Survey of simple sequence repeats in completed fungal genomes
Survey of simple sequence repeats in completed fungal genomes
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DOI：
10.1093/molbev/msi057
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发表时间：
2005-03-01
影响因子：
10.7
通讯作者：
Meyer, W
中科院分区：
文献类型：
--
作者：
Karaoglu, H;Lee, CMY;Meyer, W
简单重复序列或微卫星作为遗传标记的使用已经变得非常流行，因为它们在不同个体之间的丰度和长度变化。SSR是1至6个碱基对的串联重复单元，在许多原核和真核基因组中大量发现。这是第一个研究和比较完整测序的真菌基因组中的SSR。我们分析和比较的发生率，相对丰度，相对密度，最常见的，和最长的SSR在9个分类学上不同的真菌物种：构巢曲霉，新型隐球菌，脑炎，禾谷镰刀菌，稻瘟病菌，粗糙脉孢菌，酿酒酵母，粟酒裂殖酵母，玉米黑粉菌。我们的分析表明，在研究的所有基因组中，SSR的发生、丰度和相对密度各不相同，并且不受基因组大小的影响。相对丰度与基因组大小之间没有相关性，但N。crassa是分析的最大基因组，具有最高的SSR相对丰度。在大多数基因组中，单核苷酸，二核苷酸和三核苷酸重复比更长的重复SSR更丰富。一般来说，在每种生物体中，SSR的发生率、相对丰度和相对密度随着重复单位的增加而降低。此外，每种生物都有自己共同的和最长的SSR。我们的分析表明，与人类基因组相比，真菌中SSR的相对丰度较低，并且真菌中较长的SSR很少。除了提供关于这些真菌中每一种的SSR丰度的新信息外，这些结果还提供了分子标记的一般来源，这些分子标记可用于各种应用，如真菌生物的群体遗传学和菌株鉴定。
The use of simple sequence repeats or microsatellites as genetic markers has become very popular because of their abundance and length variation between different individuals. SSRs are tandem repeat units of 1 to 6 base pairs that are found abundantly in many prokaryotic and eukaryotic genomes. This is the first study examining and comparing SSRs in completely sequenced fungal genomes. We analyzed and compared the occurrences, relative abundance, relative density, most common, and longest SSRs in nine taxonomically different fungal species: Aspergillus nidulans, Cryptococcus neoformans, Encephalitozoon cuniculi, Fusarium graminearum, Magnaporthe grisea, Neurospora crassa, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Ustilago maydis. Our analysis revealed that, in all of the genomes studied, the occurrence, abundance, and relative density of SSRs varied and was not influenced by the genome sizes. No correlation between relative abundance and the genome sizes was observed, but it was shown that N. crassa, the largest genome analyzed had the highest relative abundance of SSRs. In most genomes, mononucleotide, dinucleotide, and trinucleotide repeats were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. Our analysis showed that the relative abundance of SSRs in fungi is low compared with the human genome and that longer SSRs in fungi are rare. In addition to providing new information concerning the abundance of SSRs for each of these fungi, the results provide a general source of molecular markers that could be useful for a variety of applications such as population genetics and strain identification of fungal organisms.