Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers
Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers
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DOI：
10.1007/s00294-010-0328-9
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发表时间：
2011-04-01
期刊：
影响因子：
2.5
通讯作者：
Martin, Francis
中科院分区：
文献类型：
--
作者：
Labbe, Jessy;Murat, Claude;Martin, Francis
越来越清楚的是，简单重复序列（SSR）在真菌基因组组织中起着重要作用，它们是群体遗传学和减数分裂图谱的遗传标记的重要来源。通过计算机模拟技术鉴定了双色蜡蚧基因组中的SSR位点，并分析了它们在基因组不同区域的分布。比较了L.与以下真菌基因组的那些同源：黄孢原毛平革菌、灰盖鬼伞、玉米黑粉菌、新型隐球菌、构巢曲霉、稻瘟病菌、粗糙脉孢菌和酿酒酵母。使用MISA计算机程序，我们在L.双色基因组代表8%的组装基因组序列。在所分析的担子菌中，L. bicolor的SSR密度最高，但相对丰度与基因组大小之间没有相关性。在大多数基因组中，短基序（单到三核苷酸）比长重复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。在L.在双色基因组中，大部分SSR位于基因间区域（73.3%），其中转座元件（TEs）的SSR密度最高，为6，706个SSR/Mb。然而，81%的蛋白质编码基因在其外显子中含有SSR，这表明SSR多态性可能会改变基因表型。在L。双色后代中，78个SSR的序列多态性主要分布在非TE基因间区。与以前开发的微卫星标记不同，这些新的微卫星标记分布在整个基因组中;这些标记可以立即应用于群体遗传学。
It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) 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. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.