ZHANG Hong-lei,ZHU Jie-hua,HU Zhen-zhu,et al.Detection and Analysis of Microsatellites in the Phytophthora infestans Genome[J].Northern Horticulture,2013,37(17):110-114.
致病疫霉基因组序列微卫星的发掘与开发分析
- Title:
- Detection and Analysis of Microsatellites in the Phytophthora infestans Genome
- 文章编号:
- 1001-0009(2013)17-0110-05
- Keywords:
- Phytophthora infestans; genome; microsatellite
- 分类号:
- Q 813
- 文献标志码:
- A
- 摘要:
- 利用SciRoKo软件,确定了致病疫霉整个基因组及其不同区域完美型和复合型微卫星的数量，并分析其分布规律。结果表明：在致病疫霉基因组中共发现了5 010个完美型微卫星位点，其出现频率平均为26.35个/Mb，最偏好基元类型为ACGG、AT和AAG;外显子区域仅含3~6个碱基的微卫星基元，其中3和6个碱基的微卫星基元占93.68%;复合型位点275个，82.18%为中断完美类型。通过SciRoKo软件对致病疫霉基因组不同区域的序列进行分析，共获得了430个适合开发高多态性微卫星标记位点，其中包括83个外显子编码区微卫星位点和264个非编码区位点;分别对32个编码区和105非编码区的微卫星位点进行验证，结果表明其开发成功率和多态性明显提高。
- Abstract:
- The amount and distribution of pure and compound microsatellite in the whole genome and its different regions of Phytophthora infestans were identified by software SciRoKo.The results showed that,a total of 5 010 loci for perfect microsatellites were detected in the genome,whose density was 26.35 SSRs/Mb,and the perfect motifs were ACGG,AT and AAG.Only motif for 3 to 6 bases occurred in the exons,in which the percent of microsatellites with 3 and 6 bases motif accounted for 93.68%.The number of compound microsatellites were 275,accounting for 82.18% was interrupted perfect microsatellites.The loci suitable for microsatellite markers were identified according to the software of SciRoKo.At last,430 loci suitable for the development of microsatellites were acquired,in which the coding regions were 83 and non-coding regions were 264.In the coding region and non-coding regions,which were respectively selected 32 and 105 microsatellite loci for validation.The results showed that the success rate of its development and polymorphism significantly increased.This provided a reliable method for the development of microsatellite in genome of high repetition.
参考文献/References:
[1] Goodwin S B.The population genetics of Phytophthora[J].Phytopathology,1997,87(4):462-473.
[2] Rassmann K,Schlotterer C,Tautz D.Isolation of simple-sequence loci for use in polymerase chain reaction-based DNA fingerprinting[J].Electrophoresis,1991,12(2-3):113-118.
[3] Ostrander E A,Jong P M,Rine J,et al.Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences[J].Proceedings of the National Academy of Sciences,1992,89(8):3419-3423.
[4] Kandpal R P,Kandpal G,Weissman S M.Construction of libraries enriched for sequence repeats and jumping clones,and hybridization selection for region-specific markers[J].Proceedings of the National Academy of Sciences,1994,91(1):88-92.
[5] 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.
[6] Zane L,Bargelloni L,Patarnello T.Strategies for microsatellite isolation:a review[J].Molecular Ecology,2002,11(1):1-16.
[7] Kofler R,Schlotterer C,Lelley T.SciRoKo:a new tool for whole genome microsatellite search and investigation[J].Bioinformatics,2007,23(13):1683-1685.
[8] Thiel T,Michalek W,Varshney R,et al.Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)[J].Theoretical and Applied Genetics,2003,106(3):411-422.
[9] Benson G.Tandem repeats finder:a program to analyze DNA sequences[J].Nucleic Acids Research,1999,27(2):573-580.
[10] Temnykh S,Declerck G,Lukashova A,et al.Computational and experimental analysis of microsatellites in rice (Oryza sativa L.):frequency,length variation,transposon associations,and genetic marker potential[J].Genome Research,2001,11(8):1441-1452.
[11] Blanchette M,Kent W J,Riemer C,et al.Aligning multiple genomic sequences with the threaded blockset aligner[J].Genome Research,2004,14(4):708-715.
[12] Bhargava A,Fuentes F F.Mutational dynamics of microsatellites[J].Molecular Biotechnology,2010,44(3):250-266.
[13] Weber J L.Informativeness of human (dC-dA)n·(dG-dT)n polymorphisms[J].Genomics,1990,7(4):524-530.
[14] Cho Y G,Ishii T,Temnykh S,et al.Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.)[J].Theoretical and Applied Genetics,2000,100(5):713-722.
[15] Kofler R,Jan Bartos J,Gong L,et al.Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1[J].Theoretical and Applied Genetics,2008,117(6):915-926.
[16] 李小白,张明龙,崔海瑞.油菜EST资源的SSR信息分析[J].中国油料作物科学,2007,29(1):20-25.
[17] Kelkar Y D,Eckert K A,Chiaromonte F,et al.A matter of life or death:How microsatellites emerge in and vanish from the human genome[J].Genome Research,2011,21(12):2038-2048.
[18] Labbe J,Murat C,Morin E,et al.Survey and analysis of simple sequence repeats in the Laccaria bicolor genome,with development of microsatellite markers[J].Current Genetics,2011,57(2):75-88.
[19] Jin L,Macaubas C,Hallmayer J,et al.Mutation rate varies among alleles at a microsatellite locus:phylogenetic evidence[J].Proceedings of the National Academy of Sciences,1996,93(26):15285-15288.
[20] Haas B J,Kamoun S,Zody M C,et al.Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans[J].Nature,2009,61(7262):393-398.
相似文献/References:
[1]姜生秀,兰海燕.杏仁基因组DNA微量提取的改良方法[J].北方园艺,2012,36(20):105.
JIANG Sheng-xiu,LAN Hai-yan.The Improved Method of Apricot Genomic DNA Trace Extraction[J].Northern Horticulture,2012,36(17):105.
[2]王峰,丁云花,李成琼,等.植物异源附加系研究进展[J].北方园艺,2012,36(19):195.
WANG Feng,DING Yun-hua,LI Cheng-qiong,et al.Research Progress in Alien Plant Additional Lines[J].Northern Horticulture,2012,36(17):195.
[3]高兴旺,王贤磊,杨雅婷,等.甜瓜基因组SSR位点分布规律与多态性初探[J].北方园艺,2014,38(15):93.
GAO Xing-wang,WANG Xian-lei,YANG Ya-ting,et al.Distribution and Polymorphism Characteristics of SSR Loci in Melon Genome[J].Northern Horticulture,2014,38(17):93.
[4]王晓娥,姚方杰.真菌降解木质纤维素酶系的研究进展[J].北方园艺,2015,39(03):176.[doi:10.11937/bfyy.201503051]
WANG Xiao-e,YAO Fang-jie.Research Progress on Lignocellulose Degradation Enzyme System of Fungi[J].Northern Horticulture,2015,39(17):176.[doi:10.11937/bfyy.201503051]
[5]吴新义,徐沛,吴晓花,等.瓠瓜基因组测定[J].北方园艺,2016,40(02):110.[doi:10.11937/bfyy.201602029]
WU Xinyi,XU Pei,WU Xiaohua,et al.Estimation of Genome of Bottle Gourd[J].Northern Horticulture,2016,40(17):110.[doi:10.11937/bfyy.201602029]
[6]许瑞瑞,高明刚,刘春香.苹果基因组中转录因子的鉴定与分析[J].北方园艺,2018,42(09):42.[doi:10.11937/bfyy.20173398]
XU Ruirui,GAO Minggang,LIU Chunxiang.Identification and Analysis of Transcription Factors in Apple Genome[J].Northern Horticulture,2018,42(17):42.[doi:10.11937/bfyy.20173398]
[7]高耀辉,马斌,肖凤洁,等.CRISPR/Cas9系统在园林植物中的研究展望[J].北方园艺,2019,43(15):133.[doi:10.11937/bfyy.20183493]
GAO Yaohui,MA Bin,XIAO Fengjie,et al.Prospect of Research on CRISPR/Cas9 System in Garden Plants[J].Northern Horticulture,2019,43(17):133.[doi:10.11937/bfyy.20183493]
[8]李雪松,华蓉,孙达锋,等.基于花脸香蘑基因组的SSR分子标记开发[J].北方园艺,2023,(02):112.[doi:10.11937/bfyy.20222019]
LI Xuesong,HUA Rong,SUN Dafeng,et al.Development of SSR Molecular Markers Based on Whole Genome of Lepista sordida[J].Northern Horticulture,2023,(17):112.[doi:10.11937/bfyy.20222019]
[9]焦枥禾,王凤利,马银鹏,等.黑木耳分子生物学研究进展[J].北方园艺,2023,(17):124.[doi:10.11937/bfyy.20230365]
JIAO Lihe,WANG Fengli,MA Yinpeng,et al.Research Progress on Molecular Biology of Auricularia heimuer[J].Northern Horticulture,2023,(17):124.[doi:10.11937/bfyy.20230365]
[10]张春雨,李小宇,王晨,等.百合斑驳病毒靖宇分离物全基因组序列测定与进化分析[J].北方园艺,2023,(24):59.[doi:10.11937/bfyy.20232243]
ZHANG Chunyu,LI Xiaoyu,WANG Chen,et al.Sequencing and Analysis of the Genome of Lily mottle virus (LMoV) Jingyu Isolate[J].Northern Horticulture,2023,(17):59.[doi:10.11937/bfyy.20232243]
备注/Memo
第一作者简介：张宏磊（1986-），男，河北唐山人，硕士研究生，研究方向为植物病理学。E-mail:bdzhl2013@163.com.
责任作者：杨志辉（1975-），男，河北藁城人，博士，副教授，硕士生导师，研究方向为植物病理学。E-mail:bdyzh2002@yahoo.com.cn.
基金项目：国家自然科学基金资助项目（31000833）。
收稿日期：2013-04-15