SRP326948 PRJNA743793 The transcriptomics of trophic muscle modularity: Malawi cichlid fish gene expression and a crushing key innovation The developmental genomic basis of craniofacial muscle diversity in the unparalleled trophic radiations of cichlids fishes is likely to be extensive. Using RNA-seq, we examined gene expression in five of the largest cichlid craniofacial muscles including: the adductor mandibulae 1, adductor mandibulae 2, sternohyoideus, epaxial, and levator posterior/levator externus IV. Gene expression in these muscles was contrasted between a pelagic planktivore, Copadichromis borleyi, and benthic molluscivore, Mylochromis mola that are both endemic to Lake Malawi in Africa. Consistent with the muscles of these species diverging along a pharyngeal jaw force production axis, a greater number of differentially expressed genes were found in the pharyngeal muscles than in any of the other muscles contrasted. Additionally, very few genes were found to be differentially expressed in the sternohyoideus, epaxial, and adductor mandibulae 2. Surprisingly, the adductor mandibulae 1 which exhibits extensive coevolution in muscle mass with adductor mandibulae 1 also shows extensive divergence in gene expression between the Malawi species. The vast majority of the 637 differentially expressed genes identified tended to only show differential expression in a single muscle. However, we found 11 genes that showed differential expression both in the levator posterior/levator externus IV and in at least one other muscle examined including the adductor mandibulae 1. The developmental genomic basis of individual muscle differentiation in Malawi cichlids is largely, but not completely, independent of gene expression divergence in other muscles.