Biodiv Sci ›› 2012, Vol. 20 ›› Issue (1): 51-58.DOI: 10.3724/SP.J.1003.2012.08168

• Original Papers • Previous Articles     Next Articles

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

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

  1. 1 School of Life Sciences, Anhui University, Hefei 230039
    2 School of Life Sciences, Nanjing Normal University, Nanjing 210046
  • Received:2011-09-02 Accepted:2011-10-16 Online:2012-01-20 Published:2012-02-14
  • Contact: Baowei Zhang

Abstract:

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.

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