The pattern of polymorphism in Arabidopsis thaliana.
The pattern of polymorphism in Arabidopsis thaliana.
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DOI：
10.1371/journal.pbio.0030196
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发表时间：
2005-07
期刊：
影响因子：
9.8
通讯作者：
Bergelson J
中科院分区：
文献类型：
--
作者：
Nordborg M;Hu TT;Ishino Y;Jhaveri J;Toomajian C;Zheng H;Bakker E;Calabrese P;Gladstone J;Goyal R;Jakobsson M;Kim S;Morozov Y;Padhukasahasram B;Plagnol V;Rosenberg NA;Shah C;Wall JD;Wang J;Zhao K;Kalbfleisch T;Schulz V;Kreitman M;Bergelson J
我们对96个拟南芥个体的876个短片段进行了重测序，其中包括库存中心的加入以及来自自然群体的分层样品。虽然A. thaliana是一种自交杂草，多态性的模式一般同意什么是广泛分布，有性繁殖的物种的预期。连锁不平衡在50 kb内迅速衰减。尽管种群结构和因距离而造成的隔离是明显的，但全世界都有变异。这些数据在几个方面都不符合标准的中性模型。基因组范围内稀有等位基因过剩，至少部分原因是选择。在多态性水平上，基因组区域之间存在太多的变异。局部多态性水平与基因密度呈负相关，与片段重复呈正相关。由于数据不符合理论零分布，因此尝试从多态性数据推断自然选择将需要全基因组多态性调查，以识别异常区域。尽管如此，我们的数据支持A. thaliana作为进化功能基因组学的模型。拟南芥基因组DNA序列多态性的系统性全球调查显示，标准的遗传测试选择不适用于这个物种，但支持其作为模式生物的地位。
We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics. A systematic global survey of genomic DNA sequence polymorphism in Arabidopsis thaliana reveals that standard genetic tests for selection do not apply to this species but supports its status as a model organism.
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影响因子：
9.8
作者：
Akey JM;Eberle MA;Rieder MJ;Carlson CS;Shriver MD;Nickerson DA;Kruglyak L
通讯作者：
Kruglyak L
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作者：
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