|Table of Contents|

Microsatellite Characteristic Analysis of Chloroplast Genome of Actinidia kolomikta

《北方园艺》[ISSN:1001-0009/CN:23-1247/S]

Issue:
2018年09
Page:
30-35
Research Field:
Publishing date:

Info

Title:
Microsatellite Characteristic Analysis of Chloroplast Genome of Actinidia kolomikta
Author(s):
WU Dongyang1; 2; YE Ning2; XU Yiqing2; ZHANG Li2; ZHOU Xiaoliang2
(1.College of Forest Resouces and Environment，Nanjing Forestry University，Nanjing，Jiangsu 210037;2.College of Information Science and Technology,Nanjing Forestry University，Nanjing，Jiangsu 210037)
Keywords:
Actinidia kolomikta; chloroplast genome; microsatellite
PACS:
-
DOI:
10.11937/bfyy.20174592
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.

References:

 

[1]ZIETKIEWICZ E，RAFALSKI A，LABUDA D.Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification[J].Genomics,1994,20(2):176-183.

[2]van BELKUM A，SCHERER S，van ALPHEN L，et al.Short-sequence DNA repeats in prokaryotic genomes[J].Microbiol Mol Biol Rev,1998,62(2):275-293.

[3]TRIVEDI S.Comparison of simple sequence repeats in 19 Archaea[J].Genetics & Molecular Research Gmr,2006,5(4):741.

[4]杨纪青,袁磊,杨凤.马铃薯X病毒完整基因组上微卫星分布[J].基因组学与应用生物学，2010,29(6):1064-1071.

[5]MRZEK J,GUO X,SHAH A.Simple sequence repeats in prokaryotic genomes[J].Proceedings of the National Academy of Sciences of the United States of America，2007，104(20):8472-8428.

[6]PIQUEMAL J，CINQUIN E，COUTON F，et al.Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers[J].Theoretical & Applied Genetics,2005,111(8):1514-1523.

[7]GUPTA P，BALYAN H，EDWARDS K，et al.Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat[J].Theoretical & Applied Genetics,2002,105(2-3):413.

[8]赵会彦,肖麓,杜德志.青海大黄油菜黄籽基因SSR标记开发和图谱构建[J].江苏农业科学，2014,42(1):32-35.

[9]CHENG B S，WAN Z B，HONG D L.Establishment of SSR fingerprint map and analysis of genetic similarity among 35 varieties in japonica rice(Oryza sativa L.)[J].Journal of Nanjing Agricultural University,2007,30(3):1-8.

[10]YANG J，LI S，SUN G，et al.Population structure and genetic variation in the genus Dipteronia Oliv.(Aceraceae) endemic to China as revealed by cpSSR analysis[J].Plant Systematics & Evolution,2008,272(1-4):97-106.

[11]NANNI L，FERRADINI N，TAFFETANI F，et al.Molecular phylogeny of Anthyllis spp.[J].Plant Biology,2004,6(4):454-464.

[12]OZYIGIT I I，DOGAN I，FILIZ E.In silico analysis of simple sequence repeats (SSRs) in chloroplast genomes of glycine species[J].Plant Omics,2015,8(1):24-29.

[13]严仲铠,李万林.中国长白山药用植物彩色图志[M].北京:人民卫生出版社,1997.

[14]吉林省中医中药研究所.长白山植物药志[M].长春：吉林人民出版社，1982.

[15]ZUO L L，WANG Z Y，FAN Z L，et al.Evaluation of antioxidant and antiproliferative properties of three actinidia(Actinidia kolomikta,Actinidia arguta,Actinidia chinensis) extracts in vitro[J].International Journal of Molecular Sciences,2012,13(5):5506-5518.

[16]GUAN D,ZHANG Z,YANG Y，et al.Antioxidant and antitumor activities of water extracts from the root of Actinidia kolomikta[J].Experimental & Therapeutic Medicine,2011,2(1):33-39.

[17]王振兴,曹建冉,秦红艳,等.狗枣猕猴桃彩叶色素含量和结构共同影响叶色[J].植物生理学报,2016(12):1921-1926.

[18]常清泉,杨宗毅,褚友情,等.狗枣猕猴桃叶多糖分离纯化及抗氧化活性研究[J].长春师范大学学报,2017,36(2):49-54.

[19]史洁,尹佟明,管宏伟,等.油茶基因组微卫星特征分析[J].南京林业大学学报(自然科学版),2012,36(2):47-51.

[20]WEBER J L.Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms[J].Genomics,1990,7(4):524.

[21]胡建斌,李建吾,梁芳芳,等.黄瓜叶绿体基因组全序列微卫星分布特征与标记开发[J].中国细胞生物学学报,2009(1):69-74.

[22]王化坤,乔玉山,娄晓鸣,等.拟南芥叶绿体DNA全序列微卫星分布规律的分析[J].中国生物化学与分子生物学报,2006,22(10):845-850.

[23]蔡小彦,刘方,周忠丽,等.棉花叶绿体基因组全序列微卫星分布规律研究[J].棉花学报,2015,27(6):570-575.

[24]贺圆,王兵益,廖声熙,等.云南松基因组微卫星序列特征分析[J].西北林学院学报，2017(3):104-107.

[25]阮桢媛,王兵益,欧阳志勤,等.极度濒危植物巧家五针松基因组微卫星特征分析[J].植物研究,2016,36(5):775-781.

[26]党少飞,王占林,张得芳,等.枸杞基因组微卫星特征分析[J].西北林学院学报,2016,31(1):97-102.

[27]郑燕,张耿,吴为人.禾本科植物微卫星序列的特征分析和比较[J].基因组学与应用生物学，2011,30(5):513-520.

[28]BIET E，SUN J，DUTREIX M.Conserved sequence preference in DNA binding among recombination proteins:An effect of ssDNA secondary structure[J].Nucleic Acids Research,1999,27(2):596-600.

[29]骈瑞琪,李伟,李娜,等.蒺藜苜蓿叶绿体微卫星分布规律的研究[J].安徽农业科学,2008,36(9):3531-3534.

[30]廖礼彬,杨时宇,王兵益,等.甜酸角基因组微卫星序列特征分析[J].云南大学学报(自然科学版),2016,38(6):982-988.

[31]SCHORDERET D F，GARTLER S M.Analysis of CpG suppression in methylated and nonmethylated species[J].Proceedings of the National Academy of Sciences of the United States of America,1992,89(3):957.

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Last Update: 2018-05-23