Detecting and characterizing gene conversions between multigene family members
Detecting and characterizing gene conversions between multigene family members
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DOI：
10.1093/oxfordjournals.molbev.a026047
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发表时间：
1999-10-01
影响因子：
10.7
通讯作者：
Clarke, GDP
中科院分区：
文献类型：
--
作者：
Drouin, G;Prat, F;Clarke, GDP
我们使用了多种方法来检测已知的基因转换的肌动蛋白基因家族的5个被子植物物种，β-珠蛋白基因家族的两个灵长类动物物种，和Zfx/Zfy基因家族的7个哺乳动物物种。我们的目标是设计一种工作策略，它将允许分析多基因家族的成员，以确定其成员之间是否存在基因转换，识别参与基因转换的基因，确定转换区域的长度，并确定基因转换的极性。我们发现，三种系统发育方法和同源性测试的梅纳德史密斯和史密斯在我们的数据集上表现相对较差，因为我们分析的序列有大量的多个取代。索耶的方法、Jakobsen和Easteal的相容性方法、Jakobsen、Wilson和Easteal的划分矩阵方法以及Balding、Nichols和Hunt的共双方法可用于鉴定参与基因转换的基因。共双方法比其他方法更强大，但需要来自相关物种的正向序列。相容性、系统发育和核苷酸取代分布统计方法可用于鉴定转化区域的位置。也可以使用逐站点兼容性分析来确定转换事件的方向。因此，这些方法的组合可用于确定多基因家族成员之间基因转换的存在、位置和极性。
We used a variety of methods to detect known gene conversions in the actin gene families of five angiosperm species, the beta-globin gene families of two primate species, and the Zfx/Zfy gene families of seven mammalian species. Our goal was to devise a working strategy which would allow the analysis of the members of a multigene family in order to determine whether there had been gene conversions between its members, identify the genes involved in the gene conversions, establish the lengths of the converted regions, and determine the polarities of the gene conversions. We show that three phylogenetic methods and the homoplasy test of Maynard Smith and Smith perform relatively poorly on our data sets because the sequences we analyzed had large levels of multiple substitutions. The method of Sawyer, the compatibility method of Jakobsen and Easteal, the partition matrix method of Jakobsen, Wilson, and Easteal, and the co-double method of Balding, Nichols, and Hunt can be used to identify the genes which have been involved in gene conversions. The co-double method is more powerful than other methods but requires orthologous sequences from related species. Compatibility, phylogenetic, and nucleotide substitution distribution statistics methods can be used to identify the location of the converted region(s). Site-by-site compatibility analyses can also be used to identify the direction of the conversion event(s). Combinations of these methods can therefore be used to establish the presence, locations, and polarities of gene conversions between multigene family members.