Rapid development of microsatellite markers for the endangered fish Schizothorax biddulphi (Günther) using next generation sequencing and cross-species amplification

International Journal of Molecular Sciences

Volumn 13, Issue 11, 2012, Pages 14946-14955

  Luo, Wei ^a   Nie, Zhulan ^a   Zhan, Fanbin ^a   Wei, Jie ^b   Wang, Weimin ^a   Gao, Zexia ^a  

^a Huazhong Agricultural University   (China)

^b Tarim University   (China)

Author keywords

Microsatellite (SSR); PGM sequencing; Polymorphism; Schizothorax biddulphi

Indexed keywords

ARTICLE; COST EFFECTIVENESS ANALYSIS; DINUCLEOTIDE REPEAT; ENDANGERED SPECIES; FISH; GENE AMPLIFICATION; GENE LOCUS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; MICROSATELLITE MARKER; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMORPHIC LOCUS; SCHIZOTHORAX BIDDULPHI; ANIMAL; GENE FREQUENCY; GENETIC MARKER; GENETICS; GENOTYPE; NUCLEIC ACID AMPLIFICATION; NUCLEOTIDE MOTIF;

GENETIC MARKER; MICROSATELLITE DNA;

ANIMALS; ENDANGERED SPECIES; FISHES; GENE FREQUENCY; GENETIC LOCI; GENETIC MARKERS; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSATELLITE REPEATS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEOTIDE MOTIFS; POLYMORPHISM, GENETIC;

EID: 84870679222     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms131114946     Document Type: Article

References (30)

1. Zhang, R.M.; Guo, Y.; Ma, Y.W. Turxun (2007) A survey on the resource and distribution of Schizothorax biddulphi Günther. Freshw. Fish. 2007, 37, 76-78.
2. Liu, X.J.; Hu, G.F. Threatened fishes of the world: Schizothorax (Schizopyge) biddulphi Günther, 1876 (Cyprinidae). Environ. Biol. Fish 2009, 85, 97-98.
3. Yue, P.Q.; Chen, Y.Y. China Red Databook of Endangered Animals (Pisce.); Science Press: Beijing, China, 1998; pp. 153-155.
4. Mariette, S.; Le Corre, V.; Austerlitz, F.; Kremer, A. Sampling within the genome for measuring within-population diversity: Tradeoffs between markers. Mol. Ecol. 2002, 11, 1145-1156.
5. Evanno, G.; Regnaut, S.; Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 2005, 14, 2611-2620.
6. Castoe, T.A.; Poole, A.W.; Gu, W.; Koning, A.P.J.D.; Daza, J.M.; Smith, E.N.; Pollock, D.D. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Mol. Ecol. Resour. 2010, 10, 341-347.
7. Abdelkrim, J.; Robertson, B.C.; Stanton, J.-A.L.; Gemmell, N.J. Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. Biotechniques 2009, 46, 185-192.
8. Gardner, M.G.; Fitch, A.J.; Bertozzi, T.; Lowe, A.J. Rise of the machines-Recommendations for ecologists when using next generation sequencing for microsatellite development. Mol. Ecol. Resour. 2011, 11, 1093-1101.
9. Loman, N.J.; Misra, R.V.; Dallman, T.J.; Constantinidou, C.; Gharbia, S.E.; Wain, J.; Pallen, M.J. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 2012, 30, 434-439.
10. Whiteley, A.S.; Jenkins, S.; Waite, I.; Kresoje, N.; Payne, H.; Mullan, B.; Allcock, R.; O'Donnell, A. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J. Microbiol. Meth. 2012, 91, 81-88.
11. Somridhivej, B.; Wang, S.; Sha, Z.; Liu, H.; Quilang, J.; Xu, P.; Li, P.; Hu, Z.; Liu, Z. Characterization, polymorphism assessment, and database construction for microsatellites from BAC end sequences of channelcatfish (Ictalurus punctatus): A resource for integration of linkage and physical maps. Aquaculture 2008, 275, 76-80.
12. Meglécz, E.; Nève, G.; Biffin, E.; Gardner, M.G. Breakdown of phylogenetic signal: A survey of microsatellite densities in 454 shotgun sequences from 154 non-model eukaryote species. PLoS One 2012, 7, e40861.
13. Edwardsa, Y.J.K.; Elgara, G.; Clarka, M.S.; Bishop, M.J. The identification and characterization of microsatellites in the compact genome of the Japanese pufferfish, Fugu rubripes: Perspectives in functional and comparative genomic analyses. J. Mol. Biol. 1998, 278, 843-854.
14. Saarinen, E.V.; Austin, J.D. When technology meets conservation: Increased microsatellite marker production using 454 genome sequencing on the endangered okaloosa darter (Etheostoma okaloosae). J. Hered. 2010, 101, 784-788.
15. Wang, Y.; Guo, X. Development and Characterization of EST-SSR Markers in the Eastern Oyster Crassostrea virginica. Mar. Biotechnol. 2007, 9, 500-511.
16. Zhan, A.B.; Bao, Z.M.; Wang, X.L.; Hu, J.J. Microsatellite markers derived from bay scallop Argopecten irradians expressed sequence tags. Fish. Sci. 2005, 71, 1341-1346.
17. Katti, M.V.; Ranjekar, P.K.; Gupta, V.S. Differential distribution of simple sequence repeats in eukaryotic fenome sequences. Mol. Biol. Evol. 2001, 18, 1161-1167.
18. Tóth, G.; Gáspári, Z.; Jurka, J. Microsatellites in different eukaryotic genomes: Survey and analysis. Genome Res. 2000, 10, 967-981.
19. Schorderet, D.F.; Gartler, S.M. Analysis of CpG suppression in methylated and nonmethylated species. Proc. Natl. Acad. Sci. USA 1992, 89, 957-961.
20. Perry, J.C.; Rowe, L. Rapid Microsatellite Development for Water Striders by Next-Generation Sequencing. J. Hered. 2011, 102, 125-129.
21. Csencsics, D.; Brodbeck, S.; Holderegger, R. Cost-effective, species-specific microsatellite development for the endangered Dwarf Bulrush (Typha minima) using next-generation sequencing technology. J. Hered. 2010, 101, 789-793.
22. Chabot, C.L.; Nigenda, S. Characterization of 13 microsatellite loci for the tope shark, Galeorhinus galeus, discovered with next-generation sequencing and their utility for eastern Pacific smooth-hound sharks (Mustelus). Conservation Genet. Resour. 2011, 3, 553-555.
23. Gong, X.; Cui, Z.; Wang, C. Isolation and characterization of polymorphic microsatellite loci from the endangered Tarim schizothoracin (Schizothorax biddulphi Günther). Conserv. Genet. Resour. 2012, 4, 795-797.
24. Liu, X.; Luo, W.; Zeng, C.; Wang, W.; Gao, Z. Isolation of new 40 microsatellite markers in mandarin fish (Siniperca chuatsi). Int. J. Mol. Sci. 2011, 12, 4180-4189.
25. Sambrook, J.; Russell, D.W. Molecular Cloning: A Laboratory Manual, 3rd ed.; Cold Spring Harbor Laboratory Press: New York, NY, USA, 2002; pp. 479-483.
26. You, F.M.; Huo, N.; Gu, Y.Q.; Luo, M.; Ma, Y.; Hane, D.; Lazo, G.R.; Dvorak, J.; Anderson, O.D. BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 2008, 9, 253.
27. Jurka, J.; Pethiyagoda, C. Simple repetitive DNA sequences from primates: Compilation and Analysis. J. Mol. Evol. 1995, 40, 120-126.
28. Yeh, F.C.; Yang, R.C.; Boyle, T. POPGENE, version 1.32; Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, AB, Canada, 1999.
29. Raymond, M.; Rousset, F. GENEPOP (version 1.2): Population genetic software for exact tests and ecumenicism. J. Hered. 1995, 86, 248-249.
30. Van oosterhout, C.; Hutchinson, W.F.; Wills, D.P.M.; Shipley, P. MICRO-CHECKER: Software for identifying and correcting genotype errors in microsatellite data. Mol. Ecol. Notes 2004, 4, 535-538.