中华鲟生长速率差异个体肌肉组织转录组测序分析

Transcriptome sequencing analysis of individual muscle tissues with differences in growth rate of Chinese sturgeon(Acipenser sinensis

  • 摘要: 【目的】 基于转录组测序挖掘出与中华鲟生长相关的基因和信号通路,揭示其个体生长差异的分子调控机制,为中华鲟的亲鱼选育、人工保种群体培育及种群梯队建设提供参考依据。【方法】 将养殖于相同环境和营养条件下的同批次中华鲟F2代个体分为快生长组(FGM)和慢生长组(SGM),每组随机选取3尾中华鲟,采集其背部肌肉,通过转录组测序筛选出差异表达基因(DEGs),然后分别进行GO功能注释分析、KEGG代谢通路富集分析及实时荧光定量PCR验证。【结果】 从FGM组和SGM组6个中华鲟肌肉组织样本共测序得到34.86 Gb的有效数据(Clean data),以中华鲟基因组序列为参考基因组,共挖掘出16037个新基因,其中有6953个新基因在COG、GO、KEGG、KOG、Pfam、SWISS-PROT、TrEMBL、EggNOG、Nr等数据库中得到注释。根据FDR<0.01且Fold Change≥2的筛选标准,从中华鲟肌肉组织中鉴定出247个DEGs,其中142个DEGs呈上调表达、105个DEGs呈下调表达。有191个DEGs获得GO功能注释,主要注释到细胞过程、代谢过程、细胞结构组件、结合、催化活性等功能条目;有100个DEGs富集在88个特定的KEGG代谢通路上,包括糖酵解/糖异生、氨基酸生物合成、碳代谢、蛋白酶体、磷酸戊糖通路等。综合GO功能注释分析和KEGG代谢通路富集分析,鉴定出20个与中华鲟生长相关的候选基因,分别是PKMPGML1TPIGAPDHLDHGPIFBPasePGK1ALDOAenolaseTTNMYBPC3PLA2G6CXCL10MICALL1GPC6CLASP1CARNS1PSMD7CDO1。实时荧光定量PCR检测结果与转录组测序结果基本一致,表明转录组测序筛选获得的DEGs结果可靠。【结论】 中华鲟以糖类利用效率和能量分配策略为主导,耦合肌肉生长、营养代谢及信号传导等基因功能,协同调控个体生长速率的差异化。

     

    Abstract: 【Objective】 Based on transcriptome sequencing technology, genes and signaling pathways related to the growth of Chinese sturgeon(Acipenser sinensis) were excavated, and the molecular regulatory mechanisms of individual growth differences in Chinese sturgeon were revealed, which could provide technical references for the breeding of Chinese sturgeon, the cultivation of artificial conservation populations and the construction of population echelons. 【Method】 The F2 generation individuals of Chinese sturgeon from the same batch and cultured under the same environmental and nutritional conditions were divided into a fast-growing group(FGM) and a slow-growing group(SGM). Three Chinese sturgeons were randomly selected from each group, and their dorsal muscle samples were collected. Differentially expressed genes(DEGs) were screened through transcriptome sequencing, followed by GO functional annotation analysis and KEGG metabolic pathway enrichment analysis. Additionally, real-time fluorescence quantitative PCR was performed to validate the sequencing results. 【Result】 A total of 34.86 Gb of clean data were obtained through sequencing from the muscle tissue samples of 6 Chinese sturgeons in the FGM and SGM groups. Using the Chinese sturgeon genome sequence as the reference genome, 16037 new genes were identified, of which 6953 were annotated in databases such as COG, GO, KEGG, KOG, Pfam, SWISS-PROT, TrEMBL, EggNOG and Nr. According to the screening criteria of FDR < 0.01 and Fold Change ≥ 2, 247 DEGs were identified in the muscle tissues of Chinese sturgeon, including 142 up-regulated and 105 down-regulated DEGs. A total of 191 DEGs were annotated with GO functions, mainly annotated to functional terms such as cellular processes, metabolic processes, cellular structural components, binding, and catalytic activity. Additionally, 100 DEGs were enriched in 88 specific KEGG metabolic pathways, including glycolysis/gluconeogenesis, amino acid biosynthesis, carbon metabolism, proteasome and pentose phosphate pathway. Through comprehensive GO functional annotation and KEGG metabolic pathway enrichment analysis, 20 candidate genes related to the growth of Chinese sturgeon were identified: PKM, PGML1, TPI, GAPDH, LDH, GPI, FBPase, PGK1, ALDOA, enolase, TTN, MYBPC3, PLA2G6, CXCL10, MICALL1, GPC6, CLASP1, CARNS1, PSMD7 and CDO1. The results of real-time fluorescence quantitative PCR were consistent with those of transcriptome sequencing, indicating the reliability of the DEGs identified through transcriptome sequencing. 【Conclusion】 Chinese sturgeon takes carbohydrate utilization efficiency and energy allocation strategy as the leading factors, couples the gene functions such as muscle growth, nutritional metabolism and signal transduction, and coordinately regulates the differentiation of individual growth rates.

     

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