极度濒危植物巧家五针松基因组微卫星特征分析

doi:10.7525/j.issn.1673-5102.2016.05.020

植物研究 ›› 2016, Vol. 36 ›› Issue (5): 775-781.doi: 10.7525/j.issn.1673-5102.2016.05.020

极度濒危植物巧家五针松基因组微卫星特征分析

阮桢媛¹, 王兵益², 欧阳志勤³, 廖礼彬², 苏腾伟¹, 乔璐¹

1. 云南林业职业技术学院, 昆明 650224;
2. 中国林业科学研究院资源昆虫研究所, 昆明 650224;
3. 云南省环境科学研究院, 昆明 650034

收稿日期:2016-03-16 出版日期:2016-09-15 发布日期:2016-09-27
通讯作者: 王兵益,E-mail:wangbykm@gmail.com E-mail:wangbykm@gmail.com
作者简介:阮桢媛(1983-),女,博士,讲师,主要从事植物生理与分子生物学研究。
基金资助:
云南省教育厅科学研究基金项目（2014Y569）；云南省生物多样性保护专项资金资助项目（2013-004）；云南林业职业技术学院博士基金项目（KY（BS）201402）；云南省教育厅科学研究基金项目（2014Y571）

Characterization of Microsatellites in Genome of Pinus squamata, a Critically Endangered Species in the World

RUAN Zhen-Yuan¹, WANG Bing-Yi², OUYANG Zhi-Qin³, LIAO Li-Bin², SU Teng-Wei¹, QIAO Lu¹

1. Department of Landscape Architecture, Yunnan Forestry Technologicl College, Kunming 650224;
2. The Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224;
3. Yunnan Institute of Environmental Science, Kunming 650034

Received:2016-03-16 Online:2016-09-15 Published:2016-09-27
Supported by:
Science Research Fund of Yunnan Provincial Education Department(2014Y569);Special Fund for the Protection of Biological Diversity in Yunnan(2013-004);Doctoral Program of Yunnan Forestry Technological College(KY(BS)201402);Science Research Fund of Yunnan Provincial Education Department(2014Y571)

摘要/Abstract

摘要： 巧家五针松是世界极度濒危植物，对其SSR引物的开发有助于其遗传学研究以及物种的保护。本研究通过Illumina高通量测序技术获得巧家五针松全基因组序列，并以MISA软件查找得到2 651个微卫星序列，其中单核苷酸重复最多，可能预示了其悠久的进化历史。不同重复类型中，A/T含量显著高于G/C；在不同长度重复单元中，二核苷酸重复微卫星长度变异程度最高；各重复类型微卫星长度与微卫星出现的频率成反比。获得的微卫星序列能够满足巧家五针松的种群遗传学研究，而且反映了该物种的偏好性及对应的潜在功能，并且对该物种的保护提供了资料。

关键词: 巧家五针松, 基因组, 微卫星

Abstract: Pinus squamata is a critically endangered species in the world, therefore, developing simple sequence repeat(SSR) primers will facilitate the species genetic research and conservation. The complete genome sequence of P.squamaia was determined through Illumina genome analyzer, and 2 651 microsatellites were discovered by MISA software. Single nucleotide repeat number occupied the highest proportion of these microsatellites which may indicate a long evolution history of P.squamata. Among different repeat types, A/T contents was significantly higher than G/C contents. In terms of distinct length repeat units, the length of dinucleotide repeat microsatellite varies with the highest degree. The length of SSRs with different repeat type was negatively correlated with frequency of occurrences. The available microsatellite sequences can satisfy P.squamaia population genetics, and reveal the species bias and corresponding potential functions.

Key words: Pinus squamata X.W.Li, genome, microsatellite

中图分类号:

S791.24

阮桢媛, 王兵益, 欧阳志勤, 廖礼彬, 苏腾伟, 乔璐. 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.

RUAN Zhen-Yuan, WANG Bing-Yi, OUYANG Zhi-Qin, LIAO Li-Bin, SU Teng-Wei, QIAO Lu. Characterization of Microsatellites in Genome of Pinus squamata, a Critically Endangered Species in the World[J]. Bulletin of Botanical Research, 2016, 36(5): 775-781.

参考文献

1. 李乡旺.云南松属一新系一新种[J].云南植物研究,1992,14(3):259-260.Li Xiangwang.A new series and a new species of Pinus from Yunnan[J].Acta Botanica Yunnanica,1992,14(3):259-260.
2. 李文虎.巧家五针松列入全球最濒危物种名录[J].云南林业,2012,33(6):37.Li Wenhu.Pinus squamata is listed on the most endangered species in the world[J].Yunnan Forestry,2012,33(6):37.
3. 陆素娟,邓莉兰,李乡旺.五针白皮松濒危原因初步研究[J].西北林学院学报,1999,14(1):42-44.Lu Sujuan,Deng Lilan,Li Xiangwang.A study on endangered causes of Pinus squamata[J].Journal of Northwest Forestry University,1999,14(1):42-44.
4. 张志勇,李德铢.极度濒危植物五针白皮松的保护遗传学研究[J].云南植物研究,2003,25(5):544-550.Zhang Zhiyong,Li Dezhu.Conversation genetics of an extremely endangered pine,Pinus squamata[J].Acta Botanica Yunnanica,2003,25(5):544-550.
5. Wright S.Evolution in populations in approximate equilibrium[J].Journal of Genetics,1935,30:257.
6. 刘列钊,林呐.油菜简单重复序列SSR(simple sequence repeat)研究进展[J].生命科学,2004,16(3):173-176.Liu Liezhao,Lin Na.Research advances of SSR(simple sequence of repeat) in canola[J].Chinese Bulletin of Life Sciences,2004,16(3):173-176.
7. 田路明,曹玉芬,董星光,等.SSR分子标记在梨种质资源研究中的应用[J].生物学杂志,2013,30(6):91-94.Tian Luming,Cao Yufen,Dong Xingguang,et al.Application of SSR molecular marker in pear germplasm resources[J].Journal of Biology,2013,30(6):91-94.
8. 杨爱红,张金菊,田华,等.鹅掌楸贵州烂木山居群的微卫星遗传多样性及空间遗传结构[J].生物多样性,2014,22(3):375-384.Yang Aihong,Zhang Jinju,Tian Hua,et al.Microsatellite genetic diversity and fine-scale spatial genetic structure within a natural stand of Liruiodendron chinense(Magnoliaceae) in Lanmushan,Duyun City,Guizhou Province[J].Biodiversity Science,2014,22(3):375-384.
9. 贺梁琼,熊发前,韩柱强,等.花生种间杂种异源多倍化早期世代性状和SSR变化研究[J].中国油料作物学报,2013,35(5):499-507.He Liangqiong,Xiong Faqian,Han Zhuqiang,et al.Traits and microsatellites variation of early generations during allopolyploidization of Arachis interspecific hydridization[J].Chinese Journal of Oil Crop Sciences,2013,35(5):499-507.
10. 胡紫璟,毛娟,赵长增,等.利用SSR标记分析27份扁桃种质资源的亲缘关系[J].甘肃农业大学学报,2015,50(4):56-62.Hu Zijing,Mao Juan,Zhao Changzeng,et al.Idetification of genetic relationship of almond by SSR markers[J].Journal of Gansu Agricultural University,2015,50(4):56-62.
11. 李婷,覃道凤,戴璨.利用SSR荧光标记对野慈姑异交率的估测[J].植物科学学报,2015,33(4):554-563.Li Ting,Qin Daofeng,Dai Can.An estimation of the outcrossing rate in Sagitlaria trifolia using SSR fluorescence markers[J].Plant Science Journal,2015,33(4):554-563.
12. 李淑娴,张新叶,王英亚,等.桉树EST序列中微卫星含量及相关特征[J].植物学报,2010,45(3):363-371.Li Shuxian,Zhang Xinye,Wang Yingya,et al.Content and characteristics of microsatellites detected in expressed sequence tag sequences in Eucalyptus[J].Chinese Bulletin of Botany,2010,45(3):363-371.
13. 秦海峰,龙宁,吴建国,等.甜叶菊微卫星富集文库的构建与多态性标记的筛选[J].作物学报,2014,40(3):447-456.Qin Haifeng,Long Ning,Wu Jianguo.Construction of microsatellite-enriched library and isolation of icrosatellite markers in Stevia rebaudiana[J].ACTA Agronomica Science,2014,40(3):447-456.
14. 曾庆国,陈艺燕.微卫星位点筛选方法综述[J].生态科学,2005,24(4):368-372.Zeng Qinguo,Chen Yiyan.The methods of isolating microsatellite loci[J].Ecologic Science,2005,24(4):368-372.
15. 袁阳阳,王青锋,陈进明.基于转录组测序信息的水生植物莕菜SSR标记开发[J].植物科学学报,2013,31(5):485-492.Yuan Yangyang,Wang Qingfeng,Chen Jinming.Development of SSR markers in aquatic plant Nymphoides peltata Menyanthaceae based on information from transcriptom sequencing[J].Plant Science Journal,2013,31(5):485-492.
16. Aggarwal R K,Hendre P S,Varshney R K,et al.Identification,characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species[J].Theoretical and Applied Genetics,2007,114(2):359-372.
17. 张晗,王雪梅,王东建,等.谷子基因组SSR信息分析和标记开发[J].分子植物育种,2013,11(1):30-36.Zhang Han,Wang Xuemei,Wang Dongjian,et al.Survey of SSRs in foxtail millet genome and development of SSR markers[J].Molecular Plant Breeding,2013,11(1):30-36.
18. 孔凡明,王小龙,陈赢男,等.松属编码区微卫星特征和相应基因功能分析[J].南京林业大学学报:自然科学版,2014,38(2):47-51.Kong Fanming,Wang Xiaolong,Chen Yingnan,et al.Characterization of microsatellites in coding genes and functional analysis of these genes in pines[J].Journal of Nanjing Forestry University:Natural Sciences Edition,2014,38(2):47-51.
19. 吴敏,杜红岩,乌云塔娜,等.杜仲基因组微卫星特征及SSR标记开发[J].林业科学研究,2015,28(3):387-393.Wu Ming,Du Hongyan,Wuyun Tana,et al.Characterization of genomic microsatellites and development of SSR markers of Eucommia ulmoides[J].Forest Research,2015,28(3):387-393.
20. 黄志成,雷树凡,胡景涛,等.利用优化的SSR分子标记技术检测杂交水稻万优481纯度[J].安徽农业科学,2014,42(22):7321-7322.Huang Zhicheng,Lei Shufan,Hu Jingtao,et al.Identification and purity test of hybrid rice Wanyou 481 with optimized SSR markers[J].Journal of Anhui Agricultural Sciences,2014,42(22):7321-7322.
21. Tóth G,Gáspári Z,Jurka J.Microsatellites in different eukaryotic genomes:survey and analysis[J].Genome Research,2000,10(7):967-981.
22. Harr B,Schl tterer C.Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times,which cause their genome-wide underrepresentation[J].Genetics,2000,155(3):1213-1220.
23. 高亚梅,韩毅强,汤辉,等.根瘤菌基因组内简单重复序列的分析[J].中国农业科学,2008,41(10):2992-2998.Gao Yamei,Han Yiqiang,Tang Hui,et al.Anlysis of simple sequence repeats in Rhizobium genomes[J].Scientia Agricultura Sinica,2008,41(10):2992-2998.
24. 吴征镒,王荷生.中国自然地理--植物地理[M].北京:科学出版社,1983:1-129.Wu Zhengyi,Wang Hesheng.Chinese physical geography-Plant geography[M].Beijing:Science Press,1983:1-129.
25. 樊国盛,李乡旺,邓莉兰.五针白皮松林区系特点研究[J].中南林学院学报,1996,16(2):23-27,33.Fan Guosheng,Li Xiangwang,Deng Lilan.A study of floristic geography of Pinus squamata flora[J].Journal of Central-South Forestry University,1996,16(2):23-27.
26. 张炜.利用小麦SSR研究其近缘物种的遗传多样性及其微卫星序列的进化[D].成都:四川农业大学,2008.Zhang Wei.Genetic diversity and evolution of microsatellite segment among triticeae species as revealed by wheat microsatellite markers[D].Chengdu:Sichuan Agricultural University,2008.
27. Song Q J,SHI J R,SINGH S,et al.Development and mapping of microsatellite(SSR) markers in wheat[J].Theoretical and Applied Genetics,2005,110(3):550-560.
28. Jiao Y,Jia H M,Li X W,et al.Development of simple sequence repeat(SSR) markers from a genome survey of Chinese bayberry(Myrica rubra)[J].BMC Genomics,2012,13:201.
29. Lawson M J,Zhang L Q.Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes[J].Genome Biology,2006,7(2):R14.
30. 关玲,章镇,王新卫,等.苹果基因组SSR位点分析与应用[J].中国农业科学,2011,44(21):4415-4428.Guan Ling,Zhang Zhen,Wang Xinwei,et al.Evaluation and application of SSR loci in apple genome[J].Scientia Agricultura Science,2011,44(21):4415-4428.
31. 刘公秉,季孔庶.基于松树EST序列的马尾松SSR引物开发[J].分子植物育种,2009,7(4):833-838.Liu Gongbing,Ji Kongshu.Designing Pinus massoniana SSR promers from Pinus EST sequences[J].Molecular Plant Breeding,2009,7(4):833-838.
32. Li S X,Yin T M.Map and analysis of microsatellites in the genome of Populus:The first sequenced perennial plant[J].Science in China Series C:Life Science,2007,50(5):690-699.
33. 雷淑云,高庆波,付鹏程,等.基于Solexa高通量测序的唐古特红景天(Rhodiola algida)微卫星信息分析[J].植物研究,2014,34(6):829-834.Lei Shuyun,Gao Qingbo,Fu Pengcheng,et al.Analysis on microsatellites in Rhodiola algida based on Solexa sequencing[J].Bulletin of Botanical Research,2014,34(6):829-834.
34. Schl tterer C,Tautz D.Slippage synthesis of simple sequence DNA[J].Nucleic Acids Research,1992,20(2):211-215.

[1]	王子寅, 刘秉儒, 李子豪, 王继飞, 杨鹏斌. 基于Survey分析的濒危植物四合木基因组研究[J]. 植物研究, 2023, 43(2): 186-193.
[2]	王飞, 赵文植, 董章宏, 马路遥, 李卫英, 李宗艳, 辛培尧. 丝兰属6种植物叶绿体基因组特征分析[J]. 植物研究, 2023, 43(1): 109-119.
[3]	芦永昌, 张鑫, 张璐燕, 王久利. 辽东丁香完整叶绿体基因组的结构与特征[J]. 植物研究, 2023, 43(1): 120-130.
[4]	穆赢通, 樊东昌, 吕丽娟, 李晓杰, 路景诗, 张晓明. 毛茛科和芍药科叶绿体基因组密码子特征和系统发育比较[J]. 植物研究, 2022, 42(6): 964-975.
[5]	钟鑫爱, 孟诗琪, 周婉婷, 姚琦, 张琼, 兴旺, 刘大丽. 甜菜谷胱甘肽S-转移酶基因家族鉴定及在镉胁迫下的响应分析[J]. 植物研究, 2022, 42(5): 790-801.
[6]	张雨, 苏旭, 刘玉萍, 刘涛, 郑长远, 苏丹丹, 王亚男, 吕婷. 喜马红景天叶绿体基因组特征及其系统发育分析[J]. 植物研究, 2022, 42(4): 602-612.
[7]	夏铭泽, 张发起, 迟晓峰, 韩霜, 陈世龙. 梅花草属叶绿体基因组进化分析[J]. 植物研究, 2022, 42(4): 626-636.
[8]	杨晨, 姚雪莹, 陈志祥, 王奇志. 红花变豆菜叶绿体基因组结构及同属种间关系研究[J]. 植物研究, 2022, 42(3): 437-445.
[9]	苏丹丹, 刘玉萍, 刘涛, 郑长远, 张雨, 王亚男, 秦娜, 苏旭. 苦马豆叶绿体基因组结构及其特征分析[J]. 植物研究, 2022, 42(3): 446-454.
[10]	王梦姣, 曹钰雪, 徐永盛, 丁风鹅, 苏乔. 过表达海洋微生物宏基因组MbCSP提高转基因拟南芥的抗旱和耐寒性[J]. 植物研究, 2022, 42(2): 243-251.
[11]	田双慧, 程赫, 张洋, 刘聪, 夏德安, 魏志刚. 毛果杨类胡萝卜素裂解双加氧酶基因家族全基因组水平鉴定及其干旱与盐胁迫响应分析[J]. 植物研究, 2021, 41(6): 993-1005.
[12]	杨斌, 孟庆瑶, 张凯, 段义忠. 孑遗濒危植物矮扁桃叶绿体全基因组特征分析及亲缘关系鉴定[J]. 植物研究, 2020, 40(5): 686-695.
[13]	宁馨, 姜小龙, 邓敏, 徐刚标. 基于简化基因组数据开发岭南青冈微卫星引物[J]. 植物研究, 2020, 40(4): 629-634.
[14]	张珊珊, 康洪梅, 杨文忠. 基于简化基因组技术的云南蓝果树群体遗传分析[J]. 植物研究, 2019, 39(6): 899-907.
[15]	杨赟, 陈梦娇, 杜庆鑫, 朱景乐, 杜红岩, 杨绍彬. 基于全基因组重测序技术的‘红叶’杜仲SNP位点开发[J]. 植物研究, 2019, 39(6): 947-954.

极度濒危植物巧家五针松基因组微卫星特征分析

Characterization of Microsatellites in Genome of Pinus squamata, a Critically Endangered Species in the World

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

本文评价