doi:

DOI: 10.3724/SP.J.1003.2012.08168

Biodiversity Science (生物多样性) 2012/20:1 PP.51-58

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


Abstract:
A low success ratio is often encountered in the microsatellite isolation from the species of Caudata. In the present study, dinucleotide/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 dinucleotide 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 re-flect 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.

Key words:microsatellite, structure characteristics, microsatellite DNA family, Pachyhynobius shangchengensis, isolation efficiency

ReleaseDate:2014-07-21 16:18:26



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

Bruford MW, Wayne RK (1993) Microsatellites and their application to population genetic studies. Current Opinion in Genetics and Development, 3, 939-943.

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

Devitt TJ, Pereira R, Jakkula L, Alexandrino J, Bardeleben C, Moritz C (2009) Isolation and characterization of 15 polymorphic microsatellites in the Plethodontid salamander Ensatina eschscholtzii. Molecular Ecology Resources, 9, 966-969.

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, 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 Chinese Amphibians (中国两栖动物检索及图解), p. 23. Sichuan Publishing House of Science and Technology, Chengdu. (in Chinese)

Garner TWJ (2002) Genome size and microsatellites: the 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, Kullman B, Kullman K, Leitch IJ, Murray BG, Kapraun DF, Greilhuber J, Bennett MD (2007) Eukaryotic genome size databases. Nucleic Acids Research, 35, D332-D338.

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

Ji YJ (吉亚杰), Zhang DX (张德兴) (2004) Characteristics of microsatellite DNA in lepidopteran genomes and implications for their isolation. Acta Zoologica Sinica (动物学报), 50, 608-614. (in Chinese with English abstract)

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 and Internet Report, 1, 270-272.

Purrenhage JL, Niewiarowski PH, Moore FBG (2009) Population structure of spotted salamanders (Ambystoma maculatum) in a fragmented landscape. Molecular Ecology, 18, 235-247.

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

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

Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K, White RE, Rodriguez-Tomé P, Aggarwal A, Bajorek E, Bentolila S, Birren BB, Butler A, Castle AB, Chiannilkulchai N, Hudson TJ (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.

Tay WT, Behere GT, Batterham P, Heckel DG (2010) Generation of microsatellite repeat families by RTE retrotrans-posons in lepidopteran genomes. BMC Evolutionary Biology, 10, 144.

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.

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

van de Vliet MS, Diekmann OE, Serrão ETA, Beja P (2009) Isolation of highly polymorphic microsatellite loci for a species with a large genome size: sharp-ribbed salamander (Pleurodeles waltl). Molecular Ecology Resources, 9, 425-428.

van Dongen S, Backeljau T, Matthysen E, Dhondt AA (1998) Genetic population structure of the winter moth (Operophtera brumata L.) (Lepidoptera, Geometridae) in a fragmented landscape. Heredity, 80, 92-100.

Wang IJ, Savage WK, Shaffer HB (2009) Landscape genetics and least-cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense). Molecular Ecology, 18, 1365-1374.

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

Zhang DX (2004) Lepidopteran microsatellite DNA: redundant but promising. Trends in Ecology and Evolution, 19, 507-509.

Zhang P, Chen YQ, Zhou H, Liu YF, Wang XL, Papenfuss TJ, Wake DB, Qu LH (2006) Phylogeny, evolution, and bio-geography of Asiatic salamanders (Hynobiidae). Proceedings of the National Academy of Sciences, USA, 103, 7360-7365.

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