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Background  Passionflowers  Passiflora edulis  and  Passiflora alata  are diploid, outcrossing and understudied fruit bearing species. In Brazil, passion fruit cultivation began relatively recently and has earned the country an outstanding position as the world’s top producer of passion fruit. The fruit’s main economic value lies in the production of juice, an essential exotic ingredient in juice blends. Currently, crop improvement strategies, including those for underexploited tropical species, tend to incorporate molecular genetic approaches. In this study, we examined a set of  P. edulis  transcripts expressed in response to infection by  Xanthomonas axonopodis , (the passion fruit’s main bacterial pathogen that attacks the vines), aiming at the development of putative functional markers, i.e. SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms).    Results  A total of 210 microsatellites were found in 998 sequences, and trinucleotide repeats were found to be the most frequent (31.4%). Of the sequences selected for designing primers, 80.9% could be used to develop SSR markers, and 60.6% SNP markers for  P. alata . SNPs were all biallelic and found within 15 gene fragments of  P. alata . Overall, gene fragments generated 10,003 bp. SNP frequency was estimated as one SNP every 294 bp. Polymorphism rates revealed by SSR and SNP loci were 29.4 and 53.6%, respectively.    Conclusions    Passiflora edulis  transcripts were useful for the development of putative functional markers for  P. alata , suggesting a certain level of sequence conservation between these cultivated species. The markers developed herein could be used for genetic mapping purposes and also in diversity studies.    Electronic supplementary material  The online version of this article (doi:10.1186/s13104-017-2771-x) contains supplementary material, which is available to authorized users.

Report on the development of putative functional SSR and SNP markers in passion fruits