WU Dongyang,YE Ning,XU Yiqing,et al.Microsatellite Characteristic Analysis of Chloroplast Genome of Actinidia kolomikta[J].Northern Horticulture,2018,42(09):30-35.[doi:10.11937/bfyy.20174592]
狗枣猕猴桃叶绿体基因组微卫星特征分析
- Title:
- Microsatellite Characteristic Analysis of Chloroplast Genome of Actinidia kolomikta
- Keywords:
- Actinidia kolomikta; chloroplast genome; microsatellite
- 文献标志码:
- A
- 摘要:
- 利用 NCBI 数据库收录的狗枣猕猴桃(Actinidia kolomikta)叶绿体基因组序列，应用MISA工具对其序列中的微卫星进行查找并对其分布规律进行分析。结果表明：狗枣猕猴桃叶绿体中共有41个重复单元长度为1～6碱基的微卫星重复序列，主要分布在LSC和SSC区域。其中单碱基重复的微卫星单元最为丰富，共28个，占重复序列总数的68.3%；二碱基重复单元次之，约占重复序列总数的19.5%，三碱基重复单元和六碱基重复单元个数相同，均约占重复序列总数的4.9%；五碱基重复单元个数最少，约占2.4%。在单碱基重复、二碱基重复和三碱基重复类型中，A/T、AT/TA、AAT/ATT为最主要的重复单元。分析还发现，该研究结果中单碱基重复单元变化次数最高，说明在狗枣猕猴桃叶绿体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。研究结果可为开发猕猴桃属植物叶绿体通用引物提供理论依据。
- Abstract:
- The chloroplast genome sequences of Actinidia kolomikta was used to analyze the distribution of microsatellite from GenBank Database.It was analyzed with bioinformatics software MISA.The results showed that it owned a total of 41 microsatellites in the chloroplast genome of Actinidia kolomikta with 1-6 base repeating units，mainly distributed in the large single-copy region(LSC) and the small single-copy region(SSC).Among them，the mononucleotide repeats(28)，were the most abundant accounting for 68.3% of the total microsatellites.The number of dinucleotide，trinucleotide，pentanucleotide and hexanucleotide repeats，were found to account for 19.5%，4.9%，2.4%，4.9% of the total microsatellites，respectively.In mononucleotide repeats，dinucleotide repeats and trinucleotide repeats，A/T，AT/TA and AAT/ATT were the main repeating motifs.It was noteworthy that the mononucleotide repeats were the most frequent of all types of microsatellites in terms of changes in the number of repeat motifs，which suggested that the microsatellites with longer repeat motifs would change faster than those with shorter repeat motifs.This study provided a theoretical basis for the development of general primers from chloroplast DNA in Actinidia Lindl.
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备注/Memo
第一作者简介：吴东洋（1978-），女，博士，讲师，研究方向为生物信息学。E-mail:eassun2000@sina.com.cn.基金项目：国家重点研究发展计划资助项目（2016yfd0600101）；国家自然科学基金资助项目（31570662，31500533，61401214）；南京林业大学大学生创新基金资助项目（2017NFUSPITP230）；江苏省自然科学基金资助项目(BK20170934)；南京林业大学青年科技创新基金资助项目(CX2017032)。收稿日期：2017-02-24