Present address: Key Laboratory of Child Development and Learning Science, Southeast University, Ministry of Education, Nanjing 210096, China.
Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence
Article first published online: 30 JUL 2009
© 2009 Blackwell Publishing Ltd
Molecular Ecology Resources
Volume 10, Issue 2, pages 341–347, March 2010
How to Cite
CASTOE, T. A., POOLE, A. W., GU, W., JASON de KONING, A. P., DAZA, J. M., SMITH, E. N. and 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: 341–347. doi: 10.1111/j.1755-0998.2009.02750.x
The first two authors contributed equally.
- Issue published online: 5 FEB 2010
- Article first published online: 30 JUL 2009
- Received 14 April 2009; revision received 4 June 2009; accepted 12 June 2009
- high-throughput marker identification;
- next-generation sequencing;
- simple sequence repeats;
- snake genomics;
Optimal integration of next-generation sequencing into mainstream research requires re-evaluation of how problems can be reasonably overcome and what questions can be asked. One potential application is the rapid acquisition of genomic information to identify microsatellite loci for evolutionary, population genetic and chromosome linkage mapping research on non-model and not previously sequenced organisms. Here, we report on results using high-throughput sequencing to obtain a large number of microsatellite loci from the venomous snake Agkistrodon contortrix, the copperhead. We used the 454 Genome Sequencer FLX next-generation sequencing platform to sample randomly ∼27 Mbp (128 773 reads) of the copperhead genome, thus sampling about 2% of the genome of this species. We identified microsatellite loci in 11.3% of all reads obtained, with 14 612 microsatellite loci identified in total, 4564 of which had flanking sequences suitable for polymerase chain reaction primer design. The random sequencing-based approach to identify microsatellites was rapid, cost-effective and identified thousands of useful microsatellite loci in a previously unstudied species.