中国中药杂志

2019, v.44(21) 4605-4611

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冬虫夏草转录组SSR位点信息分析研究
SSR loci information analysis in transcriptome of Cordyceps sinensis

张涵;王芳;白静;董强;童锌芯;袁媛;国锦琳;
ZHANG Han;WANG Fang;BAI Jing;DONG Qiang;TONG Xin-xin;YUAN Yuan;GUO Jin-lin;Key Laboratory of Standardization of Chinese Medicine,Ministry of Education,Key Laboratory of Systematic Research,Development and Utilization of Chinese Medicine,Resources Breeding Base of Co-founded by Sichuan Province and MOST,Chengdu University of Traditional Chinese Medicine;Chinese Medicine Resource Center,China Academy of Chinese Medical Sciences;

摘要(Abstract):

为探究冬虫夏草转录组中简单重复序列(simple sequence repeats,SSR)位点信息,开发冬虫夏草SSR分子标记奠定基础,该研究利用MISA(MicroSatellite)软件对冬虫夏草转录组拼接获得的16 875 unigene进行SSR位点数据挖掘,并使用Primer 3. 0软件设计引物。研究发现,冬虫夏草转录组中4 252条unigene含有5 899个SSR位点,出现频率为34. 99%,平均每7 952 bp出现1个SSR位点,以单核苷酸和三核苷酸重复为主,分别占总数的42. 5%,38. 48%。SSR序列中共包括74种基序类型,C/G和CCG/CGG是优势重复单元。6种SSR重复类型的重复次数集中于5~12次,长度大多小于24 bp。通过引物设计软件,共筛选得到12 282对引物,随机挑选的20对引物用于有效性检测,19对引物扩增出条带,引物有效率为95%。10对引物扩增出清晰、可重复特异性条带,其中引物P1具显著多态性。此外,经GO与KEGG功能注释后发现,含有SSR位点的unigene主要与遗传和环境功能相关。上述结果表明冬虫夏草转录组SSR位点出现频率较高、基元类型丰富、多态性较高,具有较高的可用性,为其遗传多样性分析、资源鉴定保护、基因功能研究等方面提供了丰富的候选分子标记。
To analysis the SSR loci information in the transcriptome of Cordyceps sinensis and develop SSR molecular markers,MISA(MicroSatellite) software was used to analyze the microsatellites information from 16 875 unigene sequences and SSR primer designed by Primer 3. 0. In total,5 899 SSRs were detected in 4 252 unigene with the distribution frequency of 34. 99%,which was represented by 74 repeat motifs and SSR loci occurred per 7 952 bp in length. In the SSRs,the mono-nucleotide was the most abundant repeat motif(42. 5%),followed by tri-nucleotide(34. 48%),C/G and CCG/CGG were the dominant repeat motifs,respectively. The number of repetitions of the six SSR repeat types was concentrated on 5 to 12 times,and the length was mostly less than 24 bp. A total of 12 282 pairs of primers were screened and selected 20 pairs of primers for validity detection randomly,10 pairs of primers amplified the expected specific bands,and primer P1 has significant polymorphism. Moreover,it was found that unigene containing SSR loci is mainly related to genetic and environmental functions after GO and KEGG annotation. In conclusion,these SSR loci in the transcriptome of O. sinensis are high in frequency,rich in primitive types,high in polymorphism,and highly available,which will provides abundant candidate molecular markers for its genetic diversity analysis,resource identification protection,and gene function research.

关键词(KeyWords): 冬虫夏草;转录组;SSR位点信息
Cordyceps sinensis;transcriptome;SSR loci information

Abstract:

Keywords:

基金项目(Foundation): 国家自然科学基金项目(81872959,81373920,30801522);; 四川省青年科技创新团队项目(19CXTD0055);; 国家留学基金委项目(201708570027)

作者(Author): 张涵;王芳;白静;董强;童锌芯;袁媛;国锦琳;
ZHANG Han;WANG Fang;BAI Jing;DONG Qiang;TONG Xin-xin;YUAN Yuan;GUO Jin-lin;Key Laboratory of Standardization of Chinese Medicine,Ministry of Education,Key Laboratory of Systematic Research,Development and Utilization of Chinese Medicine,Resources Breeding Base of Co-founded by Sichuan Province and MOST,Chengdu University of Traditional Chinese Medicine;Chinese Medicine Resource Center,China Academy of Chinese Medical Sciences;

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