Borevitz Justin O, Hazen Samuel P, Michael Todd P, Morris Geoffrey P, Baxter Ivan R, Hu Tina T, Chen Huaming, Werner Jonathan D, Nordborg Magnus, Salt David E, Kay Steve A, Chory Joanne, Weigel Detlef, Jones Jonathan D G, Ecker Joseph R
Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12057-62. doi: 10.1073/pnas.0705323104. Epub 2007 Jul 12.
We used hybridization to the ATH1 gene expression array to interrogate genomic DNA diversity in 23 wild strains (accessions) of Arabidopsis thaliana (arabidopsis), in comparison with the reference strain Columbia (Col). At <1% false discovery rate, we detected 77,420 single-feature polymorphisms (SFPs) with distinct patterns of variation across the genome. Total and pair-wise diversity was higher near the centromeres and the heterochromatic knob region, but overall diversity was positively correlated with recombination rate (R(2) = 3.1%). The difference between total and pair-wise SFP diversity is a relative measure contrasting diversifying or frequency-dependent selection, similar to Tajima's D, and can be calibrated by the empirical genome-wide distribution. Each unique locus, centered on a gene, has a diversity and selection score that suggest a relative role in past evolutionary processes. Homologs of disease resistance (R) genes include members with especially high levels of diversity often showing frequency-dependent selection and occasionally evidence of a past selective sweep. Receptor-like and S-locus proteins also contained members with elevated levels of diversity and signatures of selection, whereas other gene families, bHLH, F-box, and RING finger proteins, showed more typical levels of diversity. SFPs identified with the gene expression array also provide an empirical hybridization polymorphism background for studies of gene expression polymorphism and are available through the genome browser http://signal.salk.edu/cgi-bin/AtSFP.
我们利用与ATH1基因表达阵列的杂交技术，检测了23个拟南芥野生株系（种质）相对于参考株系哥伦比亚（Col）的基因组DNA多样性。在错误发现率低于1%的情况下，我们检测到77420个单特征多态性（SFP），其在全基因组中呈现出不同的变异模式。着丝粒附近和异染色质结区域的总多样性和成对多样性较高，但总体多样性与重组率呈正相关（R² = 3.1%）。总SFP多样性与成对SFP多样性之间的差异是一种对比多样化或频率依赖性选择的相对指标，类似于 Tajima's D，并且可以通过全基因组的经验分布进行校准。每个以基因为中心的独特位点都有一个多样性和选择得分，这表明其在过去进化过程中的相对作用。抗病（R）基因的同源物包括多样性特别高的成员，它们通常表现出频率依赖性选择，偶尔还能发现过去选择性清除的证据。类受体蛋白和S位点蛋白也包含多样性水平升高和选择特征的成员，而其他基因家族，如bHLH、F-box和环指蛋白，则表现出更典型的多样性水平。通过基因表达阵列鉴定的SFP也为基因表达多态性研究提供了一个经验性杂交多态性背景，可通过基因组浏览器http://signal.salk.edu/cgi-bin/AtSFP获取。
