Large-scale isolation of Eastern spiny mouse Acomys dimidiatus microsatellite loci through GS-FLX 454 titanium sequencing
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We isolated and characterized Eastern spiny mouse, Acomys dimidiatus microsatellite loci. A microsatellite-enriched library was created and A. dimidiatus fragments sequenced using 454 sequencing. In total, 1,221 primer-designable microsatellite sequences were identified. We designed primer sets for 20 loci. Loci were characterized in A. dimidiatus individuals from a semi-isolated desert wadi (valley) in St. Katherine Protectorate, Egypt. After initial trails, 18 microsatellite loci were genotyped in 67 mice. The number of alleles displayed in the 18 markers ranged from three to nine (mean = 6) with mean expected and observed heterozygosities of 0.63 and 0.65, respectively. All 18 selected loci were in Hardy–Weinberg equilibrium (P > 0.01). These markers will be used to investigate the fine-scale spatial patterns of genetic diversity and divergence of A. dimidiatus populations. The isolated loci are of potential utility in other murines, including 260 threatened species.
KeywordsEastern spiny mouse Pyrosequencing Microsatellite markers Muridae Rodent Simple sequence repeats (SSRs)
We thank Mohammed Shaker of St. Katherine Protectorate for the permission to collect spiny mice and the staff of the Rangers office for providing vehicles and drivers that enabled access to remote locations. The fieldwork was supported by a grant from the Teaching Quality Enhancement Fund of the University of Nottingham, for which we are most grateful. Marker development and genotyping was supported by the UK Natural Environment Research Council (NERC) and performed at the NERC Biomolecular Analysis Facility at the Universities of Liverpool and Sheffield. We thank Christian Bourne, John Kenny and Xuan Li for 454 sequencing at the NERC Biomolecular Analysis Facility at the University of Liverpool. Andy Krupa provided genotyping advice and Francis Gilbert helped with logistics in Egypt. We thank Terry Burke for project support. SA is funded by the Government of Kuwait and thanks Prof. M. Bou-Resli (retired) and Drs A. Al-Lanqawi, F. Al-Balool, F. Alsidrawi (retired), M. Al-Salameen and S. Al-Mohanna for their endless moral support. Finally, the fieldwork could not have been undertaken without the enthusiastic participation of undergraduate students from the School of Biology at the University of Nottingham.
- Bates PJ (1994) The distribution of Acomys (Rodentia: Muridae) in Africa and Asia. Israel J Zool 40:199–214Google Scholar
- Myers P, Espinosa R, Parr CS, Jones T, Hammond GS, Dewey TA (2006) Family Muridae. The Animal Diversity Web. http://www.arlis.org/docs/vol1/52386062/muridae.html#b4b85fac760ab2d318cdd0cbe91a1662 Accessed 24 October 2012
- Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenism. J Hered 86:248–249Google Scholar
- Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar