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Background  The smooth marron,  Cherax cainii  is an important freshwater crustacean species for aquaculture and for a local wild fishery.  C. tenuimanus , commonly known as the hairy marron is under threat from environmental impacts and genetic introgression from  C. cainii  that is hampering the survival of wild  C. tenuimanus  stocks. Marron are endemic to the south-west of Western Australia and  C. tenuimanus  is restricted to only the Margaret River.    Results  To isolate microsatellite sequences, shotgun 454 pyrosequencing was performed resulting in 184,981 DNA sequence reads. Following screening for microsatellites, 8799 putative microsatellite loci were detected and PCR primers were designed for 968 of these. Ten microsatellite loci were screened in 30 captive  C. cainii  individuals with eight loci producing unambiguous results. The average number of alleles per locus was 4.7 and average  H   e   was 0.474. Following an analysis of relatedness, 79 % of captive dyads were assigned as unrelated. Utilising  C.  quadricarinatus  and  C. destructor , cross-species amplification tests were conducted and amplification was achieved at four of the eight loci.    Conclusions  Using next-generation sequencing methods, eight polymorphic microsatellite loci were developed from  C. cainii , with potential for cross amplification in other  Cherax  species. The markers can be utilised for studies of natural genetic stock structure and for monitoring relatedness levels and genetic variation in both wild and captive populations.    Electronic supplementary material  The online version of this article (doi:10.1186/s13104-015-1345-z) contains supplementary material, which is available to authorized users.

bmc research notes

Microsatellite marker development based on next-generation sequencing for the smooth marron (Cherax cainii, Austin) and cross-species amplification in other Cherax species