Tissue-specific transcriptomics uncovers novel craniofacial genes underlying jaw divergence in specialist pupfishes
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Oct 28, 2024 version files 54.56 MB
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README.md
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Abstract
The regulation of gene expression is one of the key evolutionary processes driving phenotypic divergence among species. Here, we investigate the tissue-specific gene expression of a non-model adaptive radiation of Cyprinodon pupfishes, characterized by their divergent dietary niches and exceptionally fast rates of craniofacial evolution. By comparing tissue-specific gene expression in the most morphologically divergent skeletal structure, the oral jaws, with the relatively morphologically conserved caudal tail region, we identified genes that were differentially expressed exclusively in the developing jaws of each of the three trophic specialists at hatching (8 dpf) and not in any other species. We then assessed their overlap (as transcriptionally-regulated genes) with adaptive regulatory variants identified in previous genomic studies. Our analysis identified pycr3 and atp8a1 as the most promising for craniofacial evolution in the scale-eaters, both genes with no known previous craniofacial function. We functionally confirmed the craniofacial expression of these genes by in situ mRNA hybridization chain reaction and demonstrated their species-specific expression in branchial and muscle tissues between sister species of this young radiation. Our work underscores the power of integrating tissue-specific transcriptomics with speciation genomics to identify novel craniofacial candidate genes controlling divergent morphogenesis in a natural ‘evolutionary mutant’ system.
https://doi.org/10.5061/dryad.dncjsxm8c
Description of the data and file structure
Counts for 7 tissue-specific pupfish transcriptomes at hatching (8 dpf)
Tissues: Jaw (J), Tail (T).
Populations: Crescent Pond (C), Osprey Lake (O), Little Lake (L), Chihuahua (F), North Carolina (N).
Species: Cyprinodon desquamator (P), Cyprinodon variegatus (A), Cyprinodon brontotheroides (M), Cyprinodon fontinalis (F), Cyprinodon sp. ‘wide-mouth’ (S).
Diet: Generalist (A), Scale-eater (P), Molluscivore (M), Intermediate scale-eater (S).
Files and variables
The file name is,
First character: Pupfish population
Second character: Pupfish Species
Third character: Replicate
Fifth character: Tissue
Access information
https://www.biorxiv.org/content/10.1101/2024.10.02.616385v1.full
https://github.com/fishfena/JAWesome_RNAproject
Description here https://github.com/fishfena/JAWesome_RNAproject and in the manuscript