National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute (IARI), New Delhi, India.
PLoS One. 2011;6(6):e21298. doi: 10.1371/journal.pone.0021298. Epub 2011 Jun 21.
Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice) and dicots (Arabidopsis, Medicago and Populus) was performed. A total of 797,863 simple sequence repeats (SSRs) were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database 'BraMi' (Brachypodium microsatellite markers) of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot-dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium and related grass species, especially for the map based cloning of the candidate gene(s).
植物基因组复杂，含有大量重复 DNA，包括分布在整个基因组中的微卫星。几种单子叶和双子叶植物的全基因组序列在公共领域可用，为研究微卫星的起源、分布和进化提供了机会，也为新的分子标记的开发提供了便利。本研究对单子叶植物（短柄草、高粱和水稻）和双子叶植物（拟南芥、紫花苜蓿和杨树）的微卫星分布进行了全基因组分析。在 6 种植物的全基因组序列中共鉴定出 797863 个简单序列重复（SSR）。这些 SSR 的特征表明，单核苷酸重复是最丰富的重复，在单子叶植物和双子叶植物中，重复的频率随着基序长度的增加而降低。然而，无论是核基因组还是叶绿体基因组，双子叶植物的 SSR 频率都高于单子叶植物。有趣的是，富含 GC 的重复仅在单子叶植物中占主导地位，其中大多数存在于编码区。这些编码 GC 丰富的重复被发现参与不同的生物过程，主要是结合活性。此外，还开发了一套 22879 个经 e-PCR 验证的 SSR 标记，并首次在短柄草的不同染色体上进行了定位，每个 Mb 有 101 个 SSR 标记。对 55 个标记的实验验证表明，在 16 个短柄草品系中，80%的 SSR 标记成功扩增。开发了一个名为“BraMi”（短柄草微卫星标记）的这些全基因组 SSR 标记的在线数据库，并在公共领域提供。观察到的 SSR 标记分布的差异模式将有助于研究单子叶植物-双子叶植物系统中的微卫星进化。本研究开发的 SSR 标记将有助于短柄草和相关禾本科物种的基因组研究，特别是候选基因（s）的图谱克隆。
