Biodiversity Science ›› 2012, Vol. 20 ›› Issue (1): 51-58.doi: 10.3724/SP.J.1003.2012.08168

• Original Papers • Previous Article     Next Article

Structural characteristics of di-nucleotide/tetra-nucleotide repeat microsatellite DNA in Pachyhynobius shangchengensis genomes and its effect on isolation

Hui Wang1, Baowei Zhang1*, Wenbo Shi1, Xia Luo1, Lizhi Zhou1, Demin Han1, Qing Chang2   

  1. 1School of Life Sciences, Anhui University, Hefei 230039

    2School of Life Sciences, Nanjing Normal University, Nanjing 210046
  • Received:2010-07-01 Revised:2011-09-01 Online:2012-02-14
  • Baowei Zhang

A low success ratio is often encountered in the microsatellite isolation from the species of Caudata. In the present study, di-nucleotide/tetra-nucleotide repeat microsatellite loci were isolated following the FLASCO (fast isolation by AFLP of sequences containing repeats) approach and the sequences were analyzed for the purpose of learning how microsatellite structure impacted on isolation efficiency. We found that most di-nucleotide repeat microsatellite loci were involved in the microsatellite DNA family, which resulted in low isolation efficiency. In contrast, no microsatellite DNA family members were found in the tetra-nucleotide repeat microsatellite loci. On the basis of analysis of the three microsatellite DNA families found in the present study, there were significant differences in the extent of variation between the upstream and downstream flanking sequences in same microsatellite DNA family. This variation was the highest in the sequence sections adjacent to the core repeated units, but more conservative in other regions, which might reflect the complexity of the microsatellite DNA family evolution. These results suggest that in the process of microsatellite development for Caudata, we must pay attention to interference from microsatellite DNA family evolution. The choice of appropriate nucleotide repeats is key to obtaining a high isolation efficiency.

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

Devitt TJ, Pereira R, Jakkula L, et al. (2009) Isolation and characterization of 15 polymorphic microsatellite in the Plethodontid salamander Ensatina eschscholtzii. Molecular Ecology Resources.

Garner TWJ (2002) Genome size and microsatellites: effect of nuclear size on amplification potential. Genome 45, 212-215.

Gonser RA, Collura RV (1996) Waste Not, Want Not: Toe-clips as a Source of DNA Journal of Herpetology 30, 445-447.

Gregory TR, Nicol JA, Tamm H (2007) Eukaryotic genome size databases. Nucleic Acids Research 35, 332-338.

Hanski I (1998) Metapopulation dynamics. Nature 396, 41-49.

Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. TRENDS in Ecology and Evolution 11, 424-429.

Kumar S, Tamura K, Nei M (2004) MEGA: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5, 150-163.

Lalitha S (2000) Primer premier 5. Biotech Software & Internet Report 1, 270.

Rowe G, Beebee TJC, Burke T (2000) A microsatellite analysis of natterjack toad (Bufo calamita) metapopulation. Oikos 88, 641-651.

Sambrook J, Fritsch EF, Maniatis T (1999) Molecular Cloning: A Laboratory Manual (2nd). Cold Spring Harbor Laboratory Press, 463-469.

Schuler GD, Boguski MS, Stewart EA (1996) A gene map of the human genome. Science 274, 540-546.

Sequeira F, Rocha S, Ferrand N, Weiss S (2005) Isolation and characterization of seven microsatellite loci in Chioglossa lusitanica(Urodela:Salamandridae). Molecular Ecology Notes 5, 212-214.

Singh VK, Mangalam AK, Dwivedi S, Naik S (1998) Primer premier: program for design of degenerate primers from a protein sequence. Biotechniques 24, 318-319.

Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic acids research 25, 4876-4882.

Toth G, Gáspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analisis. Genome Research 10, 967-981.

Vandevliet MS, Diekann OE, Serrsao ETA, Beja P (2009) Isolation of highly polymorphic mircosatellite loci for a species with a large genome size:sharp-ribbed salamander(Pleurodeles waltl). Molecular Ecology Resources 9, 425-428.

Wang H, Shi W, Zhu L, et al. (2010) Isolation and characterization of fourteen polymorphic tetranucleotide microsatellites for Shangcheng Stout Salamander (Pachyhynobius shangchengensis). Conservation Genetics Resources, in press.

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

Wang H (王慧), Shen FF (沈菲菲), Chang Q (常青), Han DM (韩德民), Zhang BW (张保卫) (2009) Isolation and characterization of dinucleotide microsatellite loci in Pachyhynobius shangchengensis. Herpetologica Sinica (两栖爬行动物学研究) 12, pp. 357-362. Publishing House of Southeast University, Nanjing. (in Chinese with English abstract)

Ji YJ (吉亚杰),Zhang DX (张德兴)(2004) Characteristics of microsatellite DNA in lepidopteran genomes and implications for their isolation. Current Ecology (动物学报) 50, 608-614.

Wang S (汪松), Xie Y (谢焱) (2004) China Species Red List (中国红色物种名录), pp. 190. Higher Education Press, Beijing. (in Chinese)

Zhang BW (张保卫), Shi WB (史文博), Zhao K (赵凯) (2009) The preliminary investigation of Pachyhynobius shangchengensis distribution, with remarks on the injury and malformation phenomenon. Herpetologica Sinica (两栖爬行动物学研究) 12, pp. 311-317. Publishing House of Southeast University, Nanjing. (in Chinese with English abstract)

Fei L (费梁), Qu WY (瞿文元), Wu SH (吴淑辉) (1985) Description of a new genus and species of Hynobiidae of China. Zoological Research (动物学研究) 6(4), 389-404. (in Chinese with English abstract)

Fei L (费梁), Ye CY (叶昌媛), Huang YS (黄永韶) (2005) An illustrated key to Chianese Amphibians (中国两栖动物检索及图解), pp. 23. Sichuan Publishing Group?Sichuan Publishing House of Science and Technology. (in Chinese)

Chen BH (陈壁辉) (1991) The Amphibiam and Reptilian fauna of Anhui(安徽两栖爬行动物志), pp. 34-36. Anhui Science & Technology Publishing House, Hefei. (in Chinese)
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