枣基因组的微卫星特征

doi:10.11707/j.1001-7488.20131212

摘要/Abstract

摘要：

利用454高通量测序技术对枣基因组进行部分测序。经序列拼接，共获得总长约为8.4 Mb的基因组序列，从中找到15 036个微卫星重复序列。其中六碱基重复类型的重复数目最丰富，共6 033个，占重复序列总数的40.1%；其次是复合型碱基2 707个和单碱基2 575个，分别占重复序列总数的18.0%和17.1%。另外，二碱基重复1 118个，三碱基1 050个，四碱基1 218个，五碱基335个，分别占重复序列总数的7.5%，7.0%，8.1%，2.2%。通过分析发现六碱基重复类型所占比例最多，但微卫星重复单元的重复次数变化却是二碱基微卫星显著高于其他各重复类型。在单碱基重复和二碱基重复这2种类型中，A/T以及AT/TA为最主要的重复单元；（AAN）_n，（AAAN）_n，（AAAAN）_n和（AAAAAN）_n为三碱基、四碱基、五碱基、六碱基重复类型中对应的优势重复单元，这些优势重复单元中富含A和T碱基。分析还发现，枣基因组微卫星长度变化的多样性与重复单元长度呈负相关（二碱基重复类型除外），这意味着枣基因组中重复单元较短的微卫星变异速率较快，而重复单元较长的微卫星变异速率较慢。对枣基因组微卫星侧翼序列分析发现，左侧序列与右侧序列GC含量相差不大；设计的引物序列中，有86%的引物可以特异扩增出含有SSR序列的位点。研究结果为枣的遗传研究提供丰富的序列信息和标记资源。

关键词: 枣, 基因组, 454测序, 微卫星

Abstract:

In this study, the genome of Ziziphus jujuba was partially sequenced using the Roche 454 FLX sequencer. The assembled sequences were totally 8.4 Mb, from which 15 036 microsatellites repeats were detected. Among them, the hexanucleotide repeats were the most abundant (6 033), accounting for 40.1% of the total microsatellites, following by the compound (2 707) and mononucleotide(2 575) repeats that accounted for 18.0% and 17.1% of the total microsatellites, respectively. The number of dinucleotide (1 118), trinucleotide (1 218), tetranucleotide (1 050), and pentanucleotide repeats (335), were found to account for 7.5%, 7.0%, 8.1%, 2.2% of the total microsatellites, respectively. While hexanucleotide repeats were the most abundant, dinucleotide repeats were more frequent than the other types of microsatellites in terms of changes in the number of repeat motifs. In mononucleotide and dinucleotide repeats, A/T and AT/TA were the main repeating motifs, while (AAN)_n, (AAAN)_n, (AAAAN)_n and (AAAAAN)_n were the dominant repeat motifs in tri-, tetra-, penta-and hexanucleotide repeats, respectively. All the dominant repeat motifs in different types of microsatellites were rich in A and T. It is noteworthy that the variation of microsatellites was found to be negatively correlated with the lengths of repeat motifs, which suggested that the microsatellites with longer repeat motifs would change faster than those with shorter repeat motifs. This study provided abundant genome sequences and marker resources for different aspects of genetic studies on Z. jujuba.

Key words: Ziziphus jujuba, genome, 454 sequencing, microsatellite

中图分类号:

S718.46

马秋月, 戴晓港, 陈赢男, 张得芳, 廖卓毅, 李淑娴. 枣基因组的微卫星特征[J]. 林业科学, 2013, 49(12): 81-87.

Ma Qiuyue, Dai Xiaogang, Chen Yingnan, Zhang Defang, Liao Zhuoyi, Li Shuxian. Characterization of Microsatellites in the Genome of Ziziphus jujuba[J]. Scientia Silvae Sinicae, 2013, 49(12): 81-87.

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