Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim

doi:10.1186/1471-2164-11-94

CORC > 武汉植物园 > 中国科学院武汉植物园

	Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim
	Zeng, Shaohua 1,2; Xiao, Gong 1,2; Guo, Juan 1,2; Fei, Zhangjun 3,4; Xu, Yanqin 1; Roe, Bruce A.5; Wang, Ying 1
刊名	BMC GENOMICS
	2010-02-08
卷号	11 页码:11
ISSN号	1471-2164
DOI	10.1186/1471-2164-11-94
英文摘要	Background: Epimedium sagittatum (Sieb. Et Zucc.) Maxim, a traditional Chinese medicinal plant species, has been used extensively as genuine medicinal materials. Certain Epimedium species are endangered due to commercial overexploition, while sustainable application studies, conservation genetics, systematics, and marker-assisted selection (MAS) of Epimedium is less-studied due to the lack of molecular markers. Here, we report a set of expressed sequence tags (ESTs) and simple sequence repeats (SSRs) identified in these ESTs for E. sagittatum. Results: cDNAs of E. sagittatum are sequenced using 454 GS-FLX pyrosequencing technology. The raw reads are cleaned and assembled into a total of 76,459 consensus sequences comprising of 17,231 contigs and 59,228 singlets. About 38.5% (29,466) of the consensus sequences significantly match to the non-redundant protein database (E-value < 1e-10), 22,295 of which are further annotated using Gene Ontology (GO) terms. A total of 2,810 EST-SSRs is identified from the Epimedium EST dataset. Trinucleotide SSR is the dominant repeat type (55.2%) followed by dinucleotide (30.4%), tetranuleotide (7.3%), hexanucleotide (4.9%), and pentanucleotide (2.2%) SSR. The dominant repeat motif is AAG/CTT (23.6%) followed by AG/CT (19.3%), ACC/GGT (11.1%), AT/AT (7.5%), and AAC/GTT (5.9%). Thirty-two SSR-ESTs are randomly selected and primer pairs are synthesized for testing the transferability across 52 Epimedium species. Eighteen primer pairs (85.7%) could be successfully transferred to Epimedium species and sixteen of those show high genetic diversity with 0.35 of observed heterozygosity (Ho) and 0.65 of expected heterozygosity (He) and high number of alleles per locus (11.9). Conclusion: A large EST dataset with a total of 76,459 consensus sequences is generated, aiming to provide sequence information for deciphering secondary metabolism, especially for flavonoid pathway in Epimedium. A total of 2,810 EST-SSRs is identified from EST dataset and similar to 1580 EST-SSR markers are transferable. E. sagittatum EST-SSR transferability to the major Epimedium germplasm is up to 85.7%. Therefore, this EST dataset and EST-SSRs will be a powerful resource for further studies such as taxonomy, molecular breeding, genetics, genomics, and secondary metabolism in Epimedium species.
资助项目	Chinese Academy of Sciences[KSCX2-YW-N-030]
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000275291900001
内容类型	期刊论文
源URL	[http://202.127.146.157/handle/2RYDP1HH/978]
专题	中国科学院武汉植物园
通讯作者	Wang, Ying
作者单位	1.Chinese Acad Sci, Wuhan Bot Garden, Key Lab Pant Germplasm Enhancement & Special Agr, Wuhan 430074, Hubei, Peoples R China 2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China 3.Cornell Univ, Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA 4.USDA, Robert W Holley Ctr Agr & Hlth, Ithaca, NY 14853 USA 5.Univ Oklahoma, Stephenson Res & Technol Ctr, Norman, OK 73019 USA
推荐引用方式 GB/T 7714	Zeng, Shaohua,Xiao, Gong,Guo, Juan,et al. Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim[J]. BMC GENOMICS,2010,11:11.
APA	Zeng, Shaohua.,Xiao, Gong.,Guo, Juan.,Fei, Zhangjun.,Xu, Yanqin.,...&Wang, Ying.(2010).Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim.BMC GENOMICS,11,11.
MLA	Zeng, Shaohua,et al."Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim".BMC GENOMICS 11(2010):11.