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Article(id=1194652709719610094, tenantId=1146029695717560320, journalId=1149651085930835976, issueId=1194652705147822651, articleNumber=null, orderNo=null, doi=10.12284/hyxb2025010, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1705248000000, receivedDateStr=2024-01-15, revisedDate=1731254400000, revisedDateStr=2024-11-11, acceptedDate=null, acceptedDateStr=null, onlineDate=1762757001571, onlineDateStr=2025-11-10, pubDate=1738252800000, pubDateStr=2025-01-31, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1762757001571, onlineIssueDateStr=2025-11-10, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1762757001571, creator=13701087609, updateTime=1762757001571, updator=13701087609, issue=Issue{id=1194652705147822651, tenantId=1146029695717560320, journalId=1149651085930835976, year='2025', volume='47', issue='1', pageStart='1', pageEnd='132', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1762757000481, creator=13701087609, updateTime=1762757000481, updator=13701087609, preIssue=null, nextIssue=null, ext=null, issueFiles=null}, startPage=63, endPage=73, ext={EN=ArticleExt(id=1194652710042571504, articleId=1194652709719610094, tenantId=1146029695717560320, journalId=1149651085930835976, language=EN, title=Transcriptome analysis of liver of juvenile Rachycentron canadum under low temperature stress, columnId=1194652705852465724, journalTitle=Haiyang Xuebao, columnName=Article, runingTitle=null, highlight=null, articleAbstract=

To investigate the effect of low temperature stress on juvenile cobia (Rachycentron canadum), the fish were reared under normal temperature [(30.5 ± 1.0)℃] and low temperature [(20.0 ± 0.5)℃] for 7 days, followed by genome-based transcriptome sequencing of there liver tissues. Each group included 3 biological replicates. The results showed that a total of approximately 243 694 134 raw reads were obtained from the 6 sequencing samples, with Q30 scores exceeding 94% for all samples and GC content raging between 47.65% and 48.16%. A total of 4 362 differentially expressed genes (DEGs) were identified, including 2 793 up-regulated and 1 569 down-regulated genes. KEGG pathway enrichment analysis revealed that in lipid metabolism, a significant number of DEGs were enriched in biological processes such as lipid metabolism, lipid biosynthesis, glycerophospholipid metabolism, phospholipid metabolism and glycerideid metabolism. Key lipid metabolism-related genes, including pparα, pparβ, scd1, cpt1, and cpt2 in the PPAR signaling pathway, played crucial roles in the response of juvenile cobia to low temperature stress. In glucose metabolism, numerous genes were enriched in pathways such as glycolysis/gluconeogenesis, galactose metabolism, starch and sucrose metabolism, and pentose and glucuronate interconversions. Among these, genes such as g6pc and eno were found to play important roles in the adaptation of juvenile cobia to low temperature stress.

, correspAuthors=Jing Zhang, authorNote=null, correspAuthorsNote=null, copyrightStatement=Haiyang Xuebao, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Baogui Tang, Runjia Cai, Jing Zhang), CN=ArticleExt(id=1194652925608825645, articleId=1194652709719610094, tenantId=1146029695717560320, journalId=1149651085930835976, language=CN, title=低温胁迫下军曹鱼幼鱼肝脏转录组测序分析, columnId=1149698756456657529, journalTitle=海洋学报, columnName=论文, runingTitle=null, highlight=null, articleAbstract=

为研究低温胁迫对军曹鱼幼鱼的影响，将军曹鱼幼鱼饲养于常温[（30.5 ± 1.0）℃]和低温[（20.0 ± 0.5）℃]7 d后对军曹鱼肝脏进行有参转录组测序，每组3个生物学重复。结果显示，6个测序样品共检测到约243 694 134个raw reads，所有样品Q30均超过94%，GC在47.65%～48.16%范围内。共筛选出4 362个差异表达基因，其中2 793个基因上调，1 569个基因下调。KEGG通路富集分析结果显示，在脂质代谢中，大量差异基因富集在脂代谢过程、脂质生物合成过程、甘油磷脂代谢过程、磷脂代谢过程和甘油脂代谢过程等生物过程中， PPAR信号通路中pparα、pparβ、scd1、cpt1和cpt2等多个脂代谢相关基因对军曹鱼幼鱼应对低温胁迫具有关键作用；在糖代谢中，大量基因富集于糖酵解/糖异生、半乳糖代谢、淀粉和蔗糖代谢、戊糖和葡萄糖醛酸酯的相互转化等生物过程，其中g6pc、eno等基因在军曹鱼幼鱼应对低温胁迫时发挥重要调节作用。

, correspAuthors=张静, authorNote=null, correspAuthorsNote=
*张静，副教授，主要研究方向为渔业生态环境与保护。E-mail：
, copyrightStatement=版权所有©《海洋学报》编辑部 2025
汤保贵，蔡润佳，张静. 低温胁迫下军曹鱼幼鱼肝脏转录组测序分析[J]. 海洋学报，2025，47(1)：63–73Tang Baogui，Cai Runjia，Zhang Jing. Transcriptome analysis of liver of juvenile Rachycentron canadum under low temperature stress[J]. Haiyang Xuebao，2025, 47(1)：63–73
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汤保贵（1975— ），男，湖北省襄阳市人，副教授，主要研究方向为鱼类养殖与遗传育种。E-mail：

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汤保贵（1975— ），男，湖北省襄阳市人，副教授，主要研究方向为鱼类养殖与遗传育种。E-mail：

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汤保贵（1975— ），男，湖北省襄阳市人，副教授，主要研究方向为鱼类养殖与遗传育种。E-mail：

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Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China), AuthorCompanyExt(id=1194975301051597328, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, companyId=1194975301039014414, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.广东省水产经济动物病原生物学及流行病学重点实验室，广东 湛江，524088)])], figs=[ArticleFig(id=1194975302712541742, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=EN, label=Fig. 1, caption=CG vs LG volcano plot, figureFileSmall=qqO0wM1G/meoNak1ehVQcQ==, figureFileBig=MoWsUMJiN1JzW83G0d1wCQ==, tableContent=null), ArticleFig(id=1194975302783844911, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=CN, label=图1, caption=CG vs LG火山图, figureFileSmall=qqO0wM1G/meoNak1ehVQcQ==, figureFileBig=MoWsUMJiN1JzW83G0d1wCQ==, tableContent=null), ArticleFig(id=1194975302871925296, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=EN, label=Fig. 2, caption=The first 20 enriched GO terms

The first circle: the first 20 enriched GO terms, outside the circle is the coordinate ruler of gene number, and different colors represent different Ontology. The second circle: the number and Q value of the GO term in the background gene, the more genes, the longer the bars, and the smaller the Q value, the redder the color. The third circle: bar chart of the proportion of up and down genes, dark purple represents the proportion of up genes, light purple represents the proportion of down genes, and specific values are displayed below. The fourth circle: RichFactor value of each GO term (the number of differential genes in the GO term divided by all the numbers), and each grid line of the background represents 0.1

, figureFileSmall=cF8LcKsM+26C+onqjNeLPg==, figureFileBig=Az7NAh9sacSjb+SLVYpU/w==, tableContent=null), ArticleFig(id=1194975302930645553, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=CN, label=图2, caption=富集前20的GO terms

第一圈：富集前20的GO term，圈外为基因数目的坐标尺，不同的颜色代表不同的Ontology；第二圈：背景基因中该GO term的数目以及Q值，基因越多条形越长，Q值越小颜色越红；第三圈：上下调基因比例条形图，深紫色代表上调基因比例，浅紫色代表下调基因比例，下方显示具体的数值；第四圈：各GO term的RichFactor值(该GO term中差异基因数量除以所有数量)，背景网格线每一格代表0.1

, figureFileSmall=cF8LcKsM+26C+onqjNeLPg==, figureFileBig=Az7NAh9sacSjb+SLVYpU/w==, tableContent=null), ArticleFig(id=1194975303014531634, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=EN, label=Fig. 3, caption=The first 20 enriched pathways, figureFileSmall=+h77HAiweMyFz+VSBY9BMA==, figureFileBig=BfP4UDu0M+NeN48WAkdmcg==, tableContent=null), ArticleFig(id=1194975303085834803, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=CN, label=图3, caption=富集前20的通路, figureFileSmall=+h77HAiweMyFz+VSBY9BMA==, figureFileBig=BfP4UDu0M+NeN48WAkdmcg==, tableContent=null), ArticleFig(id=1194975303140360756, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=EN, label=Fig. 4, caption=PPAR signaling pathway

The red box indicates that the genes in this box are up-regulated compared with the control group; the green box indicates that the genes in this box are down-regulated compared with the control group; the red-green box indicates that some genes in this box are up-regulated and some are down-regulated compared with the control group

, figureFileSmall=ghItrN6IXIODLscXvl2TNA==, figureFileBig=KF9/345WvLx5VAPQkE7DuA==, tableContent=null), ArticleFig(id=1194975303203275317, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=CN, label=图4, caption=PPAR信号通路

红色框线表示：该框中的基因对比对照组，表达上调；绿色框线表示：该框中的基因对比对照组，表达下调；红−绿框线表示：该框中的基因对比对照组，部分表达上调，部分下调

, figureFileSmall=ghItrN6IXIODLscXvl2TNA==, figureFileBig=KF9/345WvLx5VAPQkE7DuA==, tableContent=null), ArticleFig(id=1194975303266189878, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=EN, label=Fig. 5, caption=Verification of transcriptome results, figureFileSmall=vV2LFiIqzGz61zeoHJrY/w==, figureFileBig=bKnHw/LipbAov7TNUkIYyQ==, tableContent=null), ArticleFig(id=1194975304348320311, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=CN, label=图5, caption=转录组结果验证, figureFileSmall=vV2LFiIqzGz61zeoHJrY/w==, figureFileBig=bKnHw/LipbAov7TNUkIYyQ==, tableContent=null), ArticleFig(id=1194975304448983608, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=EN, label=Table 1, caption=

Primer sequences of genes used for RT-qPCR

, figureFileSmall=null, figureFileBig=null, tableContent=
基因名称基因编号上游引物(5′−3′)下游引物(5′−3′)
accRca011875TCGCCAGTCTCCCAACTCCTATACCTGTCCACCTCCTCCTTCAT
fasRca019519AGCATCCTGTATCGCCCGTTTGAGTCGGTCCTGTGGGTCTCCTTGT
hslRca015361AGCAGTCTGGTTTGGGTTTGGCAGGTTCTGGGTAATGCGTTCA
cpt1Rca009591TACCGCTTGGCTATGACTGGACTTGCTGGAGATGTGGAAGTTGATG
mglRca013017CACTGCGACCTTTGACCTCTTTGAACCATCCTTCTGGGCGTAATC
pparαRca010067GAGTTCTCATCTTCCTCCTCATCGCGGCACTTGTTGCGGTTCTTCTTT
β-actinGU584189AGGGAAATTGTGCGTGACAGGCAGCTCGTAGCTCTT
), ArticleFig(id=1194975304566424121, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=CN, label=表1, caption=

实时荧光定量PCR引物序列

, figureFileSmall=null, figureFileBig=null, tableContent=
基因名称基因编号上游引物(5′−3′)下游引物(5′−3′)
accRca011875TCGCCAGTCTCCCAACTCCTATACCTGTCCACCTCCTCCTTCAT
fasRca019519AGCATCCTGTATCGCCCGTTTGAGTCGGTCCTGTGGGTCTCCTTGT
hslRca015361AGCAGTCTGGTTTGGGTTTGGCAGGTTCTGGGTAATGCGTTCA
cpt1Rca009591TACCGCTTGGCTATGACTGGACTTGCTGGAGATGTGGAAGTTGATG
mglRca013017CACTGCGACCTTTGACCTCTTTGAACCATCCTTCTGGGCGTAATC
pparαRca010067GAGTTCTCATCTTCCTCCTCATCGCGGCACTTGTTGCGGTTCTTCTTT
β-actinGU584189AGGGAAATTGTGCGTGACAGGCAGCTCGTAGCTCTT
), ArticleFig(id=1194975304637727290, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=EN, label=Table 2, caption=

Statistical table of sequencing quality evaluation after sample filtering

, figureFileSmall=null, figureFileBig=null, tableContent=
处理样品Raw readsClean reads (Ratio)Clean data/bpGC/%Q20/%Q30/%
对照GC−14105219440443694 (98.52%)603380558147.9198.3694.96
GC−23940524238872552 (98.65%)580279564847.6698.2494.66
GC−33827745437694004 (98.48%)562381950248.0398.3094.85
低温LG−14176483241190146 (98.62%)614861546047.6598.2394.74
LG−24202515641532498 (98.83%)620607819547.9498.1994.63
LG−34116925640660388 (98.76%)607578307148.1698.3394.90
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样品过滤后测序质量评估统计表

, figureFileSmall=null, figureFileBig=null, tableContent=
处理样品Raw readsClean reads (Ratio)Clean data/bpGC/%Q20/%Q30/%
对照GC−14105219440443694 (98.52%)603380558147.9198.3694.96
GC−23940524238872552 (98.65%)580279564847.6698.2494.66
GC−33827745437694004 (98.48%)562381950248.0398.3094.85
低温LG−14176483241190146 (98.62%)614861546047.6598.2394.74
LG−24202515641532498 (98.83%)620607819547.9498.1994.63
LG−34116925640660388 (98.76%)607578307148.1698.3394.90
), ArticleFig(id=1194975304830665276, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=EN, label=Table 3, caption=

Statistics table of sequencing results compared to the genome

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处理样品Unmapped (Ratio)Unique_Mapped (Ratio)Multiple_Mapped (Ratio)Total_Mapped (Ratio)
对照GC−12505363 (6.20%)35435211 (87.67%)2477732 (6.13%)37912943 (93.80%)
GC−22677482 (6.89%)34013307 (87.56%)2154317 (5.55%)36167624 (93.11%)
GC−32784477 (7.39%)32773501 (87.02%)2103880 (5.59%)34877381 (92.61%)
低温LG−12918520 (7.10%)36014174 (87.60%)2177240 (5.30%)38191414 (92.90%)
LG−22690715 (6.49%)36329768 (87.62%)2440121 (5.89%)38769889 (93.51%)
LG−32159254 (5.32%)35571430 (87.60%)2875492 (7.08%)38446922 (94.68%)
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测序结果比对基因组情况统计表

, figureFileSmall=null, figureFileBig=null, tableContent=
处理样品Unmapped (Ratio)Unique_Mapped (Ratio)Multiple_Mapped (Ratio)Total_Mapped (Ratio)
对照GC−12505363 (6.20%)35435211 (87.67%)2477732 (6.13%)37912943 (93.80%)
GC−22677482 (6.89%)34013307 (87.56%)2154317 (5.55%)36167624 (93.11%)
GC−32784477 (7.39%)32773501 (87.02%)2103880 (5.59%)34877381 (92.61%)
低温LG−12918520 (7.10%)36014174 (87.60%)2177240 (5.30%)38191414 (92.90%)
LG−22690715 (6.49%)36329768 (87.62%)2440121 (5.89%)38769889 (93.51%)
LG−32159254 (5.32%)35571430 (87.60%)2875492 (7.08%)38446922 (94.68%)
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Differential gene enrichment analysis of lipid metabolism-related biological processes and pathways

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数据库功能/通路基因数编号
GO脂质代谢过程 （lipid metabolic process）294GO:0006629
细胞脂质代谢过程 （cellular lipid metabolic process）218GO:0044255
脂质生物合成过程 （lipid biosynthetic process）82GO:0008610
细胞脂质分解代谢过程 （cellular lipid catabolic process）26GO:0044242
脂质分解代谢过程 （lipid catabolic process）30GO:0016042
中性脂质代谢过程 （neutral lipid metabolic process）38GO:0006638
脂质稳态 （lipid homeostasis）23GO:0055088
脂质定位 （lipid localization）60GO:0010876
蛋白−脂质复合物亚基组织 （protein-lipid complex subunit organization）11GO:0071825
脂质贮藏的积极调节 （positive regulation of lipid storage）7GO:0010884
脂质储存的调节 （regulation of lipid storage）14GO:0010883
脂质储存 （lipid storage）15GO:0019915
脂质代谢过程的正向调节 （positive regulation of lipid metabolic process）13GO:0045834
脂质代谢过程的调节 （regulation of lipid metabolic process）55GO:0019216
甘油脂代谢过程 （glycerolipid metabolic process）79GO:0046486
磷脂代谢过程 （phospholipid metabolic process）82GO:0006644
脂质转运 （lipid transport）48GO:0006869
脂质过氧化氢反应 （response to lipid hydroperoxide）2GO:0006982
KEGG类固醇生物合成 （Steroid biosynthesis）16ko00100
脂肪酸降解 （Fatty acid degradation）25ko00071
类固醇激素的合成 （Steroid hormone biosynthesis）24ko00140
初级胆汁酸生物合成 （Primary bile acid biosynthesis）11ko00120
脂肪酸生物合成 （Fatty acid biosynthesis）10ko00061
花生四烯酸代谢 （Arachidonic acid metabolism）19ko00590
), ArticleFig(id=1194975305078129215, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=CN, label=表4, caption=

脂代谢相关生物过程及通路的差异基因富集分析

, figureFileSmall=null, figureFileBig=null, tableContent=
数据库功能/通路基因数编号
GO脂质代谢过程 （lipid metabolic process）294GO:0006629
细胞脂质代谢过程 （cellular lipid metabolic process）218GO:0044255
脂质生物合成过程 （lipid biosynthetic process）82GO:0008610
细胞脂质分解代谢过程 （cellular lipid catabolic process）26GO:0044242
脂质分解代谢过程 （lipid catabolic process）30GO:0016042
中性脂质代谢过程 （neutral lipid metabolic process）38GO:0006638
脂质稳态 （lipid homeostasis）23GO:0055088
脂质定位 （lipid localization）60GO:0010876
蛋白−脂质复合物亚基组织 （protein-lipid complex subunit organization）11GO:0071825
脂质贮藏的积极调节 （positive regulation of lipid storage）7GO:0010884
脂质储存的调节 （regulation of lipid storage）14GO:0010883
脂质储存 （lipid storage）15GO:0019915
脂质代谢过程的正向调节 （positive regulation of lipid metabolic process）13GO:0045834
脂质代谢过程的调节 （regulation of lipid metabolic process）55GO:0019216
甘油脂代谢过程 （glycerolipid metabolic process）79GO:0046486
磷脂代谢过程 （phospholipid metabolic process）82GO:0006644
脂质转运 （lipid transport）48GO:0006869
脂质过氧化氢反应 （response to lipid hydroperoxide）2GO:0006982
KEGG类固醇生物合成 （Steroid biosynthesis）16ko00100
脂肪酸降解 （Fatty acid degradation）25ko00071
类固醇激素的合成 （Steroid hormone biosynthesis）24ko00140
初级胆汁酸生物合成 （Primary bile acid biosynthesis）11ko00120
脂肪酸生物合成 （Fatty acid biosynthesis）10ko00061
花生四烯酸代谢 （Arachidonic acid metabolism）19ko00590
), ArticleFig(id=1194975305162015296, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=EN, label=Table 5, caption=

Differential gene enrichment analysis of glucose metabolism-related biological processes and pathways

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数据库功能/通路基因数编号
GO单糖代谢过程78GO:0005996
己糖代谢过程71GO:0019318
KEGG糖酵解/糖异生30ko00010
半乳糖代谢15ko00052
淀粉和蔗糖代谢16ko00500
戊糖和葡萄糖醛酸酯的相互转化17ko00040
), ArticleFig(id=1194975305279455809, tenantId=1146029695717560320, journalId=1149651085930835976, articleId=1194652709719610094, language=CN, label=表5, caption=

糖代谢相关生物过程及通路的差异基因富集分析

, figureFileSmall=null, figureFileBig=null, tableContent=
数据库功能/通路基因数编号
GO单糖代谢过程78GO:0005996
己糖代谢过程71GO:0019318
KEGG糖酵解/糖异生30ko00010
半乳糖代谢15ko00052
淀粉和蔗糖代谢16ko00500
戊糖和葡萄糖醛酸酯的相互转化17ko00040
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低温胁迫下军曹鱼幼鱼肝脏转录组测序分析
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汤保贵 1, 2 , 蔡润佳 1 , 张静 1, 2, *
海洋学报 | 论文 2025,47(1): 63-73
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海洋学报 | 论文 2025, 47(1): 63-73
低温胁迫下军曹鱼幼鱼肝脏转录组测序分析
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汤保贵1, 2 , 蔡润佳1, 张静1, 2, *
作者信息
  • 1.广东海洋大学 水产学院，广东 湛江，524088
  • 2.广东省水产经济动物病原生物学及流行病学重点实验室，广东 湛江，524088

    • 汤保贵（1975— ），男，湖北省襄阳市人，副教授，主要研究方向为鱼类养殖与遗传育种。E-mail：

通讯作者:

*张静，副教授，主要研究方向为渔业生态环境与保护。E-mail：
Transcriptome analysis of liver of juvenile Rachycentron canadum under low temperature stress
Baogui Tang1, 2 , Runjia Cai1, Jing Zhang1, 2, *
Affiliations
  • 1. Fishery College, Guangdong Ocean University, Zhanjiang 524088, China
  • 2. Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China
出版时间: 2025-01-31 doi: 10.12284/hyxb2025010
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摘要
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为研究低温胁迫对军曹鱼幼鱼的影响，将军曹鱼幼鱼饲养于常温[（30.5 ± 1.0）℃]和低温[（20.0 ± 0.5）℃]7 d后对军曹鱼肝脏进行有参转录组测序，每组3个生物学重复。结果显示，6个测序样品共检测到约243 694 134个raw reads，所有样品Q30均超过94%，GC在47.65%～48.16%范围内。共筛选出4 362个差异表达基因，其中2 793个基因上调，1 569个基因下调。KEGG通路富集分析结果显示，在脂质代谢中，大量差异基因富集在脂代谢过程、脂质生物合成过程、甘油磷脂代谢过程、磷脂代谢过程和甘油脂代谢过程等生物过程中， PPAR信号通路中pparα、pparβ、scd1、cpt1和cpt2等多个脂代谢相关基因对军曹鱼幼鱼应对低温胁迫具有关键作用；在糖代谢中，大量基因富集于糖酵解/糖异生、半乳糖代谢、淀粉和蔗糖代谢、戊糖和葡萄糖醛酸酯的相互转化等生物过程，其中g6pc、eno等基因在军曹鱼幼鱼应对低温胁迫时发挥重要调节作用。

低温胁迫  /  军曹鱼  /  转录组  /  脂代谢  /  糖代谢

To investigate the effect of low temperature stress on juvenile cobia (Rachycentron canadum), the fish were reared under normal temperature [(30.5 ± 1.0)℃] and low temperature [(20.0 ± 0.5)℃] for 7 days, followed by genome-based transcriptome sequencing of there liver tissues. Each group included 3 biological replicates. The results showed that a total of approximately 243 694 134 raw reads were obtained from the 6 sequencing samples, with Q30 scores exceeding 94% for all samples and GC content raging between 47.65% and 48.16%. A total of 4 362 differentially expressed genes (DEGs) were identified, including 2 793 up-regulated and 1 569 down-regulated genes. KEGG pathway enrichment analysis revealed that in lipid metabolism, a significant number of DEGs were enriched in biological processes such as lipid metabolism, lipid biosynthesis, glycerophospholipid metabolism, phospholipid metabolism and glycerideid metabolism. Key lipid metabolism-related genes, including pparα, pparβ, scd1, cpt1, and cpt2 in the PPAR signaling pathway, played crucial roles in the response of juvenile cobia to low temperature stress. In glucose metabolism, numerous genes were enriched in pathways such as glycolysis/gluconeogenesis, galactose metabolism, starch and sucrose metabolism, and pentose and glucuronate interconversions. Among these, genes such as g6pc and eno were found to play important roles in the adaptation of juvenile cobia to low temperature stress.

low temperature stress  /  Rachycentron canadum  /  transcriptome  /  lipid metabolism  /  glucose metabolism
汤保贵, 蔡润佳, 张静. 低温胁迫下军曹鱼幼鱼肝脏转录组测序分析. 海洋学报, 2025 , 47 (1) : 63 -73 . DOI: 10.12284/hyxb2025010
Baogui Tang, Runjia Cai, Jing Zhang. Transcriptome analysis of liver of juvenile Rachycentron canadum under low temperature stress[J]. Haiyang Xuebao, 2025 , 47 (1) : 63 -73 . DOI: 10.12284/hyxb2025010
正文
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1 引言
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水温作为影响鱼类生存的最重要环境因子之一，深刻影响着鱼类的多种生命活动。即使不同物种之间的适温范围存在差异，但是一旦水温过低，都会对鱼类生长、代谢等产生影响[1–2]。低温胁迫对鱼类的脂代谢调节具有显著影响，如He等研究表明，低温胁迫会显著提高吉富罗非鱼（GIFT Oreochromis niloticus）肌肉脂肪酸的不饱和度[3]；Sun等研究发现，斜带石斑鱼（Epinephelus coioides）通过抑制肝脏cpt1、fabp10等脂代谢相关基因的表达来响应低温胁迫[4]；Mininni等应用转录组测序技术对低温胁迫下的金头鲷（Sparus aurata）进行肝脏转录组分析，发现肝脏在低温下产生的大量差异基因富集在脂代谢的相关通路上[5]。近年来，测序技术不断更新换代，组学技术的发展为很多生物学机制分析提供了重要的研究手段。转录组测序通过监测生物体在不同条件下的基因变化来分析基因响应情况，已应用于多个物种对低温胁迫或低温适应机制的研究中，如鲤鱼（Cyprinus carpio）、尼罗罗非鱼（Oreochromis niloticus）、暗纹东方鲀（Takifugu fasciatus）等，并筛选出较多关于应对低温胁迫的关键基因[6–8]。虽然目前已对多种鱼类应对低温胁迫的机制展开研究，但对军曹鱼（Rachycentron canadum）脂代谢在低温胁迫下的分子调节机制仍不清楚。
军曹鱼是鲈形目、军曹鱼科、军曹鱼属鱼类，属于暖水广盐性鱼类，适宜温度为21～31℃，适宜盐度为8～35，一直被认为是具有巨大潜力的海洋水产养殖品种，随着种苗生产技术的发展已成为我国南方沿海一带的重要海水网箱养殖对象之一[9]，但其应对低温的适应能力较差，而培育耐低温品种能有效地提高军曹鱼的耐低温能力。肝脏是脊椎动物代谢调控的主要器官，也是分析鱼类生理活动变化时的重要组织[7]，本研究以军曹鱼幼鱼肝脏为实验材料进行转录组测序，了解和分析军曹鱼幼鱼在20℃低温条件下肝脏脂代谢调节网络，为军曹鱼应对低温胁迫关键基因的挖掘和耐低温品种的培育提供参考。
2 材料和方法
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2.1 实验动物与管理
实验动物为广东海洋大学鱼类种子工程与养殖实验室人工繁殖的军曹鱼幼鱼（211.17 ± 9.51） g，将90尾军曹鱼幼鱼随机均分为常温对照组和低温组，每组3个平行，每天饱食投喂两次（08：00和16：00），暂养7 d后开始正式实验。常温对照组水温为自然水温[（30.5 ± 1.0） ℃]，低温实验组采用密封瓶装冰块按照0.5℃/h匀速降温，并维持在（20.0 ± 0.5）℃，间隔30 min检测一次水温，静水养殖且每天更换50%等温新鲜海水。预实验过程中发现军曹鱼幼鱼在20℃时完全无食欲，为避免残余饲料污染水质故低温组不投喂，对照组保持每天两次正常喂食。低温组和对照组采样后适当降低水位以保持鱼密度相对一致，且均维持溶氧在5 mg/L以上，pH值在7.4～7.8范围内，氨氮小于0.02 mg/L，亚硝酸盐小于0.01 mg/L。
2.2 样品采集
由预实验结果可知，军曹鱼幼鱼在20℃低温下半致死时间为7 d，所以在第7天时随机采集低温组和常温对照组各3尾幼鱼的肝脏作为转录组分析样品，采样时每尾鱼用丁香酚麻醉后取大约100 mg的肝脏样品放入冻存管中并用液氮速冻。采样结束后将所有肝脏样品保存于−80℃冰箱中。
2.3 RNA提取和cDNA文库构建
采用北京全式金生物技术有限公司的RNA提取试剂盒（TransZOL Up Plus RNA Kit）提取每个样品的总RNA，操作过程严格按照说明书进行。RNA提取后采用1%琼脂糖凝胶电泳检验RNA的降解程度，RNA定量采用Nano Drop 2000分光光度计对RNA做初步分析并使用Agilent 2100 RNA 6000 Nano kit做精确分析。总RNA提取后采用常规试剂盒去除rRNA，用带Oligo(dT)的磁珠对mRNA进行富集。将富集得到的mRNA用超声波打断作为模板，随机寡核苷酸作为引物，利用M-MuLV逆转录酶体系合成第一链cDNA。降解RNA链后以第一链为模板，以dNTP为合成原料，利用DNA polymerase I体系合成第二链cDNA。修复双链cDNA末端、加上Poly A尾和测序接头，用AMPure XP beads把200 bp左右的cDNA筛选出来进行PCR扩增，最后再次利用AMPure XP beads纯化产物，完成文库构建。
2.4 转录组数据质控与参考基因组比对
将含adapter、含N比例大于10%、全部为A碱基和质量值Q≤20的碱基数占整条read的50%以上的reads定义为低质量数据，对下机的raw reads利用fastp进行质控，过滤低质量数据得到clean reads，再进行碱基组成和质量分布分析，利用bowtie2软件将clean reads比对到该物种的核糖体数据库，去除比对上核糖体的reads，再利用HISAT2软件，开展基于参考基因组（未公布）的比对分析。参考基因组（575.35 Mb）由广东海洋大学鱼类种子工程与健康养殖实验室提供。
2.5 基因表达分析
根据HISAT2软件的比对结果，利用Stringtie重构转录本，并利用RSEM计算每个样本中所有基因的表达量。对测序深度、转录本长度进行校正后得到基因的FPKM值，再进一步分析各基因的表达分布情况。把基因表达水平分析中得到的表达矩阵数据利用DESeq2软件进行差异基因分析。基于差异分析结果，筛选FDR < 0.05且|log2FC| > 1的基因作为显著差异基因。
2.6 差异基因GO富集和KEGG富集分析
将差异基因向GO数据库（http://www.geneontology.org/）的条目映射，统计每个term的差异基因数量，再应用超几何检验找出显著富集的GO条目。将差异基因注释到KEGG数据库得到注释信息，再以KEGG Pathway为单位，同样应用超几何检验完成Pathway显著性富集分析。该假设检验的p-value计算公式为
$ P=1-\sum _{i=0}^{m-1}\frac{\left(\begin{array}{c}M\\ i\end{array}\right)\left(\begin{array}{c}N-M\\ n-i\end{array}\right)}{\left(\begin{array}{c}N\\ n\end{array}\right)}， $
式中：N为所有背景蛋白中具有GO注释的蛋白数目；n为N中差异表达蛋白的数目；M为所有背景蛋白中注释为某特定GO term的蛋白数目；m为注释为某特定GO term的差异表达蛋白数目。
2.7 qRT-PCR验证
通过对表达量高且差异性大的基因进行背景调查，筛选出以下几个基因进行qRT-PCR验证。根据acc、cpt1、fas、hsl、mgl、pparα等基因和肌动蛋白(β-actin)基因，用primer 5.0设计各个基因的引物(引物序列如表1所示)，再用实时荧光定量PCR仪检测基因表达量，以β-actin基因表达量为内参使用2−△△Ct计算各基因的相对表达量。
3 结果
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3.1 转录组测序与比对
通过对军曹鱼肝脏进行转录组测序，6个样品（常温对照组和低温组各3个生物学重复）的下机raw datas及过滤后各质量指标如表2所示，各样品clean reads数占raw reads的98%以上，过滤后各样品GC含量在47.65%～48.16%之间，较为一致，Q20超过98%，Q30超过94%，表明本次测序结果的有效数据量占比高且质量较好。将获得的clean reads去除比对上核糖体RNA（rRNA）后，进行参考基因组比对，结果如表3所示，各样品reads在基因组上的总比对率均在92%以上，比对率在不同处理组之间无显著差异且较为一致。
3.2 差异表达分析
为了消除基因长度和测序深度差异对分析基因表达的影响，采用基因的FPKM值对不同样品间的基因表达差异情况进行比较。基于差异分析结果，筛选出差异表达基因。差异表达分析结果如图1所示，本次分析共获得4 362个差异表达基因，其中2 793个基因表达上调，1 569个基因表达下调。
3.3 差异表达基因的GO和KEGG富集分析
Gene Ontology（GO）共有3个ontology（本体），分别描述基因的分子功能（molecular function）、细胞组分（cellular component）、参与的生物过程（biological process）。将富集前20的GO term进行统计（图2），发现有4个term属于分子功能条目，7个term属于细胞组分条目、9个term属于生物过程条目。在分子功能条目中，差异基因主要富集在催化活性（GO:0003824）、RNA结合（GO:0003723）、小分子结合（GO:0036094）、核苷结合（GO:0001882）；在细胞组分条目中，差异基因富集在细胞器部分（GO:0044422）、膜结合细胞器（GO:0043227）、细胞内膜结合细胞器（GO:0043231）、细胞内细胞器部分（GO:0044446）、细胞器膜（GO:0031090）、细胞器（GO:0043226）、细胞内细胞器（GO:0043229）；在生物过程条目中，差异基因主要富集在草酸代谢过程（GO:0043436）、有机酸代谢过程（GO:0006082）、羧酸代谢过程（GO:0019752）、单生物代谢过程（GO:0044710）、小分子代谢过程（GO:0044281）、细胞酮代谢过程（GO:0042180）、调节细胞酮代谢过程（GO:0010565）、细胞周期阶段（GO:0022403）、一元羧酸代谢过程（GO:0032787）。统计富集到各个term的基因表达情况发现，在富集前20的term中上调基因的数量均多于下调基因的数量（见图2第三圈）。
KEGG是有关Pathway的主要公共数据库，通过通路显著性富集来确定差异基因参与的最主要生化代谢途径和信号转导途径。统计富集差异基因最多的前20个通路（图3），主要富集的通路有蛋白酶体（ko03050）、代谢途径（ko01100）、内质网中的蛋白质加工（ko04141）、吞噬体（ko04145）、类固醇生物合成（ko00100）、柠檬酸循环（ko00020）、真核生物核糖体生物发生（ko03008）、碳代谢（ko01200）、脂肪酸降解（ko00071）、PPAR信号通路（ko03320）、戊糖和葡萄糖醛酸酯的相互转化（ko00040）等。
3.4 脂代谢相关生物过程与通路
与脂代谢相关生物过程与通路富集结果如表4所示，低温胁迫产生的差异基因主要富集到脂质代谢过程（GO:0006629）、细胞脂质代谢过程（GO:0044255）、脂质生物合成过程（GO:0008610）等生物过程以及与类固醇生物合成（ko00100）、脂肪酸降解（ko00071）、类固醇激素的合成（ko00140）、初级胆汁酸生物合成（ko00120）、脂肪酸生物合成（ko00061）等通路上。
3.5 PPAR信号通路富集结果
分析KEGG富集前20的通路中，PPAR信号通路（ko03320）对军曹鱼脂代谢在低温条件下的调节具有重要作用（如图4所示）。在该通路中共检测到83个基因，其中36个基因表达显著。军曹鱼肝脏中极低密度脂蛋白VLDL、乳糜微粒chylomicron通过脂肪酸转运蛋白fatp将信号传递至脂肪酸结合蛋白fabp，活化后的脂肪酸结合蛋白fabp在细胞核内促进pparγ转录表达同时抑制pparα表达，使下游基因中scd1、fabp3、lpl、pgar、cpt1、cpt2等基因上调，cyp7a1、cyp27、ap2等基因下调。
3.6 糖代谢相关生物过程与通路
与糖代谢相关生物过程与通路富集结果如表5所示，低温胁迫产生的差异基因主要富集到单糖代谢过程（GO:0005996）、己糖代谢过程（GO:0019318）等生物过程以及糖酵解/糖异生（ko00010）、半乳糖代谢（ko00052）、淀粉和蔗糖代谢（ko00500）、戊糖和葡萄糖醛酸酯的相互转化（ko00040）等通路上。
3.7 转录组结果验证
为了验证转录组结果，选取了acc、cpt1、fas、hsl、mgl、pparα 6个基因进行qRT-PCR检测，并从转录组中调取上述基因的检测结果进行对比。结果如图5所示，各基因在qRT-PCR和转录组中的表达变化趋势一致，说明转录组结果可靠。
4 讨论
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转录组是生物体的器官、组织或细胞在特定时空条件下所有转录产物的合集，转录组学研究不仅能够揭示生物在不同条件下的分子调节机理，也能从转录水平上分析基因的结构和功能[10]。本研究通过对常温条件和低温条件下军曹鱼肝脏的转录组分析，获得了大量的差异表达基因，为从整体上了解军曹鱼对低温的响应机制提供了资料，为培育军曹鱼耐低温品种奠定了基础。
4.1 脂质代谢
4.1.1 脂代谢相关生物过程差异表达基因
在鱼类研究中，脂肪既是机体最关键的能量来源，也是组成生物细胞膜的重要原料[11]，这两个生物功能均对鱼体抵抗低温环境具有重要作用，但目前对鱼类低温下脂代谢相关分子调节机制的认识仍然不够清晰。本研究通过对军曹鱼肝脏在低温和常温条件下的差异表达基因进行富集分析，结果发现共有294个差异基因富集到脂质代谢过程(GO:0006629)，表明低温胁迫会显著影响军曹鱼幼鱼肝脏脂代谢活动。
除了发现脂代谢过程有较多基因被显著富集之外，还发现细胞脂质代谢过程（218）、脂质生物合成过程（82）、甘油脂代谢过程（79）和磷脂代谢过程（82）等也富集到较多的差异基因。脂质是生物体内三大营养物质之一，除了为机体提供能量外，还是部分功能分子的合成原料[12]。脂质生物合成过程被显著富集可能跟军曹鱼在低温下停食有关，停食导致脂质代谢的平衡状态被打破，而提高脂质生物合成相关基因的表达可以一定程度上补偿脂质摄入减少的部分。
甘油磷脂主要包括磷脂酰胆碱和磷脂酰乙醇胺两种物质，甘油磷脂和鞘磷脂是生物膜的重要成分，细胞正常功能的行使依赖磷脂规律的结构，磷脂还是机体内脂类催化过程中的重要物质[13]。甘油作为生物体内良好的低温保护剂，具有防止体内的水分形成结晶，对维持低温条件下的正常生理功能具有较大的作用[14]。
值得注意的是，本研究中KEGG富集分析结果显示，类固醇生物合成和类固醇激素合成等两个途径分别富集到较多差异基因。类固醇生物合成途径中，lss、ebp、hsd17b7、dhcr24、fdft1、sqle等基因在低温环境中显著上调。而类固醇激素合成途径中ugt2a2、ugt2b1、akr1d1、dhrs11、cyp7a1、comtb、cyp3a27等较多基因显著下调，上调基因如sult2b1、cyp11b等基因数量较少。从军曹鱼肝脏转录组测序结果上看，低温虽然促进了类固醇生物合成，但是抑制了类固醇激素生物合成。在大黄鱼（Larimichthy crocea）应对低温胁迫的肝脏转录组研究结果中发现，类固醇激素生物合成中相关酶的基因表达显著下调[15]，与本研究结果一致。类固醇激素属于四环脂肪烃化合物，包括有糖皮质激素、孕激素、盐皮质激素、雌激素和雄激素等5类[16]。其中，糖皮质激素主要包括皮质醇和皮质酮[17]，而皮质醇是鱼类应对环境应激时用于维持生理平衡的重要激素之一[18]，也是衡量应激强弱程度的常用指标[19]。类固醇激素合成受到抑制是否导致皮质醇分泌不足，以及是否与军曹鱼低温耐受性较差有关，则有待进一步分析论证。
4.1.2 PPAR信号通路差异表达基因
作为与动物体脂代谢具有密切关系的三大途径之一[20]，过氧化物酶体增殖激活受体ppars（peroxisome proliferatos-activated receptors, ppars）信号通路对分泌脂肪因子、调控脂肪细胞的分化等过程都具有重要作用[21]。ppars具有pparα、pparβ/δ和pparγ三种亚型，均属于亲和力较高的内源性配体，且可被脂肪酸或者脂肪酸衍生物所激活，在中介代谢调控中作为脂质传感器与靶基因特异性结合并开启相关转录过程[22]。在低温胁迫后的肝脏转录组结果中，差异基因富集到PPAR信号通路的物种有金头鲷[5]、暗纹东方鲀[8]、大黄鱼[15]等，在本研究中，PPAR信号通路也在军曹鱼肝脏中被显著富集，说明PPAR信号通路对多种鱼类应对低温具有关键调节作用。Tsai等指出军曹鱼pparγ表达水平跟组织脂肪含量具有显著的正相关性[23]。在本实验的前期研究中，通过油红O染色切片观察发现低温胁迫下军曹鱼肝脏脂滴面积显著增加[24]，这可能与肝脏pparγ显著上调有关。军曹鱼肝脏PPARα显著下调，与对金头鲷的研究结果一致[5]，但与大黄鱼和卵形鲳鲹（Trachinotus ovatus）等物种的研究结果相反[15，25]，说明PPAR信号通路在不同物种应对低温过程的调控模式具有差异性。
在PPAR信号通路下游基因中，scd1受调控后显著上调，而scd1高表达可增加细胞膜中不饱和脂肪酸的比例[26]，这与前期发现军曹鱼肝脏脂肪酸不饱和度在低温下显著提高的研究结论相一致，草鱼（Ctenopharyngodon idellus）[27]、尼罗罗非鱼[28]、大黄鱼[29]等物种也发现在应对低温下scd1基因的表达显著上调，表明提高scd1基因表达对多个物种应对低温胁迫具有关键作用。PPAR信号通路下游基因cpt1和cpt2也显著上调，cpt1和cpt2是脂酰肉碱转移系统的两个重要成员[30]，也是脂肪酸β氧化过程中的关键酶，说明低温胁迫下军曹鱼肝脏通过PPAR信号通路增强脂类合成代谢的同时也增强了脂类分解代谢。
4.2 糖代谢
葡萄糖是鱼体内供能的重要物质之一。在糖异生中，g6pc基因在低温环境中表达显著上调。该基因编码的葡萄糖-6-磷酸酶（glucose-6-phosphatase）可以将肝脏中的葡糖-6-磷酸转化为葡萄糖，此时暗示葡萄糖含量可能增加，这一观点与Melis等研究一致[31]。在持续的低温环境中，肝脏葡萄糖含量会缓慢回升，即血糖升高，使军曹鱼提高了机体的御寒能力。
而在糖酵解提供能量的环节中，基因ENO编码的烯醇化酶表达下调，该酶可催化生成磷酸烯醇式丙酮酸（phosphoenolpyruvate, PEP）。磷酸烯醇式丙酮酸是一个高能磷酸分子，通过丙酮酸激酶的催化作用，它能够转化为丙酮酸，并在此过程中生成大量的ATP，为细胞提供能量[32]，同时它也是糖代谢进入三羧酸循环（tricarboxylic acid cycle, TCA）的关键物质。三羧酸循环是三大营养素（糖、氨基酸和脂质）的最终代谢途径，是氧化供能最有效的途径[33]。此时其含量降低，即暗示着以糖代谢供能的途径被抑制。
5 结论
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通过对转录组中的差异基因进行富集分析，发现大量差异基因富集在能量代谢中。在脂代谢方面，大量基因集中富集于脂代谢过程、脂质生物合成过程、甘油磷脂代谢过程、磷脂代谢过程和甘油脂代谢过程等生物过程中；PPAR信号通路中pparα、pparβ、scd1、cpt1和cpt2等多个脂代谢相关基因对军曹鱼幼鱼应对低温胁迫具有关键作用。在糖代谢方面，大量基因富集于糖酵解/糖异生、半乳糖代谢、淀粉和蔗糖代谢、戊糖和葡萄糖醛酸酯的相互转化等生物过程，其中g6pc、eno等基因在军曹鱼幼鱼应对低温胁迫时发挥重要调节作用。
基金
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  • 南方海洋科学与工程广东省实验室(湛江)项目(ZJW−2019−06)
  • 湛江市海洋经济创新发展示范市项目(XM−202008−03)
  • 国家海水鱼产业技术体系项目(CARS−47−G08)
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2025年第47卷第1期
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doi: 10.12284/hyxb2025010
  • 接收时间：2024-01-15
  • 首发时间：2025-11-10
  • 出版时间：2025-01-31
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  • 收稿日期：2024-01-15
  • 修回日期：2024-11-11
基金
南方海洋科学与工程广东省实验室(湛江)项目(ZJW−2019−06)
湛江市海洋经济创新发展示范市项目(XM−202008−03)
国家海水鱼产业技术体系项目(CARS−47−G08)
作者信息
    1.广东海洋大学 水产学院，广东 湛江，524088
    2.广东省水产经济动物病原生物学及流行病学重点实验室，广东 湛江，524088

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*张静，副教授，主要研究方向为渔业生态环境与保护。E-mail：
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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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