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Background  The unisexual Amazon molly ( Poecilia formosa ) originated from a hybridization between two sexual species, the sailfin molly ( Poecilia latipinna ) and the Atlantic molly ( Poecilia mexicana ). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely related species triggers embryogenesis of the apomictic oocytes, but typically does not contribute genetic material to the next generation. We compare for the first time the gonadal transcriptome of the Amazon molly to those of both ancestral species,  P. mexicana  and  P. latipinna .    Results  We sequenced the gonadal transcriptomes of the  P. formosa  and its parental species  P. mexicana  and  P. latipinna  using Illumina RNA-sequencing techniques (paired-end, 100 bp). De novo assembly of about 50 million raw read pairs for each species was performed using Trinity, yielding 106,922 transcripts for  P. formosa , 115,175 for  P. latipinna , and 133,025 for  P. mexicana  after eliminating contaminations. On the basis of sequence similarity comparisons to other teleost species and the UniProt databases, functional annotation, and differential expression analysis, we demonstrate the similarity of the transcriptomes among the three species. More than 40% of the transcripts for each species were functionally annotated and about 70% were assigned to orthologous genes of a closely related species. Differential expression analysis between the sexual and unisexual species uncovered 2035 up-regulated and 564 down-regulated genes in  P. formosa . This was exemplary validated for six genes by qRT-PCR.    Conclusions  We identified more than 130 genes related to meiosis and reproduction within the apomictically reproducing  P .  formosa . Overall expression of these genes seems to be down-regulated in the  P .  formosa  transcriptome compared to both ancestral species (i.e., 106 genes down-regulated, 29 up-regulated). A further 35 meiosis and reproduction related genes were not found in the  P .  formosa  transcriptome, but were only expressed in the sexual species. Our data support the hypothesis of general down-regulation of meiosis-related genes in the apomictic Amazon molly. Furthermore, the obtained dataset and identified gene catalog will serve as a resource for future research on the molecular mechanisms behind the reproductive mode of this unisexual species.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4382-2) contains supplementary material, which is available to authorized users.

bmc genomics

The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna