Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Smaistry of Agriculture, Dalian Ocean University, Dalian 116023, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China.
College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China.
Comp Biochem Physiol Part D Genomics Proteomics. 2019 Sep;31:100591. doi: 10.1016/j.cbd.2019.05.001. Epub 2019 May 2.
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.
长期近亲繁殖导致海参生长速度下降，严重影响产量和经济效益。本研究构建了三个刺参家系，并根据体重最小和最大进行筛选，包括俄罗斯、中国和它们的杂种（RC）。我们检测了杂种（RC）和纯种（CC 和 RR）的转录谱。共获得 49.69 Gb 清洁读数，Q30 碱基百分比高于 90.47%。共发现 5191 个新基因，其中 2592 个基因被注释。鉴定差异表达基因（DEGs），并进行功能注释和富集分析。在中国刺参（CC）差异组中筛选出约 1874 个 DEGs；在杂种刺参差异组（RC）中获得 2591 个 DEGs，在俄罗斯刺参差异组（RR）中获得 3006 个 DEGs。在基因本体论（GO）分析中，细胞过程和代谢过程的功能类别观察到最高的 DEG 富集。在细胞成分方面，DEG 富集在细胞部分，细胞；在分子功能方面，DEG 富集在催化活性、结合、水解酶活性、转移酶活性。根据差异表达分析，我们发现 15 个热休克蛋白（HSP）基因具有相同的表达趋势，在三个海参品系中体重最小的个体中上调。此外，还进行了防御基因的 COG 分析。所有防御基因（ATP 结合盒转运蛋白（ABCs）、多药耐药蛋白（MRPs）和β-内酰胺酶）均表现出相同的表达趋势，在 RC 品系中最小个体明显高于最大个体，这意味着最小个体在生长过程中受到更大的压力。这些结果可能导致最小个体生长缓慢。此外，我们选择了 12 个 DEGs 通过 qPCR 验证结果。这些 DEGs 包括与生长相关和抗性基因。刺参转录组测序提高了我们对控制个体发育和生长的转录调控机制的理解。
