Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing

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...

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Published inChinese journal of oceanology and limnology Vol. 35; no. 1; pp. 198 - 202
Main Author 宋娜 陈慕雁 高天翔 YANAGIMOTO Takashi
Format Journal Article
LanguageEnglish
Published Heidelberg Science Press 2017
Springer Nature B.V
Subjects
Animal populations
Biology
China
coastal water
Coastal waters
Coasts
Earth and Environmental Science
Earth Sciences
Fish
Genetic markers
Japan
loci
Marine
microsatellite repeats
Microsatellites
Oceanography
Ovoviviparity
Population genetics
Redundancy
Sebastiscus marmoratus
sequence analysis
Trinucleotide repeats
三核苷酸重复
中国沿海
二核苷酸
序列重复
微卫星标记
焦磷酸测序
近岸海域
重复序列
China, People's Rep
INW, Japan
China
Japan
microsatellite
genomic DNA
marbled rockfish
454 FLX pyrosequencing
Online AccessGet full text
ISSN0254-4059
2096-5508
1993-5005
2523-3521
DOI10.1007/s00343-016-5103-4

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Summary: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.
Bibliography:SONG Na 1, CHEN Muyan1, YANAGIMOTO Takashi3, GAO Tianxiang 1（ 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）
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.
37-1150/P
marbled rockfish microsatellite 454 FLX pyrosequencing genomic DNA
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ISSN:0254-4059
2096-5508
1993-5005
2523-3521
DOI:10.1007/s00343-016-5103-4