title: Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development.
abstract: 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 mono-nucleotide. 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.
authors.affiliation: Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.|Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
authors.forename: Fuli
authors.initials: F
authors.lastname: Liu
authors.affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
authors.forename: Zimin
authors.initials: Z
authors.lastname: Hu
authors.affiliation: Qinghai Environment Monitoring Centre, Xining, 810007, China.
authors.forename: Wenhui
authors.initials: W
authors.lastname: Liu
authors.affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Li
authors.affiliation: Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Wang
authors.affiliation: Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
authors.forename: Zhourui
authors.initials: Z
authors.lastname: Liang
authors.affiliation: Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
authors.forename: Feijiu
authors.initials: F
authors.lastname: Wang
authors.affiliation: Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
authors.forename: Xiutao
authors.initials: X
authors.lastname: Sun
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005819:Genetic Markers; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D059372:Nucleotide Motifs; D016366:Open Reading Frames; D015203:Reproducibility of Results; D044647:Sargassum / Q000235:genetics*; D059467:Transcriptome
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D005819:Genetic Markers