Twenty-First Century Plant Biology: Impacts of the Arabidopsis Genome on Plant Biology and Agriculture
Twenty-First Century Plant Biology: Impacts of the Arabidopsis Genome on Plant Biology and Agriculture
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DOI：
10.1104/pp.110.159541
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发表时间：
2010-10-01
期刊：
影响因子：
7.4
通讯作者：
Last, Robert L.
中科院分区：
文献类型：
--
作者：
Buell, C. Robin;Last, Robert L.
在20世纪80年代末和90年代初，拟南芥(Arabitopsis Thaliana)迅速成为植物生物学的模式系统，这是因为遗传方法易于研究发育、生理和基因功能，加上一个高度合作的社区。20世纪90年代初，当密歇根州立大学开始实施EST项目时，拟南芥作为主要模式植物系统的地位得到了巩固(Newman等人，1994年)。这是第一次在植物中进行这样的努力，它为拟南芥提供了大规模序列和功能基因组学资源的种子，到目前为止，这些资源在任何其他植物物种中都是无法比拟的。虽然EST项目将拟南芥的研究推向了基因组学时代，但这是植物生物界领袖们的远见卓识。以任何手段鉴定所有基因，并在2000年之前确定拟南芥基因组的完整序列“(http://www.拟南芥。Org/portals/masc/long_range_plan_1990。PDF)。由此产生的国际基因组协调努力，即拟南芥基因组倡议，为拟南芥从遗传模型系统向基因组模型系统的过渡奠定了基础。这最终公布了哥伦比亚(COL-0)加入的高质量基因组序列(拟南芥基因组倡议，2000年)。虽然在现在被称为参考基因组的高度重复的低复杂性区域中存在差距，但在可预见的未来，Col-0基因组序列的质量仍然是最高质量的植物基因组序列。当与其人工精选的注释相结合时，序列数据使拟南芥成为所有植物基因组的黄金标准。从1998年开始，Cereon Genology LLC(孟山都公司的全资子公司)利用Sanger测序技术(Jander等人，2002年)制作了Landsberg erecta基因组的低深度鸟枪序列，提供了对开花植物基因的早期观察。对于社区来说，获取Col-0和Landsberg erecta基因组序列揭示了这些地方种族之间前所未有的数量的多态，使100多项已发表的基于地图的克隆研究成为可能。据我们所知，它还为社区提供了第一个例子，说明对与高质量参考序列相关的加入或品种进行高通量测序如何使初始序列更有价值(Rounsley和Last，2010)。下一代测序技术允许以极低的成本进行高通量测序，现在对种质进行测序在巨大的规模上是可行的。分析1,001份拟南芥基因组全序列变异的计划(韦格尔和莫特，2009年)正在顺利进行，截至2010年初，已有近100个基因组完成(http://www.1001个基因组。Org/)。这一开创性的努力将导致对物种内遗传变异性的深入理解，并使基因组进化和种群生物学的分析成为可能。这说明了拟南芥的研究如何继续走在定义方法的前沿，这些方法将彻底改变我们对经济上重要的植物过程和植物物种的理解。基因表达状态受到DNA和染色质蛋白质修饰的影响。虽然仅靠标准基因组DNA序列不能直接报告这些修饰，但可以使用下一代测序方法在单核苷酸水平上评估这些表观遗传状态，并且正在出现对拟南芥表观基因组的描述性研究(Lister等人，2008年)。这些信息使对植物特有的生物学问题的研究成为可能，例如表观遗传印记和…
In the late 1980s and early 1990s, Arabidopsis (Arabidopsis thaliana) rapidly emerged as a model system for plant biology due to the ease of genetic approaches to study development, physiology, and gene function coupled with a highly collaborative community. Arabidopsis’s position as the premiere model plant system was cemented in the early 1990s when the EST project commenced at Michigan State University (Newman et al., 1994). This was the first such effort in plants and it seeded production of large-scale sequence and functional genomics resources for Arabidopsis that to this day are unmatched in any other plant species. While the EST project propelled Arabidopsis research into the genomics era, it was the foresight of leaders in the plant biology community to “... identify all of the genes by any means, and to determine the complete sequence of the Arabidopsis genome before the year 2000”(http://www. arabidopsis. org/portals/masc/Long_range_plan_1990. pdf). The resulting coordinated international genome sequence effort, the Arabidopsis Genome Initiative, laid the foundations for transition of Arabidopsis from a genetic to a genomic model system. This culminated in the publication of the high-quality genome sequence of the Columbia (Col-0) accession (Arabidopsis Genome Initiative, 2000). While there are gaps in highly repetitive lowcomplexity regions of what is now termed the reference genome, the quality of the Col-0 genome sequence is, and for the foreseeable future will remain, the highest quality plant genome sequence. When coupled with its manually curated annotation, the sequence data makes Arabidopsis the gold standard for all plant genomes. Starting in 1998, Cereon Genomics LLC (a wholly owned subsidiary of Monsanto Co.) produced a lowdepth shotgun sequence of the Landsberg erecta genome using Sanger sequencing technology (Jander et al., 2002), providing an early look at the genes of a flowering plant. For the community, access to both the Col-0 and Landsberg erecta genome sequences revealed an unprecedented number of polymorphisms between these landraces, enabling more than 100 published map-based cloning studies. To our knowledge, it also provided the community with the first example of how high-throughput sequencing of an accession or cultivar related to a high-quality reference sequence makes the initial sequence even more valuable (Rounsley and Last, 2010). Next-generation sequencing technologies permit high-throughput sequencing at greatly reduced costs and sequencing of accessions is now feasible at an enormous scale. The plan to analyze genome-wide sequence variation in 1,001 accessions of Arabidopsis (Weigel and Mott, 2009) is well under way with nearly 100 completed genomes as of early 2010 (http://www. 1001genomes. org/). This pioneering effort will result in a deep understanding of genetic variability within a species and permit analysis of genome evolution and population biology. This illustrates how Arabidopsis research continues to be at the forefront of defining approaches that will revolutionize our understanding of economically important plant processes and plant species.Gene expression states are affected by DNA and chromatin protein modification. While standard genome DNA sequence alone cannot directly report these decorations, these epigenetic states can be assessed at the single nucleotide level using next-generation sequencing approaches, and descriptive studies on the Arabidopsis epigenome are emerging (Lister et al., 2008). This information enables studies of biological problems that are unique to plants such as epigenetic imprinting …