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Background  The Amazon molly,  Poecilia formosa  (Teleostei: Poeciliinae) is an unisexual, all-female species. It evolved through the hybridisation of two closely related sexual species and exhibits clonal reproduction by sperm dependent parthenogenesis (or gynogenesis) where the sperm of a parental species is only used to activate embryogenesis of the apomictic, diploid eggs but does not contribute genetic material to the offspring.  Here we provide and describe the first  de novo  assembled transcriptome of the Amazon molly in comparison with its maternal ancestor, the Atlantic molly  Poecilia mexicana . The transcriptome data were produced through sequencing of single end libraries (100 bp) with the Illumina sequencing technique.    Results  83,504,382 reads for the Amazon molly and 81,625,840 for the Atlantic molly were assembled into 127,283 and 78,961 contigs for the Amazon molly and the Atlantic molly, respectively. 63% resp. 57% of the contigs could be annotated with gene ontology terms after sequence similarity comparisons. Furthermore, we were able to identify genes normally involved in reproduction and especially in meiosis also in the transcriptome dataset of the apomictic reproducing Amazon molly.    Conclusions  We assembled and annotated the transcriptome of a non-model organism, the Amazon molly, without a reference genome ( de novo ). The obtained dataset is a fundamental resource for future research in functional and expression analysis. Also, the presence of 30 meiosis-specific genes within a species where no meiosis is known to take place is remarkable and raises new questions for future research.

Comparative analysis of the gonadal transcriptomes of the all-female species Poecilia formosa and its maternal ancestor Poecilia mexicana