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.
Highlights
Microsatellites, known as simple sequence repeats (SSR) or short tandem repeats (STR), are repeated DNA sequences comprising tandem array of short motifs, which are widely spread in both eukaryotic and prokaryotic genomes[1,2]
The results showed that microsatellites were only presented in a small proportion of the transcripts (6.70%), consisting with the estimation that 2–11% transcripts contain microsatellite[24]
More and more ESTs or transcriptome assembled de novo were used to mine microsatellite, including several seaweeds such as Saccharina japonica[25,26], Laminaria digitata[27], Pyropia[28], etc
Summary
Microsatellites, known as simple sequence repeats (SSR) or short tandem repeats (STR), are repeated DNA sequences comprising tandem array of short motifs (generally, 1–6 nucleotides), which are widely spread in both eukaryotic and prokaryotic genomes[1,2]. Sargassum thunbergii is an ecologically and economically important brown macroalga It widely spreads in the intertidal and shallow sublittoral zone along the coasts of China, Japan, and Korea[14]. This species usually grows luxuriantly and can form seaweed forest together with other Sargassum spp. and kelp, acting as spawning, nursery and feeding ground for marine animals[15,16]. The findings will help us to better understand microsatellite evolution in S. thunbergii transcriptome, and the developed microsatellite markers can meet the urgent need for studies of population genetics, genetic mapping, and functional gene cloning in Sargassum species
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