基于454测序的油茶DNA序列微卫星观察与分析

doi:10.11707/j.1001-7488.20130807

摘要/Abstract

摘要：

采用MISA软件挖掘比较各1/4个454高通量测序反应获得的普通油茶、浙江红山茶和短柱茶EST序列及普通油茶基因组序列中的微卫星信息。结果显示: 3个种的EST序列微卫星出现频率大小相近,普通油茶EST序列的微卫星出现频率高于其基因组序列的; 在所有被检索序列的二至六碱基微卫星中,均以二碱基微卫星最多(>55%),并以(AG)_n类型为主,但三碱基微卫星在所有EST序列中以(AAG)_n类型最多,而在普通油茶基因组序列中则以(AAT)_n最多; 除六碱基微卫星外,二至五碱基微卫星均表现为不同微卫星重复单元的丰度随着微卫星碱基长度增加而减少。在转录组序列中,除六碱基微卫星之外,不同微卫星单元重复数的变异与重复单元长度呈负相关,推测二碱基微卫星理论多态性最高,而五碱基微卫星理论多态性最低; 对在无冗余独立基因各区域中的微卫星进行统计,显示分布比例依次为3'UTR >CDS>5'UTR,在相同区域内比较,UTR区域中二碱基微卫星占总数量比例最大,CDS区域内三碱基微卫星的比例最高,此外5'UTR区域的三碱基微卫星的分布比例均高于3'UTR,初步推断5'UTR区域的微卫星相对3'UTR要保守些。

关键词: 山茶属, 454高通量测序, 微卫星

Abstract:

Abstract: By using 454 pyrosequencing, the simple sequence repeats (SSRs) from DNA sequences in three Camellia species, including C. oleifera, C. brevistyla and C. chekiangoleosa, were tapped with repeats of 2 to 6 bp by MISA. In all cases, the frequency of repeat motifs in the EST was similar, while the proportion in the EST of C. oleifera was higher than that of its genome. Comparisons of all SSRs, the dinucleotide repeat microsatellites (DNRs) were most dominant (>55%) and the most common DNRs was (AG)_n. The most common trinucleotide repeat microsatellites (TNRs) was (AAG)_n in EST, while the most common TNRs was (AAT)_n in the genome of C. oleifera. Apart from the hexaucleotide repeat microsatellites (HXNRs), the abundance of the other four classes of microsatellites was negatively correlated with their repeat motif lengths. In the EST, apart from the HXNRs, diversification of microsatellite lengths (repeat number variation) was also negatively correlated with their repeat motif lengths, and we predicted that DNRs was the highest polymorphism and pentaucleotide repeat microsatellites (PTNRs) was the lowest. Subsequently, statistical analysis on SSRs within coding regions (CDS) and untranslated regions (UTR) in the Unigene showed that the ratio of motifs distribution was ranked as the following: 3'UTR>CDS>5'UTR. The DNRs were the dominant microsatellite in UTR, while the TNRs were dominant in CDS. The proportion of TNRs in the 5'UTR was higher than that in the 3'UTR, indicating that the SSRs in the 5'UTR were more conservative.

Key words: Camellia, 454 pyrosequencing, microsatellites

中图分类号:

S718.46

温强, 徐林初, 江香梅, 李江, 顾胤聪, 徐立安, 黄敏仁. 基于454测序的油茶DNA序列微卫星观察与分析[J]. 林业科学, 2013, 49(8): 43-50.

Wen Qiang, Xu Linchu, Jiang Xiangmei, Li Jiang, Gu Yincong, Xu Li'an, Huang Minren. Survey and Analysis of Microsatellites from DNA Sequences in Camellia Species Using 454 Pyrosequencing[J]. Scientia Silvae Sinicae, 2013, 49(8): 43-50.

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