（图片来源：http://dx.doi.org/10.1016/j.cell.2016.05.063）

2016年6月9日，1135个拟南芥（Arabidopsis thaliana）基因组重测序的论文在 Cell 期刊在线发表。论文的作者是 The 1001 Genomes Consortium，也就是拟南芥1001基因组计划的合作组织。这个“拟南芥1001基因组计划”是2008年启动的，旨在通过对模式植物拟南芥至少1001个品系（生态型）的全基因组序列分析，揭示其基因组上详细的序列变异。1001基因组计划收集的所有拟南芥品系种子免费对所有人开放，索取方式参见其网站（http://1001genomes.org）。自从2010年开始，1001基因组计划的部分数据就陆续发表 Genome Research, PNAS, Nature Genetics 和 Nature 上，而这篇对 1135 个拟南芥基因组全基因组序列分析的论文的发表，宣告了 1001 基因组计划项目第一阶段的结束。

这篇论文展示了 1135 个拟南芥自然近交系（naturally inbred lines）的基因组，发现拟南芥祖先栖息地依然栖息着残余群体，以及末次盛冰期（The last glacial maximum）对残余群体分布的结构具有很重要的影响。相信这些收集的拟南芥基因组数据会在整个物种水平上连接基因型和表型。

论文标题：1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana （http://dx.doi.org/10.1016/j.cell.2016.05.063）

Teaser

Genomic sequencing analysis of over 1,000 natural inbred lines of Arabidopsis thaliana reveals its global population structure, migration patterns, and evolutionary history and provides a rich genetic resource for studying phenotypic variation and adaptation.

Highlights

• The genomes of 1,135 naturally inbred lines of Arabidopsis thaliana are presented
  

• Relict populations that continue to inhabit ancestral habitats were discovered
  

• The last glacial maximum was important in structuring the distribution of relicts
  

• This collection will connect genotypes and phenotypes on a species-wide level

Summary

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

参考资料：

1. The 1001 Genomes Consortium (2016). 1135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell, June 9, 2016

2. Ossowski, S., Schneeberger, K., Clark, R.M., Lanz, C., Warthmann, N., and Weigel, D. (2008). Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research 18, 2024-2033. (MPIOssowski2008)

3. Schneeberger, K., Ossowski, S., Ott, F., Klein, J.D., Wang, X., Lanz, C., Smith, L.M., Cao, J., Fitz, J., Warthmann, N., et al. (2011). Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc. Natl. Acad. Sci. USA 108, 10249-10254. (MPISchneeberger2011)

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5. Long, Q., Rabanal, F. A., Meng, D., Huber, C. D., Farlow, A., Platzer, A., Zhang, Q., Vilhjalmsson, B. J., Korte, A., Nizhynska, V., Voronin, V., Korte, P., Sedman, L., Mandakova, T., Lysak, M. A., Seren, U., Hellmann, I., and Nordborg, M. (2013). Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nature Genetics 45, 884-890. (GMINordborg2010)

6. Schmitz, R. J., Schultz, M. D., Urich, M. A., Nery, J. R., Pelizzola, M., Libiger, O., Alix, A., McCosh, R. B., Chen, H., Schork, N. J., and Ecker, J. R. (2013). Patterns of population epigenomic diversity. Nature 495, 193-198. (Salk)

7. Gan, X., Stegle, O., Behr, J., Steffen, J. G., Drewe, P., Hildebrand, K. L., Lyngsoe, R., Schultheiss, S. J., Osborne, E. J., Sreedharan, V. T., Kahles, A., Bohnert, R., Jean, G., Derwent, P., Kersey, P., Belfield, E. J., Harberd, N. P., Kemen, E., Toomajian, C., Kover, P. X., Clark, R. M., Rätsch, G., and Mott, R. (2011). Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477, 419-423.

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