Stages and patterns of gene expression during development. A. Key stages during F. heteroclitus development. Stages (S) are in the upper left of each embryo image. S1, unfertilized egg. S2, 1 cell stage. S3, 2 cell stage. S4, 4 cell stage. S5, 8 cell stage. S7, 32 cell stage. S10, early blastula. S16, pre-mid gastrula. S21, 3-4 somites. S25, onset of circulation. S31 and S34, growth and organodiffertiantion. S35, pre-hatching. S36, hatching. S37, growth. S40, initiation of larval stage. (See Additional Files 1 and 4). AP-animal pole; AT-atrium; BD-blastoderm; BK-blastodisk; BM-blastomere; CF-caudal fin; CG-cortical granules; CH-chorion; CL-cleavage; ES-embryonic shield; H-heart; IC-inner cells; MP-micopyle; OC-outer cells; OD-oil droplet; OL-optic lobe; OR-oral cavity; PB-periblast; SO-somite; VM-vitelline membrane; VP-vegetal pole; VT-ventricle; Y-yolk. (For full atlas, see Additional Files 1, 2 and 4). B. Hierarchical clustering of 6,551 genes (95.5% of 6,857) that changed significantly between any two stages (p < 0.01). Each row represents one gene and each column represents one of forty developmental stages. Clusters of genes with similar expression patterns are shown on the right (gene tree). Red indicates high expression levels and green represents low expression levels. C. Hierarchical clustering of forty developmental stages based on shared gene expression patterns. Three majors clusters are colored yellow, red and blue and correspond to gene expression patterns. D. Pairwise differences between adjacent stages of F. heteroclitus development. Significances of differences as - log10(p-values) are plotted against log2 differences in expression of adjacent stages. - log10(p-values) range from 0 to 8 and log2 differences in expression range from -3 to 3 (-8-fold to 8-fold differences in expression). Numbers of significant genes (p < 0.01) that differ between stages are shown. Colors in these plots correspond to the colors of the gene tree in 1B.