,2012,488(7410):213-217.
[14]Xu Q,Chen L L,Ruan X,et al.The draft genome of sweet orange(Citrus sinensis)[J].Nature Genetics,2013,45(1):59-66.
[15]Guo S,Zhang J,Sun H,et al.The draft genome of watermelon(Citrullus lanatus)and resequencing of 20 diverse accessions[J].Nature Genetics,2013,45(1):51-58.
[16]Jaillon O,Aury J M,Noel B,et al.The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla[J].Nature,2007,449(7161):463-467.
[17]Ming R,Hou S,Feng Y,et al.The draft genome of the transgenic tropical fruit tree papaya(Carica papaya Linnaeus)[J].Nature,2008,452(7190):991-996.
[18]Al-Dous E K,George B,Al-Mahmoud M E,et al.De novo genome sequencing and comparative genomics of date palm(Phoenix dactylifera)[J].Nature Biotechnology,2011,29(6):521-527.
[19]Sato S,Tabata S,Hirakawa H,et al.The tomato genome sequence provides insights into fleshy fruit evolution[J].Nature,2012,485(740):635-641.
[20]Wu J,Wang Z,Shi Z,et al.The genome of the pear(Pyrus bretschneideri Rehd.)[J].Genome Research,2013,23(2):396-408.
[21]Zhang Q,Chen W,Sun L,et al.The genome of Prunus mume[J].Nature Communications,2012,3:1318.
[22]International Peach Genome Initiative,Verde I,Abbott A G,et al.The high-quality draft genome of peach(Prunus persica)identifies unique patterns of genetic diversity,domestication and genome evolution[J].Nature Genetics,2013,45(5):487-494.
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[24]Cheng S,van den Bergh E,Zeng P,et al.The tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers[J].The Plant Cell,2013,25(8):2813-2830.
[25]Huang S,Ding J,Deng D,et al.Draft genome of the kiwifruit Actinidia chinensis[J].Nature Communications,2013,4:2640.
[26]Yagi M,Kosugi S,Hirakawa H,et al.Sequence analysis of the genome of carnation(Dianthus caryophyllus L.)[J].DNA Research:an International Journal for Rapid Publication of Reports on Genes and Genomes,2014,21(3):231-241.
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[30]Cai J,Liu X,Vanneste K,et al.The genome sequence of the orchid Phalaenopsis equestris[J].Nature Genetics,2015,47(1):65-72.
[31]Eid J,Fehr A,Gray J,et al.Real-time DNA sequencing from single polymerase molecules[J].Science,2009,323(5910):133-138.
[32]Rasko D A,Webster D R,Sahl J W,et al.Origins of the E.coli strain causing an outbreak of hemolytic-uremic syndrome in Germany[J].The New England Journal of Medicine,2011,365(8):709-717.
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[35]Qi J,Liu X,Shen D,et al.A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity[J].Nature Genetics,2013,45(12):1510-1515.
[36]Shirasawa K,Fukuoka H,Matsunaga H,et al.Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato[J].DNA Research:an International Journal for Rapid Publication of Reports on Genes and Genomes,2013,20(6):593-603.
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