ArticleScientific reports2016
Distribution, function and evolution characterization of microsatellite in Sargassum thunbergii (Fucales, Phaeophyta) transcriptome and their application in marker development.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 29 citations in OpenAlex.
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- An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants?Functional & integrative genomics · 2022Article
- Physiological Responses and Metabonomics Analysis of Male and FemaleFrontiers in plant science · 2022Article
- Characterization and Development of Microsatellite Markers inFrontiers in genetics · 2020Article
- Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis.Scientific reports · 2019Article
- Analysis of microsatellites from transcriptome sequences of Phytophthora capsici and applications for population studies.Scientific reports · 2018Article
- Historical isolation and contemporary gene flow drive population diversity of the brown alga Sargassum thunbergii along the coast of China.BMC evolutionary biology · 2017Article
- Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis) for Crossbreeding.Genes · 2017Article
- Comparative Transcriptome Analysis Identified Candidate Genes Related to Bailinggu Mushroom Formation and Genetic Markers for Genetic Analyses and Breeding.Scientific reports · 2017Article
- In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa.PloS one · 2017Article
- Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species,Frontiers in plant science · 2017Article
- De novo assembly, functional annotation, and analysis of the giant reed (Biotechnology for biofuels · 2017Article
- Microsatellite markers: what they mean and why they are so useful.Genetics and molecular biologyArticle
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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