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

doi:10.7525/j.issn.1673-5102.2016.05.020

Abstract

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

CLC Number:

S791.24

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.

References

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]	Ziyin WANG, Bingru LIU, Zihao LI, Jifei WANG, Pengbin YANG. Genomic Survey Analysis of Endangered Plant Tetraena mongolica [J]. Bulletin of Botanical Research, 2023, 43(2): 186-193.
[2]	Fei WANG, Wenzhi ZHAO, Zhanghong DONG, Luyao MA, Weiying LI, Zongyan LI, Peiyao XIN. Analysis of the Chloroplast Genome Characteristics of 6 Species of Yucca [J]. Bulletin of Botanical Research, 2023, 43(1): 109-119.
[3]	Yongchang LU, Xin ZHANG, Luyan ZHANG, Jiuli WANG. Complete Chloroplast Genome Structure and Characterization of Syringa villosa subsp. wolfii [J]. Bulletin of Botanical Research, 2023, 43(1): 120-130.
[4]	Yingtong MU, Dongchang FAN, Lijuan LÜ, Xiajie LI, Jingshi LU, Xiaoming ZHANG. Comparison of Codon Characteristics and Phylogeny of Chloroplast Genome between Ranunculaceae and Paeoniaceae [J]. Bulletin of Botanical Research, 2022, 42(6): 964-975.
[5]	Xin’ai ZHONG, Shiqi MENG, Wanting Zhou, Qi YAO, Qiong ZHANG, Wang XING, Dali LIU. Identification of Glutathione S-transferase Gene Family in Sugar Beet and the Response to Cadmium Stress [J]. Bulletin of Botanical Research, 2022, 42(5): 790-801.
[6]	Yu ZHANG, Xu SU, Yuping LIU, Tao LIU, Changyuan ZHENG, Dandan SU, Yanan WANG, Ting LÜ. Characteristics of Complete Chloroplast Genome and Phylogenetic Analysis of Rhodiola himalensis (Crassulaceae) [J]. Bulletin of Botanical Research, 2022, 42(4): 602-612.
[7]	Chen YANG, Xueying YAO, Zhixiang CHEN, Qizhi WANG. Chloroplast Genome Structure and Interspecies Relationship of Sanicula rubriflora [J]. Bulletin of Botanical Research, 2022, 42(3): 437-445.
[8]	Dandan SU, Yuping LIU, Tao LIU, Changyuan ZHENG, Yu ZHANG, Yanan WANG, Na QIN, Xu SU. Structure of Chloroplast Genome and its Characteristics of Sphaerophysa salsula [J]. Bulletin of Botanical Research, 2022, 42(3): 446-454.
[9]	Mengjiao Wang, Yuxue Cao, Yongsheng Xu, Fenge Ding, Qiao Su. Overexpression of Marine Microbial Metagenomic MbCSP Enhanced Drought and Cold Tolerance of Transgenic Arabidopsisthaliana [J]. Bulletin of Botanical Research, 2022, 42(2): 243-251.
[10]	Shuang-Hui TIAN, He CHENG, Yang ZHANG, Cong LIU, De-An XIA, Zhi-Gang WEI. Genome-wide Identification and Expressional Analysis of Carotenoid Cleavage Dioxygenases(CCD) Gene Family in Populus trichocarpa under Drought and Salt Stress [J]. Bulletin of Botanical Research, 2021, 41(6): 993-1005.
[11]	YANG Bin, MENG Qing-Yao, ZHANG Kai, DUAN Yi-Zhong. Chloroplast Genome Characterization and Identification of Genetic Relationship of Relict Endangered Plant Amygdalus nana [J]. Bulletin of Botanical Research, 2020, 40(5): 686-695.
[12]	YANG Yun, CHEN Meng-Jiao, DU Qing-Xin, ZHU Jing-Le, DU Hong-Yan, YANG Shao-Bin. SNP Sites Developed by Whole Genome Resequencing Analysis in Eucommia ulmoides ‘Hongye’ [J]. Bulletin of Botanical Research, 2019, 39(6): 947-954.
[13]	DUAN Yi-Zhong, DU Zhong-Yu, WANG Hai-Tao. Chloroplast Genome Characteristics of Endangered Relict Plant Tetraena mongolica in the Arid Region of Northwest China [J]. Bulletin of Botanical Research, 2019, 39(5): 653-663.
[14]	LIU Xiong-Fang, LI Tai-Qiang, ZHANG Xu, LI Zheng-Hong, WAN You-Ming, AN Jing, LIU Xiu-Xian, MA Hong. Characteristic Analysis of Microsatellites in the Transcriptome of Phyllanthus emblica,an Important Edible and Medicinal Plant [J]. Bulletin of Botanical Research, 2019, 39(2): 294-302.
[15]	ZHOU Yu-Min, WANG Sui, LIU Yi, LI Kai-Long, YOU Xiang-Ling. Sequencing and Assembly of Populus simonii×P.nigra Genome and SSR Analysis [J]. Bulletin of Botanical Research, 2019, 39(1): 156-160.