Differentially expressed protein-coding genes (DEGs) in developing zebrafish head transcriptome. A Sample distribution according to the PCA analysis. B Volcano plots of DEGs by neighbor time point comparisons. Dark colors depict large change of genes (LFC ≥ 2) while light colors depict moderate change of genes (1 ≤ LFC < 2). C Expression patterns of DEGs by pairwise comparisons and were divided into four clusters. D GO biological process enrichment analysis of DEGs in four clusters. E RT-qPCR validation of four genes in RNA-seq datasets

Significant enrichment of brain-preference genes in head transcriptome compared to that in the whole embryo RNA-seq. A Overview of identification of developmental brain-preference genes by integrating datasets from this study and other publication. B Number of stage-specific expression genes. C The upset plots of up- and down-regulated DEGs between head and whole embryo developmental RNA-seq. D Significant enrichment of brain-preference and synaptosome genes in DEGs only detected from head transcriptome. E High correlation of DEGs detected both in head and whole embryo transcriptome based on log2-transformed fold-change. F Disease enrichment of developmental brain-preference genes. G RT-qPCR validation of genes with preferred expression in brain. H In situ hybridization of protein-coding genes, aldocb and dpysl5b

Snap25b knockout causes embryonic development defects and decreases swimming activity. A The snap25b gene structure and the schema for CRISPR-Cas9 technology to reduce snap25b expression in zebrafish. B Sanger sequencing confirms the mutations caused by CRIPSR-Cas9 in F0 and F1 generations. Primary sequence was shown. C In situ hybridization of snap25b in wild-type (WT) and snap25b mutant zebrafish. D The expression of snap25b by RT-qPCR in the head of wild-type and snap25b mutant zebrafish. E The representative abnormal phenotype included developmental delay, curled tail, and agenesis of eye. F The summary of survival rate in wild-type and snap25b mutants. G The summary of abnormality rate in wild-type and snap25b mutants. The Danio Vision system recorded the swimming behavior of wild-type and snap25b mutants (H) and analysis of total swimming distance (I). Data are presented as mean ± SD, n = 3 or n = 15–18; ** p < 0.01

Development-related miRNAs in zebrafish brain. A Expression patterns of differentially expressed miRNAs by pairwise comparisons, expression of miRNAs in adult tissues, as well as the evidence supported by the RNA in situ hybridization experiment. B Volcano plots depict differentially expressed miRNAs in comparison of 48 h vs. 24 h and 96 h vs. 48 h. C Illustration locus of four miRNA clusters. Colors in upper three clusters indicated the expression patterns in Fig. 3a, and gray color indicated miRNAs without differential expression. D RT-qPCR validation of six miRNAs in RNA-seq datasets

Potential miRNA-mRNA interacted pairs involved in nervous system development. A The workflow of screening miRNA-mRNA interacted pairs. B Functional enrichment analysis of predicted miRNA targets. C Protein–protein interaction network and densely connected network components (DCNCs). D Potential miRNA regulated genes in DCNCs (M1–M8) visualized with a “synteny”-like plot. Link colors and rectangle colors in up- or down-panel depict DCNC colors in panel C. Highly connected genes in each DCNC were labeled. E Visualization of miRNA-mRNA pairs of the top 20 connected miRNAs and highly connected genes in each DCNC and common miRNAs in regulating two key retinal differential transcription factors, crx and neurod1