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Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development
Liu, Fuli1,2; Hu, Zimin3; Liu, Wenhui4; Li, Jingjing3; Wang, Wenjun1; Liang, Zhourui1; Wang, Feijiu1; Sun, Xiutao1
2016-01-06
发表期刊SCIENTIFIC REPORTS
卷号6期号:2016页码:18947
文章类型Article
摘要Using transcriptome data to mine microsatellite and develop markers has growingly become prevalent. However, characterizing the possible function of microsatellite is relatively rare. In this study, we explored microsatellites in the transcriptome of the brown alga Sargassum thunbergii and characterized the frequencies, distribution, function and evolution, and developed primers to validate these microsatellites. Our results showed that Tri-nucleotide is the most abundant, followed by di- and mononucleotide. The length of microsatellite was significantly affected by the repeat motif size. The density of microsatellite in the CDS region is significantly lower than that in the UTR region. The annotation of the transcripts containing microsatellite showed that 573 transcripts have GO terms and can be categorized into 42 groups. Pathways enrichment showed that microsatellites were significantly overrepresented in the genes involved in pathways such as Ubiquitin mediated proteolysis, RNA degradation, Spliceosome, etc. Primers flanking 961 microsatellite loci were designed, and among the 30 pairs of primer selected randomly for availability test, 23 were proved to be efficient. These findings provided new insight into the function and evolution of microsatellite in transcriptome, and the identified microsatellite loci within the annotated gene will be useful for developing functional markers in S. thunbergii.
DOI10.1038/srep18947
收录类别SCI
语种英语
WOS记录号WOS:000368094400001
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文献类型期刊论文
条目标识符http://ir.qdio.ac.cn/handle/337002/95224
专题实验海洋生物学重点实验室
作者单位1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Key Lab Sustainable Dev Marine Fisheries, Minist Agr, Qingdao 266071, Peoples R China
2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Fisheries & Aquaculture, Qingdao 266237, Peoples R China
3.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China
4.Qinghai Environm Monitoring Ctr, Xining 810007, Peoples R China
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Liu, Fuli,Hu, Zimin,Liu, Wenhui,et al. Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development[J]. SCIENTIFIC REPORTS,2016,6(2016):18947.
APA Liu, Fuli.,Hu, Zimin.,Liu, Wenhui.,Li, Jingjing.,Wang, Wenjun.,...&Sun, Xiutao.(2016).Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development.SCIENTIFIC REPORTS,6(2016),18947.
MLA Liu, Fuli,et al."Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development".SCIENTIFIC REPORTS 6.2016(2016):18947.
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