Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Nat Genet. 2011 Aug 7;43(9):913-8. doi: 10.1038/ng.889.
Thellungiella parvula is related to Arabidopsis thaliana and is endemic to saline, resource-poor habitats, making it a model for the evolution of plant adaptation to extreme environments. Here we present the draft genome for this extremophile species. Exclusively by next generation sequencing, we obtained the de novo assembled genome in 1,496 gap-free contigs, closely approximating the estimated genome size of 140 Mb. We anchored these contigs to seven pseudo chromosomes without the use of maps. We show that short reads can be assembled to a near-complete chromosome level for a eukaryotic species lacking prior genetic information. The sequence identifies a number of tandem duplications that, by the nature of the duplicated genes, suggest a possible basis for T. parvula's extremophile lifestyle. Our results provide essential background for developing genomically influenced testable hypotheses for the evolution of environmental stress tolerance.
小盐芥是拟南芥的近缘物种，且仅生存在盐分高、资源贫瘠的环境中，这使它成为研究植物适应极端环境进化的模式生物。在这里，我们展示了这个极端环境生物的基因组草图。仅通过下一代测序，我们就获得了无间隙 1496 个连续序列，这与估计的 140Mb 基因组大小非常接近。我们在没有使用图谱的情况下，将这些连续序列锚定到了 7 个假染色体上。我们表明，对于一个缺乏遗传信息的真核生物物种，短读序列可以近乎完整地组装到染色体水平。该序列鉴定了一些串联重复序列，根据重复基因的性质，这些序列可能为小盐芥的极端环境生活方式提供了基础。我们的结果为发展具有基因组影响力的、可用于测试环境胁迫耐受性进化假说提供了重要背景。
