During the development phase of larval fish, many biological processes, such as differentiation, cellular proliferation, growth, can be regulated to obtain the phenotype of an adult fish . These regulations are carried out through the expression of genes involved in larval ontogenesis processes. Gene expression analysis can be comprehensively analyze through transcriptome using high throughput RNA-Seq tool. Previous physiologic studies showed that hybrid F1 seabream (Pagrus major♀ × Acanthopagrus schlegelii♂) grow quickly, with enhanced muscle nutritional composition [16–19]. However, the transcriptome information about the larval As, Pm and F1 are lacked. In the present study, we presented the main findings from transcriptomic investigations of As, Pm and AP during postembryonic (one month age) development 21. From the results of RNA-Seq, the whole data is nearly 6G of each sample (Table 1). The depth of sequencing is enough and the quantity of our sequencing data are convincing for next analysis.
We used the unique transcripts as the database to analysis the development processes of each sample. From the gene function annotation, KEGG results showed that most genes belongs to signal transduction, endocrine system, immune system, nervous system, signaling molecules and interaction, and so on, in each sample (Fig. 2). The molecular results were consistent with physiological development. The multiple biological processes were combined with consistencies of results obtained from the annotated expressed genes in each sample, reveals the complexity of the transcriptome regulation during larval ontogenesis processes. The authors used the transcriptome analysis to show that more than two hundred genes involved in visual pigmentation, metabolism, digestive function and epithelial development exhibited differential expression during the early development of gilthead sea bream . Form previous physiological research about As, Pm and AP samples, the fish began growing quickly, and the digest system, circulatory system, and excretory system are gradually formed during the fourth day after hatching . The transcriptome results was consistent with physiological research. Our results showed that the many genes belonged to endocrine system, immune system, nervous system development has express in each sample. As we all know, immune system is very important to juvenile fish. When the immune system formed, they can prevent the disease invading about environment change or viral infect. During the agricultural production, 25–35 days fish will be sold to farm. These fish need to face the different environment to leave off the incubation environment. In this period, the fish have good condition for transport far away. Our result supposed that the immune system of the fish is more active at this phase, and the fish body has a strong ability to resist the invasion of external pathogens. Besides, metabolism process, such as carbohydrate metabolism, lipid metabolism, amino acid metabolism, and nucleotide metabolism, all had the active gene-express (Fig. 2).
For different species have individual difference in the uniform period, different express genes (DEGs) are the focus of our attention. The DEGs between offspring (AP) transcriptome and parent sample (As♂, Pm♀) transcriptome were compared. From the top 20 pathway, AP had a high gene express in spliceosome, DNA replication, cell cycle, ribosome biogenesis in eukaryotes, parkinson’s disease, p53 signaling pathway, ECM-receptor interaction and mismatch repair pathway than Pm (Table 3). These genes in each pathway most have high expression during the individual growth. It also suggested that the cell in fish had cell multiplication to make the body grow. Then, the high expressed genes in fat digestion and absorption and oxidative phosphorylation pathway suggested that the fish need more energy for growing. Also between As and AP compared, AP also has a quickly growth. During the early development, the cell quickly divided into more cells to make body growth. The genes belong to DNA replication and cell cycle pathway can show this situation. During the replication, it need ECM-receptor interaction and mismatch repair to make the organism keep the biological function, such as cell aldhere . The developmental integrity of fish cells plays an important role in the resistance of the whole body to external viruses. Besides the quickly growth, there are much other information we can get from AP and As. There are 111 genes of viral carcinogenesis which had high expressed in AP than in As (Table 3). The high express genes showed a strong cell-proliferation ability in AP. As we know, tumor viruses can promote an abnormal cell-proliferation via modulating cellular cell-signaling pathways via expression of many potent oncoproteins [25–27]. Our results showed that 111 genes belonging to oncoproteins had high expression in AP. It can suppose that AP had stronger cell-proliferation than As, suggesting that AP maybe grow quickly than As. Another special pathway in AP compared with As, is that 106 genes of herpes simplex infection pathway had higher expression. Herpes simplex virus (HSV) is the main cause of herpes infections that lead to the formation of characteristic blistering lesion. HSV can interfere with host immune responses by expressing multiple viral accessory proteins . Influenza A is a contagious respiratory disease caused by influenza virus infection, which had 91 genes highly expressed in AP sample than in As. Influenza virus has one kind of proteins which is a multifunctional virulence factor that interfere IFN-mediated antiviral response. It can inhibit activation of transcription factors such as NF-kappa B . Except the virus infect, the parasite also can disrupt the intestinal mucus layer of fish, followed by apoptosis of host epithelial cells. 82 genes belonging to amoebiasis pathway had higher expression in AP than in As. The ingestion of contaminated water and food can lead the pathogenesis of amoebiasis. Intestinal tissue destruction causes severe dysentery and ulcerations in amoebic colitis . And several amoebic proteins, such as lectins, cysteine proteineases, and amoebapores, are associated with the invasion process . The fusion proteins have aberrant transcriptional function for fusion transcription factors alter expression of target genes, and thereby result in the tumorigenesis. They are all leaded by transcriptional misregulation. From the DEGs, There are 77 genes higher expressing in AP sample, belong to Transcriptional misregulation. During rearing, the juvenile fish often were attracted by virus in environment. These pathways maybe provided the challenge ability for fish to resist the environment. Also during these pathways, there were many immune related genes which had high express in fish. These results suggested that the AP, compared with As and Pm, has stronger immune system. The further studies about the As, Pm and AP immune response needs to be carried out in future.