National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
Genome. 2010 Jan;53(1):55-67. doi: 10.1139/g09-084.
Microsatellites present in the transcribed regions of the genome have the potential to reveal functional diversity. Unigene sequence databases are the sources of such genic microsatellites with unique flanking sequences and genomic locations even in complex polyploids. The present study was designed to assay the unigenes of Brassica napus and B. rapa for various microsatellite repeats, and to design markers and use them in comparative genome analysis and study of evolution. The average frequency of microsatellites in Brassica unigenes was one in every 7.25 kb of sequence, as compared with one in every 8.57 kb of sequence in Arabidopsis thaliana. Trinucleotide motifs coding for serine and the dinucleotide motif GA were most abundant. We designed 2374 and 347 unigene-based microsatellite (UGMS) markers including 541 and 58 class I types in B. napus and B. rapa, respectively, and evaluated their use across diverse species and genera. Most of these markers (93.3%) gave successful amplification of target microsatellite motifs, which was confirmed by sequencing. Interspecific polymorphism between B. napus and B. rapa detected in silico for the UGMS markers was 4.16 times higher in 5' untranslated regions than in coding sequences. Physical anchoring of Brassica UGMS markers on the A. thaliana genome indicated their significance in studying the evolutionary history of A. thaliana genomic duplications in relation to speciation. Comparative physical mapping identified 85% of Brassica unigenes as single copy and gave clues for the presence of conserved primordial gene order. Complex chromosomal rearrangements such as inversions, tandem and segmental duplications, and insertions/deletions were evident between A. thaliana and B. rapa genomes. The results obtained have encouraging implications for the use of UGMS markers in comparative genome analysis and for understanding evolutionary complexities in the family Brassicaceae.
微卫星存在于基因组的转录区域中，具有揭示功能多样性的潜力。基因序列数据库是此类基因微卫星的来源，这些微卫星具有独特的侧翼序列和基因组位置，即使在复杂的多倍体中也是如此。本研究旨在检测油菜和白菜的基因序列中的各种微卫星重复序列，并设计标记物，用于比较基因组分析和进化研究。与拟南芥相比，油菜基因序列中微卫星的平均频率为每 7.25kb 一个，而拟南芥为每 8.57kb 一个。编码丝氨酸的三核苷酸基序和 GA 二核苷酸基序最为丰富。我们设计了 2374 个和 347 个基于基因序列的微卫星（UGMS）标记物，分别在油菜和白菜中包括 541 个和 58 个 I 类标记物，并评估了它们在不同物种和属中的应用。这些标记物中的大多数（93.3%）成功扩增了目标微卫星基序，通过测序得到了验证。在油菜和白菜中，通过计算机预测的 UGMS 标记物的种间多态性在 5'非翻译区比编码区高 4.16 倍。将 Brassica UGMS 标记物物理定位到拟南芥基因组上，表明它们在研究拟南芥基因组重复与物种形成相关的进化历史方面具有重要意义。比较物理图谱确定了 85%的 Brassica 基因序列为单拷贝，并为保守的原始基因顺序的存在提供了线索。在拟南芥和白菜基因组之间，存在复杂的染色体重排，如倒位、串联和片段重复以及插入/缺失。这些结果为 UGMS 标记物在比较基因组分析中的应用以及理解 Brassicaceae 科的进化复杂性提供了令人鼓舞的启示。
