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Background  Differential gene expression can be translated into differing phenotypic traits. Especially during embryogenesis, specific gene expression networks regulate the development of different body structures. Cichlid fishes, with their impressive phenotypic diversity and propensity to radiate, are an emerging model system in the genomics era. Here we set out to investigate gene expression throughout development in the well-studied cichlid fish  Astatotilapia burtoni , native to Lake Tanganyika and its affluent rivers.    Results  Combining RNA-sequencing from different developmental time points as well as integrating adult gene expression data, we constructed a new genome annotation for  A. burtoni  comprising 103,253 transcripts (stemming from 52,584 genomic loci) as well as a new reference transcriptome set. We compared our transcriptome to the available reference genome, redefining transcripts and adding new annotations. We show that about half of these transcripts have coding potential. We also characterize transcripts that are not present in the genome assembly. Next, using our newly constructed comprehensive reference transcriptome, we characterized differential gene expression through time and showed that gene expression is shifted between different body parts. We constructed a gene expression network that identified connected genes responsible for particular phenotypes and made use of it to focus on genes under potential positive selection in  A. burtoni , which were implicated in fin development and vision.    Conclusions  We provide new genomic resources for the cichlid fish  Astatotilapia burtoni , which will contribute to its further establishment as a model system. Tracing gene expression through time, we identified gene networks underlying particular functions, which will help to understand the genetic basis of phenotypic diversity in cichlids.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5321-6) contains supplementary material, which is available to authorized users.

Time matters! Developmental shift in gene expression between the head and the trunk region of the cichlid fish Astatotilapia burtoni