Transcriptome analysis of body wall reveals growth difference between the largest and smallest individuals in the pure and hybrid populations of Apostichopus japonicus.

Long-term inbreeding of sea cucumber has resulted in a decrease in its growth rate, which has severely affected yield and economic efficiency. In this study, three Apostichopus japonicus families were constructed and screened into the weight of smallest and largest, which included Russian, Chinese, and their hybrids (RC). We examined the transcriptional profiles of hybrid (RC) and purebred (CC and RR). A total of 49.69 Gb clean reads were obtained, and the Q30 base percentage was above 90.47%. A total of 5191 novel genes were discovered, of which 2592 genes were annotated. Differentially expressed genes (DEGs) were identified, and functional annotation and enrichment analysis were performed. Approximately 1874 DEGs were screened in the Chinese sea cucumber (CC) difference group; 2591 DEGs were obtained in the hybrid sea cucumber difference group (RC), and 3006 DEGs were obtained in the Russian sea cucumber difference group (RR). In Gene Ontology (GO) analysis, highest DEG enrichment was observed for the functional categories of cellular process and metabolic process. In terms of cellular components, DEG enrichment was observed in cell part, cell; for molecular function, DEG enrichment was detected in catalytic activity, binding, hydrolase activity, transferase activity. According to the differential expression analysis, we found that 15 heat shock protein (HSP) genes that have the same expression trends, which were upregulated in the smallest weight of three sea cucumber lines. In addition, COG analysis of defense genes was conducted. All defense genes (ATP-binding cassette transporters (ABCs), multidrug resistance protein (MRPs), and beta-lactamase) showed the same expression trend, which was significantly upregulated in smallest individuals compared to that of largest individuals in RC lines, which implied the smallest individuals are exposed to more pressure during growth. These results may lead to the smallest individuals showing slow growth. Additionally, we selected 12 DEGs to validate the result by qPCR. Those DEGs were included in growth-related and resistance genes. Sequencing of the A. japonicus transcriptome improves our understanding of the transcriptional regulatory apparatus that controls individual development and growth.

Integration of small RNAs and mRNAs by high-throughput sequencing reveals a complex regulatory network in Chinese sea cucumber, Russian sea cucumber and their hybrids.

The body wall of the sea cucumber is an important tissue with high nutritional value. In this study, the parents of Apostichopus japonicus were derived from Russia (R) and China (C). We examined the transcriptional profiles in the body wall from F1 hybrids (CR and RC) and purebreds (CC and RR) at 9 months. In total, 34.07 G clean data were obtained from the transcriptome, 100,870 unigenes were identified, and 26,483 unigenes were annotated. Based on edgeR, 1097-4,587differentially expressed genes (DEGs) were identified. In total, 50.72 M clean data were obtained from the small RNA libraries, and 202 miRNAs were identified, including 7 known miRNAs and 195 novel miRNAs. In total, 175 miRNAs were identified as significantly differentially expressed miRNAs (diffmRNAs). Additionally, 3538 target genes were predicted, and 2243 genes were annotated in NR, COG, GO and KEGG. Furthermore, the relationships between the small RNAs and transcripts were identified, and the novel miRNA functions were predicted by integrating the small RNAs and transcriptome. According to the saponins content, RR was lower than other lines. DEGs involved in the biosynthesis of saponins were identified, including 23 DEGs involved in glycosyl, 21 DEGs involved in P450s, 5 DEGs involved in transferases and 15 DEGs involved in OSCs, from these, gdp-l-fucose, fucTcpa2 and cyp17A1 may affect the differences in the saponins development of the body wall in RR purebreds. In addition, miRNA_11347 and miRNA_32095 was associated in saponins. Our study provides fundamental information regarding the molecular mechanism of the heterosis of the sea cucumber and may suggest strategies for the selection of rapidly growing and highly nutritive strains of sea cucumber in aquaculture.

Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids.

Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.

Comparative transcriptome analysis of fast twitch muscle and slow twitch muscle in Takifugu rubripes.

Fast twitch muscle and slow twitch muscle are two important organs of Takifugu rubripes. Both tissues are of ectodermic origin, and the differences between the two muscle fibers reflect the differences in their myofibril protein composition and molecular structure. In order to identify and characterize the gene expression profile in the two muscle fibers of T. rubripes, we generated 54 million and 44 million clean reads from the fast twitch muscle and slow twitch muscle, respectively, using RNA-Seq and identified a total of 580 fast-muscle-specific genes, 1533 slow-muscle-specific genes and 11,806 genes expressed by both muscles. Comparative transcriptome analysis of fast and slow twitch muscles allowed the identification of 1508 differentially expressed genes, of which 34 myosin and 30 ubiquitin family genes were determined. These differentially expressed genes (DEGs) were also analyzed by Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. In addition, alternative splicing analysis was also performed. The generation of larger-scale transcriptomic data presented in this work would enrich the genetic resources of Takifugu rubripes, which could be valuable to comparative studies of muscles.