Low frequency of microsatellites in the avian genome
Low frequency of microsatellites in the avian genome
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DOI：
10.1101/gr.7.5.471
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发表时间：
1997-05-01
期刊：
影响因子：
7
通讯作者：
Ellegren, H
中科院分区：
文献类型：
--
作者：
Primmer, CR;Raudsepp, T;Ellegren, H
更好地了解微卫星在一系列类群中的发生可能有助于理解简单重复序列的进化。先前的研究已经发现了几种重复基序的相对丰度在哺乳动物、无脊椎动物和植物中存在差异。微卫星的绝对数量也往往与基因组大小呈正相关。我们分析了鸟类中微卫星的发生，频率和分布，紫杉醇1是脊椎动物中已知的最小的基因组大小之一。斑点杂交显示，在22种不同的二、三和四核苷酸重复基序中，约有一半在人类中比在三种鸟类（鸡、啄木鸟和燕子）中更常见。通过搜索鸟类数据库序列，我们估计鸟类基因组中有30，000 - 70，000个长度超过20 bp的微卫星。（CA）的数量（大于或等于10）将为约7000 - 9000，并且（CA）的数量（大于或等于14）将为约3000。鸟类微卫星的计算密度[总计，每20 - 39 kb一个;（CA）（大于或等于10），每136 - 150 kb一个]远低于人类基因组的估计密度[分别为每6和30 kb一个]。这可以通过以下事实来解释，即鸟类基因组包含的非编码DNA比大多数哺乳动物相对较少，并且鸟类SINE/LINE元件不终止于poly（A）尾，已知poly（A）尾为哺乳动物中简单重复序列的进化提供了资源。我们没有发现鸟类的微卫星和SINE之间的关联。引物原位标记表明，（CA）（n）重复相当均匀地分布在鸡的大染色体和中间染色体，而小染色体，大部分的Z和W染色体，大多数端粒和着丝粒有非常低的浓度（CA），微卫星。微染色体上微卫星的稀缺性与这些区域可能异常丰富的编码序列是相容的。在基因组中，特别是在微染色体上的微卫星密度低，这对鸡和其他鸟类的标记丰富的遗传图谱的开发，以及数量性状基因的定位造成了障碍。
A better insight into the occurrence of microsatellites in a range of taxa may help to understand the evolution of simple repeats. Previous studies have found the relative abundance of several repeat motifs to differ among mammals, invertebrates, and plants. Absolute numbers of microsatellites also tend to correlate positively with genome size. We analyzed the occurrence, frequency, and distribution of microsatellites in birds, a taxol 1 with one of the smallest known genome sizes among vertebrates. Dot-blot hybridization revealed that about half of 22 different di-, tri-, and tetranucleotide repeat motifs were clearly more common il 1 human than in three species of birds: chicken, woodpecker, and swallow. For the remaining motifs no clear difference was found. From searching avian database sequences we estimated there to be 30,000-70,000 microsatellites longer than 20 bp in the avian genome. The number of (CA)(greater than or equal to 10) would be around 7000-9000 and the number of (CA)(greater than or equal to 14) about 3000. The calculated density of avian microsatellites [total, one every 20-39 kb; (CA)(greater than or equal to 10), one every 136-150 kb) is much lower than that estimated for the human genome [one every 6 and 30 kb, respectively). This may be explained by the Fact that the avian genome contains relatively less noncoding DNA than most mammals and that avian SINE/LINE elements do not terminate in poly(A) tails, which are known to provide a resource for the evolution of simple repeats in mammals. We found no association between microsatellites and SINEs in birds. Primed in situ labeling suggested fairly even distribution of (CA)(n) repeats over chicken macrochromosomes and intermediate chromosomes, whereas the microchromosomes, a large part of the Z and W chromosomes, and most telomeres and centromeres had very low concentrations of (CA), microsatellites. The scarcity of microsatellites on the microchromosomes is compatible to these regions likely being unusually rich In coding sequences. The low microsatellite density in the genome in general and on the microchromosomes in particular imposes an obstacle for the development of marker-rich genetic maps of chicken and other birds, and for the localization of quantitative trait genes.