The Distribution and Characteristics of SSR in Transcriptome of <i>Psammosilene tunicoides</i>

Peng YE; Xianhuang LI; Jie CHEN; Shaohong QU; Zhanghong DONG; Han LEI; Cheng LIU; Peiyao XIN; Shengchao YANG

doi:10.12101/j.issn.1004-390X(n).201811088

JOURNAL OF YUNNAN AGRICULTURAL UNIVERSITY（Natural Science） > 2019 > 34(5): 808-814. > DOI: 10.12101/j.issn.1004-390X(n).201811088

Peng YE, Xianhuang LI, Jie CHEN, et al. The Distribution and Characteristics of SSR in Transcriptome of Psammosilene tunicoides[J]. JOURNAL OF YUNNAN AGRICULTURAL UNIVERSITY（Natural Science）, 2019, 34(5): 808-814. DOI: 10.12101/j.issn.1004-390X(n).201811088

Citation:

PDF (770 KB)

The Distribution and Characteristics of SSR in Transcriptome of Psammosilene tunicoides

1.
Southwest Forestry University, Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of Ministry of Education, Kunming 650224, China
2.
Bijie Institute of Traditional Chinese Medicine, Bijie 551700, China
3.
National-Local Joint Engineering Research Center on Gempiasm Innovation & Utillization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming 650201, China

More Information

Received Date: November 29, 2018
Revised Date: January 02, 2019
Available Online: October 08, 2019
Published Date: August 31, 2019

Graphical Abstract

Abstract

Abstract

PurposeThe distribution and sequence characteristics of SSR loci information in Psammosilene tunicoides in Yunnan-Guizhou region were analyzed, which laid a foundation for the development of SSR primers.
MethodDe novo assembly was carried out by MISA software after transcriptome sequencing with the young leaves of P. tunicoides as material. Excel software was used to analyze and Primer 3 software was used to design primers.
ResultsA total of 6 660 microsatellite loci were detected from 77 942 Unigenes sequences, with a frequency of 8.54% and an average distribution distance of 401.64 kb. Trinucleotide and dinucleotide were major repeat types, accounting for 58.69% and 35.77%, respectively. Pentanucleotide was minimum (1.24%). AG/TC, GA/CT, CTT/GAA and ACC/TGG were respectively most frequent repeated motifs in di-nucleotide and tri-nucleotide repeated types, and accounting for 12.66%, 10.45%, 3.71% and 3.60%. SSR primers were designed based on these Unigenes. The SSR loci in the P. tunicoides transcriptome showed moderate frequency of distribution, close distribution distance, rich repeated types, high repeated times and significant potention of polymorphism. 20 primers were successfully amplified which were selected randomly from 82 primers.
ConclusionThe results indicated that the Unigenes obtained from transcriptome sequence in P. tunicoides can be used as an effective way for the development of SSR loci. The SSR primers will provide more markers for the research of genetic variation of P. tunicoides.
- Psammosilene tunicoides,
- SSR,
- transcriptome

FullText(HTML)

References (35)

References

[1]	刘春丽, 刘智敏, 沈丽萍. 金铁锁植物的地理分布和区域分布特征[J]. 生物技术世界, 2015(4): 45.
[2]	王特文, 师晶丽, 王用平, 等. 西南特有药用植物—金铁锁[J]. 重庆中草药研究, 1999, 40(2): 32.
[3]	李景滨, 易继财, 张宗申. 金铁锁组培苗快繁技术研究[J]. 广东农业科学, 2011, 38(2): 29. DOI: 10.16768/j.issn.1004-874x.2011.02.037.
[4]	朱常成, 徐士奎, 钱子刚, 等. 金铁锁的地理分布及分布区的初步分析[J]. 中国现代应用药学, 2007, 24(1): 28. DOI: 10.13748/j.cnki.issn1007-7693.2007.01.011.
[5]	杨丽云, 陈翠, 赵菊, 等. 金铁锁生态学初步研究[J]. 中国农学通报, 2009, 25(18): 367.
[6]	傅立国. 中国植物红皮书—稀有濒危植物: 第一册[M]. 北京: 科学出版社, 1997.
[7]	张庆滢, 刘小烛, 毛常丽. 药用植物金铁锁的研究进展[J]. 云南农业大学学报(自然科学), 2009, 24(1): 139. DOI: 10.16211/j.issn.1004-390x(n).2009.01.018.
[8]	金虹, 谭克勤. 西南民族药金铁锁的研究现状及展望[J]. 中医药导报, 2005, 11(12): 66. DOI: 10.13862/j.cnki.cn43-1446/r.2005.12.035.
[9]	TAUTZ D. Hypervariability of simple sequences as a general source for polymorphic DNA markers[J]. Nucleic Acids Research, 1989, 17(16): 6463. DOI: 10.1093/nar/17.16.6463.
[10]	许玉兰, 蔡年辉, 白青松, 等. 基于微卫星分子标记的云南松及其近缘种遗传关系分析[J]. 西南林业大学学报, 2017, 37(1): 1. DOI: 10.11929/j.issn.2095-1914.2017.01.001.
[11]	SANCHEZ M, INGROUILLE M J, COWAN R S, et al. Spatial structure and genetic diversity of natural populations of the Caribbean pine, Pinus caribaea var bahamensis (Pinaceae), in the Bahaman archipelago[J]. Botanical Journal of the Linnean Society, 2014, 174(3): 359. DOI: 10.1111/boj.12146.
[12]	BAI T D, XU L A, XU M, et al. Characterization of masson pine (Pinus massoniana Lamb) microsatellite DNA by 454 genome shotgun sequencing[J]. Tree Genetics & Genomes, 2014, 10(2): 429. DOI: 10.1007/s11295-013-0684-y.
[13]	马金星, 剡转转, 张吉宇, 等. 20份新疆紫花苜蓿种质SSR 遗传多样性分析[J]. 云南农业大学学报(自然科学), 2018, 33(3): 397. DOI: 10.12101/j.issn.1004-390X(n).201801020.
[14]	张金旺, 李代丽, 尚峰男, 等. 15个北方杨树栽培品种倍性检测与SSR遗传分析[J]. 西南林业大学学报(自然科学), 2018, 38(5): 27. DOI: 10.11929/j.issn.2090-1914.2018.02.005.
[15]	程小毛, 黄晓霞. SSR标记开发及其在植物中的应用[J]. 中国农学通报, 2011, 27(5): 304.
[16]	陈怀琼, 隋春, 魏建和. 植物SSR引物开发策略简述[J]. 分子植物育种, 2009, 7(4): 845. DOI: 10.3969/mpb.007.000845.
[17]	苏伟敏, 靳雅惠, 杨妮, 等. 植物形态学及SSR标记在药用植物遗传分析中的应用[J]. 河北农业科学, 2016, 20(2): 48. DOI: 10.16318/j.cnki.hbnykx.2016.02.012.
[18]	杨维泽, 金航, 崔秀明, 等. 三种人参属植物的EST-SSR信息分析及其在三七中的应用[J]. 基因组学与应用生物学, 2011, 30(1): 62. DOI: 10.3969/gab.030.000062.
[19]	陈国庆. 番红花EST资源的SSR信息分析[J]. 广西植物, 2011, 31(1): 43. DOI: 10.3969/j.issn.1000-3142.2011.01.010.
[20]	李广平, 曹福亮. 银杏EST-SSR引物开发[J]. 西北农业学报, 2012, 21(12): 149. DOI: 10.7606/j.issn.1004-1389.2012.12.029.
[21]	GRABHERR M G, HAAS B J, YASSOUR M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nature Biotechnology, 2011, 29(7): 644. DOI: 10.1038/nbt.1883.
[22]	黄海燕, 杜红岩, 乌云塔娜, 等. 基于杜仲转录组序列的SSR分子标记的开发[J]. 林业科学, 2013, 49(5): 176. DOI: 10.11707/j.1001-7488.20130523.
[23]	王森, 张震, 姜倪皓, 等. 半夏转录组中的SSR位点信息分析[J]. 中药材, 2014, 37(9): 1566. DOI: 10.13863/j.issn1001-4454.2014.09.015.
[24]	陈茵, 李翠婷, 姜倪皓, 等. 灯盏花转录组中SSR位点信息分析及其多态性研究[J]. 中国中药杂志, 2014, 39(7): 1220. DOI: 10.4268/cjcmm20140714.
[25]	王东, 曹玲亚, 高建平. 党参转录组中SSR位点信息分析[J]. 中草药, 2014, 45(16): 2390. DOI: 10.7501/j.issn.0253-2670.2014.16.021.
[26]	蒋超, 袁媛, 刘贵明, 等. 基于EST-SSR的金银花分子鉴别方法研究[J]. 药学学报, 2012, 47(6): 803. DOI: 10.16438/j.0513-4870.2012.06.005.
[27]	黎晓英, 刘胜贵, 王丹, 等. 鱼腥草转录组SSR位点信息分析及其多态性研究[J]. 中草药, 2016, 47(10): 1762. DOI: 10.7501/j.issn.0253-2670.2016.10.022.
[28]	王会敏, 苏秀红, 董诚明, 等. 夏枯草转录组SSR位点信息分析[J]. 中国现代中药, 2018, 20(1): 29. DOI: 10.13313/j.issn.1673-4890.20170619003.
[29]	胡建斌, 李建吾. 甜瓜EST-SSR位点信息及标记开发[J]. 园艺学报, 2009, 36(4): 513. DOI: 10.16420/j.issn:0513-353x.2009.04.010.
[30]	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): 1441. DOI: 10.1101/gr.184001.
[31]	XU X, PENG M, FANG Z A, et al. The direction of microsatellite mutations is dependent upon allele length[J]. Nature Genetics, 2000, 24: 396. DOI: 10.1038/74238.
[32]	李翠婷, 张广辉, 马春花, 等. 野三七转录组中SSR位点信息分析及其多态性研究[J]. 中草药, 2014, 45(10): 1468. DOI: 10.7501/j.issn.0253-2670.2014.10.021.
[33]	王学勇, 周晓丽, 高伟, 等. 丹参新的EST-SSR分布规律及分子标记的建立[J]. 中国中药杂志, 2011, 36(3): 289. DOI: 10.4268/cjcmm20110313.
[34]	刘越, 岳春江, 王翊, 等. 藏茵陈川西獐牙菜转录组SSR信息分析[J]. 中国中药杂志, 2015, 40(11): 2068. DOI: 10.4268/cjcmm20151103.
[35]	杨维泽, 金航, 赵振玲, 等. 西洋参EST资源的SSR信息分析[J]. 西南农业学报, 2011, 24(1): 275. DOI: 10.16213/j.cnki.scjas.2011.01.041.

Cited By

Cited by

Periodical cited type(10)

1.	田甜，王宏霞. 暴马丁香的叶绿体微卫星特征分析. 分子植物育种. 2024(08): 2501-2507 .
2.	万小林，粱思琪，崔令军，肖强. 大叶黄精转录组中SSR位点信息分析. 北方园艺. 2024(14): 104-109 .
3.	李春霖，万小林，崔令军，肖强，李双龙. 黄精根状茎转录组SSR特点分析. 山东农业大学学报(自然科学版). 2024(06): 908-913 .
4.	张加强，史小华，刘慧春，许雯婷，周江华，朱开元. ‘京红久’忍冬叶绿体基因组微卫星序列特征分析. 分子植物育种. 2023(06): 1955-1966 .
5.	刘迪，欧阳艳飞，徐鹏，甄军波，刘琳琳，张利超，迟吉娜. 柴胡转录组SSR的分布及序列特征分析. 南方农业学报. 2022(03): 676-683 .
6.	陈虞超，李晓琳，赵玉洋，周骏辉，黄璐琦，袁媛. 珍稀濒危药用植物资源离体保存研究进展. 世界中医药. 2021(07): 1018-1030 .
7.	刘佳雪，赵一航，胡尧，衣琨，刘皓玥，王丽娜，殷秀杰. 高加索三叶草SSR序列特征分析. 分子植物育种. 2021(21): 7154-7159 .
8.	苏群，田敏，刘俊，王凌云，李春牛，李先民，黄展文，王虹妍. 基于生物信息学的睡莲SSR位点特征分析. 西南农业学报. 2021(10): 2076-2083 .
9.	辛静，辛雅萱，董章宏，瞿绍宏，姚国琼，李凤，屈亚亚，唐军荣. 云南火焰兰转录组SSR分布及其序列特征分析. 南方农业学报. 2020(07): 1634-1641 .
10.	洪克前，夏维丽，李佩玲，徐函兵，谷会，陈丽. 霍山石斛叶转录组中SSR位点信息分析. 中国农学通报. 2020(27): 106-110 .

Other cited types(1)

Get Citation

PDF

XML

Article views (2522) PDF downloads (7) Cited by(11)

Turn off MathJax

Article Contents

Abstract

References

The Distribution and Characteristics of SSR in Transcriptome of Psammosilene tunicoides

Abstract

References

Cited by

Periodical cited type(10)

Other cited types(1)

Catalog

Export File

Citation

Format

Content