Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.).
Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.).
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DOI：
10.1186/1471-2164-11-569
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发表时间：
2010-10-15
期刊：
影响因子：
4.4
通讯作者：
Weng Y
中科院分区：
文献类型：
--
作者：
Cavagnaro PF;Senalik DA;Yang L;Simon PW;Harkins TT;Kodira CD;Huang S;Weng Y
黄瓜，Cucumis sativus L.是世界上重要的蔬菜作物。直到最近，黄瓜遗传和基因组资源，特别是分子标记，一直非常有限，阻碍了黄瓜育种工作的进展。微卫星是一种短的串联重复的DNA序列，由于其高度的多态性和共显性遗传，常被用作遗传标记。来自先前表征的基因组的数据已经表明，这些重复在频率、基序序列和基因组位置方面在不同分类群中有所不同。在过去的一年中，两个黄瓜基因型，包括中国鲜食型自交系'9930'和北美腌制型自交系'Gy 14'的基因组测序。这些序列为大规模开发标记物提供了强有力的工具。在这项研究中，我们调查和特点的203 Mbp的组装Gy 14 DNA序列，占其核基因组的55%，和黄瓜EST序列中的完美微卫星的分布和频率。对其他7种植物的基因组和EST数据进行了类似的分析，并与黄瓜的结果进行了比较。在Gy 14黄瓜基因组序列中共检测到112，073个完全重复，占Gy 14基因组组装的0.9%，总密度为551.9 SSR/Mbp。四核苷酸是最常见的微卫星序列，二核苷酸重复，其中有更多的重复单位比任何其他类型的SSR，具有最高的累积序列长度。黄瓜基因组的编码区（EST）与其基因组序列相比具有较少的微卫星，EST序列中以三核苷酸为主。AAG重复序列在黄瓜EST序列中出现频率最高。总体而言，AT丰富的图案普遍存在于基因组和EST数据。与其他物种相比，黄瓜基因组序列具有最高的SSR密度（尽管与白杨，葡萄藤和水稻的密度相当），并且AT二核苷酸最丰富。利用电子PCR技术对9930和Gy 14在1,006个SSR位点上的多态性进行了研究，发现两个基因型之间的多态性高达48.3%。多态性水平似乎与微卫星重复单位的数量呈正相关。在1，006个SSR位点中的660个中，计算机PCR结果被经验验证。此外，超过83，000个新发现的黄瓜微卫星的引物序列及其在Gy 14基因组组装中的确切位置也已公开。黄瓜基因组中含有丰富的微卫星序列，AT和AAG分别是黄瓜基因组和EST序列中最丰富的重复基序。考虑到所有的物种调查，注意到一些共性，特别是在单子叶植物和双子叶植物组，虽然图案的分布和某些重复的频率是物种的特点检查。本研究开发的大量SSR标记对葫芦科植物的研究具有重要意义。
Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line '9930' and the North American pickling type inbred line 'Gy14'. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber. A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The in silico PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newly-discovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available. The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.