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Background  Early development is a key process of the life history of fish. However, the relationship between the transcriptome and the dynamic regulation of early development is still uncharacterized in the bighead carp ( Hypophthalmichthys nobilis ). In the present study, we performed transcriptome analysis of six development stages in  H. nobilis , aiming to understand the dynamic molecular regulation of early development in this fish.    Results  A total of 76,573 unigenes were assembled from clean sequence reads, with an average length of 1768 base. Among which, 41,742 (54.54%) unigenes were annotated to public protein databases, and an additional 59,014 simple sequence repeat (SSR) loci were identified among the unigenes. Furthermore, 30,199 differentially expressed transcripts (DETs) (fold change > 4 or < 0.25, and the false discovery rate FDR < 0.01) were observed in comparisons between the adjacent developmental stages, and nine expression patterns (profiles) were simulated using series-cluster analysis across six developmental stages. The unigenes expression level markedly increased after the DS1 stage (early blastula), and the numbers of DETs gradually decreased during subsequent development. The largest transcriptomic change (up- or down-regulated) was detected during the period from DS1 to DS2 (6-somite stage), which was enriched for many biological processes and metabolic pathways related to maternal to zygotic transition (MZT). Distinctly protein-protein interaction (PPI) networks were plotted for DETs during the period from DS1 to DS2. The genes (or proteins) from the same pathways were integrated together, and showed with obvious co-regulation patterns. In the series-cluster analysis, a remarkable profile of gene expression (profile_48) was identified that is probably related to the hatching during  H. nobilis  development, and the strict co-expression of a hatching enzyme gene ( hce1 ) with 33 other annotated genes was identified from this profile.    Conclusions  The results indicated that strict dynamic regulation occurs during the early development in  H. nobilis , especially in embryogenesis before hatching. This study provides valuable new information and transcriptomic resources related to  H. nobilis  early development, and for certain events such as MZT and hatching.

Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis)