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Isolation and characterization of 23 novel polymorphic microsatellite markers from the endangered Puerto Rican boa (Chilabothrus inornatus) using paired-end Illumina shotgun sequencing


We developed 23 microsatellite loci for the endangered Puerto Rican boa, Chilabothrus inornatus, from 100 bp reads obtained from a paired-end Illumina shotgun library. Importantly, these loci can be amplified using the same touchdown PCR program. All loci were highly polymorphic, with between 5 and 15 alleles found among 24 individuals genotyped from three populations. We anticipate that these loci will be extremely useful in conservation genetic studies of this species.

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We thank K. Winchell and speleological volunteers for assistance in the field. We are grateful to R. Beasley, S. Lance, and the Molecular Ecology Laboratory at the Savannah River Ecological Lab for assistance with sequencing and primer design. We are also grateful to the Puerto Rico Departamento de Recursos Naturales y Ambientales (DRNA) for permits and assistance. All samples were collected under DRNA permits 2012-EPE-001 (to RGR) and 00-EPE-16 (to ARPR), U.S. Fish and Wildlife Native Endangered Species Recovery Permit # TE63270A-0 (to RGR), and U.S. Department of Agriculture Special Use Permit # CNF-2118 (to RGR). We are grateful for funding from the United States Fish and Wildlife Service Southeast Region Endangered Species Recovery Implementation. This work was approved by the University of Massachusetts Boston Institutional Animal Care and Use Committee (IACUC) Protocol no. 2011006.

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Correspondence to R. Graham Reynolds.

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Reynolds, R.G., Puente-Rolón, A.R., Kolodzaike, K. et al. Isolation and characterization of 23 novel polymorphic microsatellite markers from the endangered Puerto Rican boa (Chilabothrus inornatus) using paired-end Illumina shotgun sequencing. Conservation Genet Resour 6, 107–109 (2014).

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  • Boidae
  • Conservation
  • Endangered species
  • Epicrates
  • Microsatellites
  • Next generation DNA sequencing