Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing

作     者：SONG Na 宋娜;陈慕雁;高天翔;YANAGIMOTO Takashi

作者机构：Fisheries College Ocean University of China Qingdao 266000 China Fisheries College Zhejiang Ocean University Zhoushan 316000 China National Research Institute of Fisheries Science Fisheries Research Agency Yokohama Japan 

出 版 物：《Chinese Journal of Oceanology and Limnology》 (中国海洋湖沼学报（英文版）)

年 卷 期：2017年第35卷第1期

页      面：198-202页

核心收录：

学科分类：0908[农学-水产] 09[农学] 

基　　金：Supported by the Special Fund for Agro-scientific Research in the Public Interest(201303048) the National Natural Science Foundation of China(Nos.41176117,31172447) the National Infrastructure of Fishery Germplasm Resources 

主　　题：marbled rockfish microsatellite 454 FLX pyrosequencing genomic DNA 

摘      要：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.