PROJECT ID: GSE130526


Data source GEO: GSE130526
Description Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates, derived from embryonic neural crest, are a useful system for elucidating mechanisms of fate specification, pattern formation, and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes, including zebrafish Danio rerio, we identified two populations of white pigment cells—leucophores—one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore-like progenitor. Single-cell transcriptomic, mutational, chemical and ultrastructural analyses of zebrafish leucophores revealed cell-type specific chemical compositions, organelle configurations and genetic requirements. At the organismal level, we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together, our studies revealed new, independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish, and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution.
Key word pigmentation; neural crest; transdifferentiation; evolution; zebrafish; neural-crest; zebrafish; kit; specification; subpopulation; morphogenesis; xanthophores; mel anocytes; orthologue; precursors
Publication Lewis VM, Saunders LM, Larson TA, Bain EJ et al. Fate plasticity and reprogramming in genetically distinct populations of <i>Danio</i> leucophores. Proc Natl Acad Sci U S A 2019 Jun 11;116(24):11806-11811. PMID: 31138706
Abstract Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates, derived from embryonic neural crest, are a useful system for elucidating mechanisms of fate specification, pattern formation, and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes, including the zebrafish Danio rerio, we identified two populations of white pigment cells-leucophores-one of which arises by transdifferentiation of adult melanophores and another of which develops from a yellow-orange xanthophore or xanthophore-like progenitor. Single-cell transcriptomic, mutational, chemical, and ultrastructural analyses of zebrafish leucophores revealed cell-type-specific chemical compositions, organelle configurations, and genetic requirements. At the organismal level, we identified distinct physiological responses of leucophores during environmental background matching, and we showed that leucophore complement influences behavior. Together, our studies reveal independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution.


Dataset Information


Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. GSE130526 (fin) Danio rerio dorsal and anal fin baseline adult, fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry GEO: GSM3741778

Clustering Result


Cluster Cell type Gene id (symbol) Marker class Evidence
1 Epidermal cells ENSDARG00000077121 (cyp26b1) marker DOI:10.1073/pnas.1901021116
1 Epidermal cells ENSDARG00000093413 (edil3a) marker DOI:10.1073/pnas.1901021116
2 Dermal skeleton ENSDARG00000021442 (cdh11) marker DOI:10.1073/pnas.1901021116
3 Epidermal cells ENSDARG00000070683 (dkk3b) marker DOI:10.1073/pnas.1901021116
4 Xanthophores ENSDARG00000045601 (cax1) marker DOI:10.1073/pnas.1901021116
4 Xanthophores ENSDARG00000071475 (aox5) marker DOI:10.1073/pnas.1901021116
4 Xanthophores ENSDARG00000025912 (bscl2l) marker DOI:10.1073/pnas.1901021116
4 Xanthophores ENSDARG00000075191 (oacyl) marker DOI:10.1073/pnas.1901021116
5 Immune cells ENSDARG00000089043 (ptpn6) marker DOI:10.1073/pnas.1901021116
5 Immune cells ENSDARG00000000767 (spi1b) marker DOI:10.1073/pnas.1901021116
5 Immune cells ENSDARG00000090783 (mfap4) marker DOI:10.1073/pnas.1901021116
6 Immune cells ENSDARG00000062152 (chaf1a) marker DOI:10.1073/pnas.1901021116
6 Immune cells ENSDARG00000040041 (mcm4) marker DOI:10.1073/pnas.1901021116
7 Melanophores ENSDARG00000006008 (dct) marker DOI:10.1073/pnas.1901021116
7 Melanophores ENSDARG00000061303 (oca2) marker DOI:10.1073/pnas.1901021116
7 Melanophores ENSDARG00000029204 (tyrp1a) marker DOI:10.1073/pnas.1901021116
8 Dermal skeleton ENSDARG00000002507 (itga10) marker DOI:10.1073/pnas.1901021116
8 Dermal skeleton ENSDARG00000017884 (bgna) marker DOI:10.1073/pnas.1901021116