Li Yanping, Lv Yunyun, Cheng Peilin, Jiang Ying, Deng Cao, Wang Yongming, Wen Zhengyong, Xie Jiang, Chen Jieming, Shi Qiong, Du Hao
Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Science, Neijiang Normal University, Neijiang 641100, China.
Animals (Basel). 2024 Nov 21;14(23):3357. doi: 10.3390/ani14233357.
The Chinese sturgeon () is an ancient, complex autooctoploid fish species that is currently facing conservation challenges throughout its distribution. To comprehensively characterize the expression profiles of genes and their associated biological functions across different tissues, we performed a transcriptome-scale gene expression analysis, focusing on housekeeping genes (HKGs), tissue-specific genes (TSGs), and co-expressed gene modules in various tissues. We collected eleven tissues to establish a transcriptomic repository, including data from Pacific Biosciences isoform sequencing (PacBio Iso-seq) and RNA sequencing (RNA-seq), and then obtained 25,434 full-length transcripts, with lengths from 307 to 9515 bp and an N50 of 3195 bp. Additionally, 20,887 transcripts were effectively identified and classified as known homologous genes. We also identified 787 HKGs, and the number of TSGs varied from 25 in the liver to 2073 in the brain. TSG functions were mainly enriched in certain signaling pathways involved in specific physiological processes, such as voltage-gated potassium channel activity, nervous system development, glial cell differentiation in the brain, and leukocyte transendothelial migration in the spleen and pronephros. Meanwhile, HKGs were highly enriched in some pathways involved in ribosome biogenesis, proteasome core complex, spliceosome activation, elongation factor activity, and translation initiation factor activity, which have been strongly implicated in fundamental biological tissue functions. We also predicted five modules, with eight hub genes in the brown module, most of which (such as , , , , , , and ) were linked to ribosome biogenesis. Our results offer insights into ribosomal proteins that are indispensable in ribosome biogenesis and protein synthesis, which are crucial in various cell developmental processes and neural development of Chinese sturgeon. Overall, these findings will not only advance the understanding of fundamental biological functions in Chinese sturgeon but also supply a valuable genetic resource for characterizing this extremely important species.
中华鲟是一种古老、复杂的同源八倍体鱼类，目前在其整个分布范围内都面临着保护挑战。为了全面表征不同组织中基因的表达谱及其相关生物学功能，我们进行了转录组规模的基因表达分析，重点关注管家基因（HKGs）、组织特异性基因（TSGs）以及不同组织中的共表达基因模块。我们收集了11个组织以建立转录组库，包括来自太平洋生物科学公司的异构体测序（PacBio Iso-seq）和RNA测序（RNA-seq）的数据，然后获得了25,434个全长转录本，长度从307到9515 bp不等，N50为3195 bp。此外，有效地鉴定出20,887个转录本，并将其分类为已知的同源基因。我们还鉴定出787个管家基因，组织特异性基因的数量从肝脏中的25个到大脑中的2073个不等。组织特异性基因的功能主要富集在某些参与特定生理过程的信号通路中，如电压门控钾通道活性、神经系统发育、大脑中的神经胶质细胞分化以及脾脏和前肾中的白细胞跨内皮迁移。同时，管家基因高度富集于一些参与核糖体生物发生、蛋白酶体核心复合体、剪接体激活、延伸因子活性和翻译起始因子活性的通路中，这些通路与基本的生物组织功能密切相关。我们还预测了五个模块，棕色模块中有八个枢纽基因，其中大多数（如、、、、、和）与核糖体生物发生相关。我们的研究结果为核糖体生物发生和蛋白质合成中不可或缺的核糖体蛋白提供了见解，这些蛋白在中华鲟的各种细胞发育过程和神经发育中至关重要。总体而言，这些发现不仅将增进对中华鲟基本生物学功能的理解，还将为表征这一极其重要的物种提供宝贵的遗传资源。
