Comparative Transcriptomics in East African Cichlids Reveals Sex- and Species-Specific Expression and New Candidates for Sex Differentiation in Fishes

Data deposition: All sequencing reads have been deposited at NCBI SRA under the accession SRP042144. Males and females of the same species differ largely in gene expression, which accounts for most of the morphological and phys-iological differences and sex-specific phenotypes. Here, we analyzed sex-specific gene expression in the brain and the gonads of cichlid fishes from Lake Tanganyika belonging to four different lineages, so-called tribes (Eretmodini, Ectodini, Haplochromini, and Lamprologini), using the outgroup Nile tilapia (Oreochromis niloticus) as reference. The comparison between male and female brains revealed few differences between the sexes, consistent in all investigated species. The gonads, on the other hand, showed a large fractionofdifferentiallyexpressedtranscriptswith themajorityof themshowingthesamedirectionofexpression inall four species.All here-studied cichlids, especially the three investigated mouth-breeding species, showed a trend toward more male- than female-biased transcripts. Transcripts, which were female-biased in expression in all four species, were overrepresented on linkage group (LG)1 in the reference genome and common male-biased transcripts showed accumulation on LG23, the presumable sex chromo-somes of the Nile tilapia. Sex-specific transcripts contained candidate genes for sex determination and differentiation in fishes, especially members of the transforming growth factor-b-superfamily and the Wnt-pathway and also prominent members of the sox-, dm-domain-, and high mobility group-box families. We further confirmed our previous finding on species/lineage-specific gene expression shifts in the sex steroid pathway, including synthesizing enzymes as the aromatase cyp19a1 and estrogen and androgen receptors