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木本植物全基因组测序研究进展

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  • 南京林业大学林木遗传与生物技术省部共建教育部重点实验室, 南京 210037

收稿日期: 2011-09-07

  修回日期: 2011-11-02

  网络出版日期: 2012-02-25

基金资助

国家自然科学基金重点项目(编号:30930077), 国家自然科学基金青年项目(编号:30901156), 国家林业局948引进项目(编号:2009-4-24), 江苏高校自然科学基金项目(编号:09KJA220001)和江苏省高校优势学科建设工程项目(PAPD)资助

Progress on whole genome sequencing in woody plants

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  • Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China

Received date: 2011-09-07

  Revised date: 2011-11-02

  Online published: 2012-02-25

摘要

近年来, 植物全基因组测序的结果正如雨后春笋般涌现, 木本植物全基因组测序也在紧锣密鼓地展开。但由于木本植物通常基因组较大, 基因组结构较为复杂, 在测序、测序后的组装、注释、功能分析等均存在较大的困难。在基因组测序分析的经费预算方面也存在着较大的压力。因此, 有必要对这方面的研究进展及其存在问题进行分析比较, 以提高林木全基因组研究方面的效率。文章在比较分析已经发展起来的3代基因测序技术(Sanger测序法、合成测序法和单分子测序法)的基础上, 选择4种已经公布的木本植物(杨树、葡萄、番木瓜、苹果), 从全基因组测序的研究背景、测序结果及应用的研究进展和存在问题等方面进行了述评, 对未来要开展的木本植物全基因组测序前的准备工作(材料选择、遗传图谱和连锁图谱的构建、测序技术的选择), 全基因组测序结果的生物信息学分析和应用进行了讨论。

本文引用格式

施季森,王占军,陈金慧 . 木本植物全基因组测序研究进展[J]. 遗传, 2012 , 34(2) : 145 -156 . DOI: 10.3724/SP.J.1005.2012.00145

Abstract

In recent years, the number of sequencing data of plant whole genome have been increasing rapidly and the whole genome sequencing has been also performed widely in woody plants. However, there are a set of obstacles in investigating the whole genome sequencing in woody plants, which include larger genome, complex genome structure, limitations of assembly, annotation, functional analysis, and restriction of the funds for scientific research. Therefore, to promote the efficiency of the whole genome sequencing in woody plants, the development and defect of this field should be analyzed. The three-generation sequencing technologies (i.e., Sanger sequencing, synthesis sequencing, and single molecule sequenc-ing) were compared in our studies. The progress mainly focused on the whole genome sequencing in four woody plants (Populus, Grapevine, Papaya, and Apple), and the application of sequencing results also was analyzed. The future of whole genome sequencing research in woody plants, consisting of material selection, establishment of genetic map and physical map, selection of sequencing technology, bioinformatic analysis, and application of sequencing results, was discussed.

参考文献

[1] Food and Agriculture Organization of the United Nations (FAO). The state of the world's forest. Food and Agriculture Organization of the United Nations, Rome, 2003, ISBN 92-5-104865- 7.
[2] Jansson S, Douglas CJ. Populus: a model system for plant biology. Annu Rev Plant Biol, 2007, 58: 435-458.
[3] Kelleher CT, Chiu R, Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin TM, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O'connor K, Prabhu AL, Smailus DE, Stott JM, Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJM, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ, Schein JE. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant J, 2007, 50(6): 1063-1078.
[4] Sterck L, Rombauts S, Jansson S, Sterky F, Rouzé P, Van de Peer Y. EST data suggest that poplar is an ancient polyploid. New Phytol, 2005, 167(1): 165-170.
[5] The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 2000, 408(6814): 796-815.
[6] Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 2006, 313(5793): 1596- 1604.
[7] Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Wincker P; French-Italian Public Consortium for Grapevine Genome Characterization. The grapevine genome sequence suggests ancestral hexap- loidization in major angiosperm phyla. Nature, 2007, 449(7161): 463-467.
Ming R, Hou SB, Feng Y, Yu QY, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen CX, Alam M. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature, 2008, 452 (7190): 991-996.
 
[8] Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Viola R. The genome of the domesticated apple (Malus ×domestica Borkh.). Nat Genet, 2010, 42(10): 833-839.
[9] International Peach Genome Initiative (IPGI). 2010. http://www.rosaceae.org/peach/genome.
[10] Sato S, Hirakawa H, Isobe S, Fukai E, Watanabe A, Kato M, Kawashima K, Minami C, Muraki A, Nakazaki N, Ta-kahashi C, Nakayama S, Kishida Y, Kohara M, Yamada M, Tsuruoka H, Sasamoto S, Tabata S, Aizu T, Toyoda A, Shin-i T, Minakuchi Y, Kohara Y, Fujiyama A, Tsuchimoto S, Kajiyama S, Makigano E, Ohmido N, Shibagaki N, Cartagena JA, Wada N, Kohinata T, Atefeh A, Yuasa S, Matsunaga S, Fukui K. Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res, 2011, 18(1): 65-76.
[11] International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature, 2005, 436(7052): 793-800.
[12] Huang SW, Li RQ, Zhang ZH, Li L, Gu XF, Fan W, Lucas WJ, Wang XW, Xie BY, Ni PX, Ren YY, Zhu HM, Li J, Lin K, Jin WW, Fei ZJ, Li GC, Staub J, Kilian A, van der Vossen EAG, Li SG. The genome of the cucumber, Cucumis sativus L. Nat Genet, 2009, 41(12): 1275-1281.
[13] Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genom Human Genet, 2008, 9(1): 387-402.
[14] Kircher M, Kelso J. High-throughput DNA sequencing--concepts and limitations. BioEssays, 2010, 32(6): 524-536.
[15] Munroe DJ, Harris TJR. Third-generation sequencing fireworks at Marco Island. Nat Biotechnol<
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