Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing

Na Song; Muyan Chen; Tianxiang Gao; Takashi Yanagimoto

doi:10.1007/s00343-016-5103-4

Your Location：

Home >

Browse articles >

Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing

Updated：2023-05-16

- Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing
- Journal of Oceanology and Limnology Vol. 35, Issue 1, Pages: 198-202(2017)
- Affiliations：
  
  1. Fisheries College Ocean University of China
  2. Fisheries College Zhejiang Ocean University
  3. National Research Institute of Fisheries Science Fisheries Research Agency
- Author bio：
- Funds：
- DOI：10.1007/s00343-016-5103-4
  CLC：
- Online First：21 April 2016，
  
  Published：2017
- Accepted：
Scan QR Code
Song, N., Chen, M., Gao, T. et al. Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing., Chin. J. Ocean. Limnol. 35, 198–202 (2017). https://doi.org/10.1007/s00343-016-5103-4
DOI：

Song, N., Chen, M., Gao, T. et al. Profile of candidate microsatellite markers in Sebastiscus marmoratus using 454 pyrosequencing., Chin. J. Ocean. Limnol. 35, 198–202 (2017). https://doi.org/10.1007/s00343-016-5103-4 DOI：

摘要

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.

关键词

Keywords

references

Barbará T, Palma-Silva C, Paggi G M, Bered F, Fay M F, Lexer C. 2007. Cross-species transfer of nuclear microsatellite markers: potential and limitations. Molecular Ecology, 16 (18): 3759–3767.

Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27 (2): 573–580.

Castoe T A, Poole A W, Gu W J, de Koning A P J, Daza J M, Smith E N, Pollock D D. 2010. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources, 10 (2): 341–347.

Chen M, Tan Z Y, Zeng G M, Peng J. 2010. Comprehensive analysis of simple sequence repeats in pre-miRNAs. Molecular Biology and Evolution, 27 (10): 2227–2232.

Chistiakov D A, Hellemans B, Volckaert F A M. 2006. Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics. Aquaculture, 255 (1-3): 1–29.

Deng H W, Li Z B, Dai G, Yuan Y, Ning Y F, Shangguan J B, Huang Y S. 2015. Isolation of new polymorphic microsatellite markers from the marbled rockfish Sebastiscus marmoratus. Genetics and Molecular Research, 14 (1): 758–762.

Dong H B, Chen G, Zhang M H, Zhang J D, Zhou H, Tang B G, Huang J S, Shi G, Jiang L. 2008. Tissue-specificities of isozymes and genetic structure of Sebastiscus marmoratus. Journal of Guangdong Ocean University, 28 (4): 15–20. (in Chinese with English abstract)

Jurka J, Kapitonov V V, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. 2005. Repbase update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research, 110 (1-3): 462–467.

Katti M V, Ranjekar P K, Gupta V S. 2001. Differential distribution of simple sequence repeats in eukaryotic genome sequences. Molecular Biology and Evolution, 18 (7): 1161–1167.

Kita J, Tsuchida S, Setoguma T. 1996. Temperature preference and tolerance, and oxygen consumption of the marbled rockfish, Sebastiscus marmoratus. Marine Biology, 125 (3): 467–471.

Li H M. 2014. New Microsatellite Satellite Markers Development Based on Whole Genome Sequencing Information and Its Application in Population Genetics in Large Yellow Croaker. Zhejiang Ocean University, Zhoushan, China. 62p. (in Chinese)

Li Q H, Li Z B, Dai G, Cao Y Y, Chen X J, Chen L N, Shangguan J B, Ning Y F. 2014. Isolation and characterization of eleven microsatellite loci in the marbled rockfish, Sebastiscus marmoratus (Scorpaenidae). Conservation Genet ics Resour ces, 6 (1): 53–55.

Li Q. 2004. Advances in studies on microsatellite markers in the Pacific abalone. Periodical of Ocean University of China, 34 (3): 365–370. (in Chinese with English abstract)

Liu H B, Liu S F, Ye J B, Yuan Y J, Ding S X, Zhuang Z M. 2014. Polymorphic microsatellite markers in the false kelpfish Sebastiscus marmoratus: isolation, characterization, and cross-species amplification. Genetics and Molecular Research, 13 (1): 134–138.

Nakamura M, Suzuki A, Hoshida H, Akada R. 2014). Minimum GC-Rich sequences for overlap extension PCR and primer annealing. In: Valla S, Lale R eds. DNA Cloning and Assembly Methods. Humana Press, New Jersey, USA. p.165–181.

Queirós J, Godinho R, Lopes S, Gortazar C, de la Fuente J, Alves P C. 2015. Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications. Molecular Ecology Resources, 15 (4): 747–760.

Rozen S, Skaletsky H. 2000). Primer3 on the WWW for general users and for biologist programmers. In: Misener S, Krawetz S A eds. Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, New Jersey, USA. p.365–386.

Su T F, Jiang S G, Zhang D C, Zhou F L, Huang J H, Zhu C Y, Yang L S. 2012. Genetic diversity of Sebastiscus marmoratus in eastern Guangdong coastal waters and its taxonomic status in Sebastidae. P rogress in Fishery Sciences, 33 (2): 1–8. (in Chinese with English abstract)

Tóth G, Gáspári Z, Jurka J. 2000. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Research, 10 (7): 967–981.

Xu T J, Quan X Q, Sun Y N, Zhao K C, Wang R X. 2010. A first set of polymorphic microsatellite loci from the marbled rockfish, Sebastiscus m armoratus. Biochemical Genetics, 48 (7-3): 680–683.

Yin L N, Zhang H, Yanagimoto T, Gao T X. 2012. Isolation and characterization of nine polymorphic microsatellite markers of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae). Russian Journal of Genetics, 48 (12): 1264–1266.

Zane L, Bargelloni L, Patarnello T. 2002. Strategies for microsatellite isolation: a review. Molecular Ecology, 11 (1): 1–16.

Zeng C, Gao Z X, Luo W, Liu X L, Wang W M. 2013. Characteristics of microsatellites in blunt snout bream (Megalobrama amblycephala) EST sequences using 454 FLX. Acta Hydrobiologica Sinica, 37 (5): 982–988.

Zhang D X, Hewitt G M. 2003. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology, 12 (3): 563–584.

Zhang H. 2013. Molecular Phylogeography of Two Marine Ovoviviparous Fishes in Northwestern Pacific. Ocean University of China, Qingdao, China. 203p. (in Chinese)

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

Profile and development of microsatellite primers for Acanthogobius ommaturus based on high-throughput sequencing technology

Analysis of novel immune-related genes and microsatellite markers in the transcriptome of Paphia undulata

Isolation and characterization of genic microsatellites from de novo assembly transcriptome in the bivalve Ruditapes philippinarum

A novel male-associated marker for sex identification in Ussuri catfish Pseudobagrus ussuriensis

Molecular cytogenetic of the Amoy croaker, Argyrosomus amoyensis (Teleostei, Sciaenidae)

Related Author

Ziyi FENG

Chunhou LI

Zhicheng SUN

Tianxiang GAO

Na SONG

Lu LIU

Chenyu SONG

Ziniu YU

Related Institution

South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences

National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University

Fisheries College, Ocean University of China

University of Chinese Academy of Sciences

Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture of China; Fisheries College, Jimei University

Address：Editorial Office of JOL, 88 Haijun Rd. Qingdao, 266000, China
Tel：+86-532-82898754 Email：jol@qdio.ac.cn
Technical support is provided by Beijing Founder electronics co., LTD 京ICP备09064830号-19 京公网安备11010802024621
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰