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SONG Na, CHEN Muyan, GAO Tianxiang, YANAGIMOTO Takashi. Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing[J]. Journal of Oceanology and Limnology, 2017, 35(1): 198-202 |
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Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing |
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| SONG Na1, CHEN Muyan1, GAO Tianxiang2, YANAGIMOTO Takashi3 |
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1 Fisheries College, Ocean University of China, Qingdao 266000, China;
2 Fisheries College, Zhejiang Ocean University, Zhoushan 316000, China;
3 National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Japan |
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| Abstract: |
| Sebastiscus marmoratus is an important sedentary ovoviparous fish distributed in near-shore coastal waters from the coast of China to Japan. Candidate S. marmoratus microsatellite markers were developed in the present study using 454 pyrosequencing, and the marker profile was analyzed. A total of 2 000 000 raw sequence reads were assembled to reduce redundancy. Among them, 1 043 dinucleotide, 925 trinucleotide, 692 tetranucleotide, and 315 pentanucleotide repeats were detected. AC repeats were the most frequent motifs among the dinucleotide repeats, and AAT was the most abundant among the trinucleotide repeats. AAAT, ATAG, and ATCC were the three most common tetranucleotide motifs, and AAGAT and AATAT were the most dominant pentanucleotide motifs. The greatest numbers of loci and potentially amplifiable loci were found in dinucleotide repeats, whereas trinucleotide repeats had the fewest. In summary, a wide range of candidate microsatellite markers were identified in the present study using a rapid and efficient 454 pyrosequencing approach. |
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| Key words:
marbled rockfish|microsatellite|454 FLX pyrosequencing|genomic DNA
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| Received: 2015-04-25 Revised: 2015-07-29 |
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