Evolution Analysis of Simple Sequence Repeats in Plant Genome.
Evolution Analysis of Simple Sequence Repeats in Plant Genome.
复制标题
植物基因组中简单重复序列的进化分析
DOI：
10.1371/journal.pone.0144108
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Zhang L
中科院分区：
文献类型：
--
作者：
Qin Z;Wang Y;Wang Q;Li A;Hou F;Zhang L
简单重复序列（SSR）是植物基因组序列上广泛存在的一种单元，在植物中起着重要的作用。为了揭示植物基因组的进化过程，我们通过对12个已测序的植物基因组序列的分析，研究了SSR在植物物种和植物界进化过程中的进化规律。首先，在所研究的12个植物基因组中，主要的SSR是那些含有1-3个核苷酸组合的重复序列。其次，在单核苷酸SSR中，A/T百分比随着植物的进化而沿着逐渐增加（展叶藓除外）。随着SSR重复数的增加，C. reinhardtii变化不明显，而陆生植物的A/T比值逐渐下降。第三，在二核苷酸SSR中，AT/TA的比例随着植物界的进化而沿着增加，陆生植物的重复数也随之增加。这种趋势在双子叶植物中比单子叶植物更明显。CG/GC与AT/TA呈相反的变化规律。第四，在三核苷酸SSR中，随着植物界的进化，包含两个或三个A/T的组合所占的比例沿着呈上升趋势;同时随着SSR重复数在植物物种中的增加，不同物种选择不同的组合作为优势SSR。SSR在C. reinhardtii，P. patens，Z. mays和A.拟南芥表现出与进化位置或基因组序列特定变化相关的特定模式。结果表明，SSR不仅具有植物界进化的一般模式，而且与特定基因组序列的进化有关。SSR分子标记的进化分析为植物基因组进化分析提供了新的思路。
Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1–3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution.