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Background  The  Passiflora  genus comprises hundreds of wild and cultivated species of passion fruit used for food, industrial, ornamental and medicinal purposes. Efforts to develop genomic tools for genetic analysis of  P. edulis , the most important commercial  Passiflora  species, are still incipient. In spite of many recognized applications of microsatellite markers in genetics and breeding, their availability for passion fruit research remains restricted. Microsatellite markers in  P. edulis  are usually limited in number, show reduced polymorphism, and are mostly based on compound or imperfect repeats. Furthermore, they are confined to only a few  Passiflora  species. We describe the use of NGS technology to partially assemble the  P. edulis  genome in order to develop hundreds of new microsatellite markers.    Results  A total of 14.11 Gbp of Illumina paired-end sequence reads were analyzed to detect simple sequence repeat sites in the sour passion fruit genome. A sample of 1300 contigs containing perfect repeat microsatellite sequences was selected for PCR primer development. Panels of di- and tri-nucleotide repeat markers were then tested in  P. edulis  germplasm accessions for validation. DNA polymorphism was detected in 74% of the markers (PIC = 0.16 to 0.77; number of alleles/locus = 2 to 7). A core panel of highly polymorphic markers (PIC = 0.46 to 0.77) was used to cross-amplify PCR products in 79 species of  Passiflora  (including  P. edulis ), belonging to four subgenera ( Astrophea, Decaloba, Distephana  and  Passiflora ). Approximately 71% of the marker/species combinations resulted in positive amplicons in all species tested. DNA polymorphism was detected in germplasm accessions of six closely related  Passiflora  species ( P. edulis ,  P. alata, P. maliformis, P. nitida, P. quadrangularis  and  P. setacea ) and the data used for accession discrimination and species assignment.    Conclusion  A database of  P. edulis  DNA sequences obtained by NGS technology was examined to identify microsatellite repeats in the sour passion fruit genome. Markers were submitted to evaluation using accessions of cultivated and wild  Passiflora  species. The new microsatellite markers detected high levels of DNA polymorphism in sour passion fruit and can potentially be used in genetic analysis of  P. edulis  and other  Passiflora  species.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3881-5) contains supplementary material, which is available to authorized users.

Microsatellite marker development by partial sequencing of the sour passion fruit genome (Passiflora edulis Sims)