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合理选择盐度驯化方式是目前虹鳟(Oncorhynchus mykiss)养殖生产所要解决的重要问题之一。本研究通过分析盐度驯化对虹鳟幼鱼外骨骼(鳞组织)中基因表达水平的影响,重点探讨了盐度对鱼类骨代谢的影响机制。首先,分别采集海水(盐度28)驯化7 d和常规淡水养殖(对照)条件下的虹鳟鳞组织,采用Illumina HiSeq 4000测序平台进行转录组测序(RNA-Seq)。以log2|fold change|≥1且P<0.05作为显著差异表达基因(DEGs)筛选条件,共筛选出1714个DEGs,其中,484个基因显著上调,1230个基因显著下调。GO功能注释分析结果显示,上述DEGs主要被注释在细胞膜、细胞质、细胞核、运输、信号转导、金属离子结合和ATP结合等功能中。KEGG通路富集分析结果显示,DEGs在氧化磷酸化、药物代谢–细胞色素P450、蛋白酶体、p53信号通路和心肌收缩等通路中显著富集。利用实时荧光定量PCR (RT-qPCR)对随机选取的8个DEGs的表达量进行验证,结果显示,RT-qPCR与RNA-Seq结果一致,表明RNA-Seq数据可靠。结果表明,以4/d的盐度提升速率对虹鳟进行盐度驯化,对其Mmp-2、Mmp-9、Acp5b、Alpl、Osteocalcin、OPG和Col12a1等骨代谢相关基因及NF-kB、MAPK-(JNK、p38、ERK1/2和STAT3)、Wnt/β-catenin、BMP/Smads和OPG-RANK-RANKL等骨代谢相关信号通路影响不显著,说明本研究所采用的驯化模式较为合理。本研究结果可为虹鳟的养殖生产实践提供参考,所获得的基因信息、功能注释和通路富集信息可为探究硬骨鱼类骨代谢的调控机理及其应对环境变化的演化规律提供新视角。 相似文献
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黑斑原鮡(Glyptosternum maculatum)是我国雅鲁藏布江中上游江段特有鱼类, 为适应雅鲁藏布江急流、低温的水域环境条件, 进化出独特的组织器官——副肝。本研究采用组织学、生物化学以及转录组学的方法开展了黑斑原鮡主肝与副肝代谢差异调控机制的研究。结果表明, 黑斑原鮡主、副肝脏在结构组成、肝细胞线粒体数量及线粒体蛋白质组成上无显著差异。转录组学结果表明, 主、副肝脏共有差异表达基因 77 个。经 GO 功能注释, 筛选出羟甲基戊二酸单酰 CoA 合成酶(Hmgcl)、血栓素合成酶(Tbxas)、钙/钙调蛋白依赖性丝氨酸蛋白激酶(Cask)、甲酰甘氨酸生成酶(Sumf1)、蛋白质酪氨酸激酶(Jak1)以及甘油酸激酶(Glxk)等差异表达基因, 这些基因富集到氨基酸代谢、脂肪代谢等过程。KEGG 通路富集结果显示, 差异表达基因富集到丁酸盐代谢通路(butanoate metabolism)、 过氧化物酶体(peroxisome)、缬氨酸, 亮氨酸和异亮氨酸降解(valine, leucine and isoleucine degradation)、赖氨酸降解(lysine degradation)、色氨酸代谢(tryptophan metabolism)以及代谢途径(metabolic pathways)等信号通路。选出 4 个差异表达基因进行实时荧光定量 PCR (qRT-PCR)检测, 结果显示 qRT-PCR 与转录组测序结果基本一致。综上所述, 黑斑原鮡主、副肝脏存在氨基酸、脂肪酸及能量代谢差异, 其代谢差异可能与 Hmgcl、Ptk2b、Gba 和 Dnm1l 等基因在主、副肝脏中的差异性表达有关(P＜0.05)。本研究筛选出调节黑斑原鮡代谢差异的关键基因和信号通路, 为揭示黑斑原鮡主、副肝脏代谢差异机制奠定了理论基础。 相似文献
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为探索枯草芽孢杆菌(Bacillus subtilis)脱氮的分子机制,筛选枯草芽孢杆菌对氨氮的分子生态学应答相关候选基因及small RNA(sRNA),本研究对处于富含氨氮环境和对照组的枯草芽孢杆菌R47进行原核链特异性转录组及sRNA分析,并采用Real-timePCR方法检测差异表达基因的相对表达量。结果显示,平均每个测序样本得到约1.40×107条reads。对照组与处理组DESeq2分析得到3918个差异表达基因,并富集在KEGG数据库中的176个信号通路,其中,包括8个与适应富含氨氮环境相关的信号通路(细菌双组分系统通路、精氨酸生物合成、嘌呤代谢等),同时发现,epsA、tasA、sinR、glnR、glnA、tnrA和ureABC基因可能参与枯草芽孢杆菌对氨氮的应答过程。经sRNA分析获得已注释的枯草芽孢杆菌sRNA 62条。对sRNA靶基因的分析结果显示,其有3960个对应的潜在靶基因,主要参与碳水化合物运输和新陈代谢、氨基酸转运和代谢、转录过程,其中,sRNA2073和sRNA2182对应的靶基因分别为sinR和tnrA。Real-time PCR结果显示,argH、codY、argG、glnA和glnR基因的相对表达量变化与转录组测序结果一致。本研究为进一步探究枯草芽孢杆菌污水脱氮的分子机理提供参考数据。 相似文献
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为探究青海湖裸鲤在盐碱耐受过程中的基因表达变化，对青海湖河口水域以及入湖淡水河——泉吉河中的青海湖裸鲤的鳃、肾脏组织进行转录组测序，筛选青海湖裸鲤耐盐碱过程中发挥作用的免疫、代谢、渗透相关基因。结果显示，使用Trinity对所有样本质控数据(clean data)进行从头组装后共得到541 429个非冗余的序列(unigene),N50平均长度达612 bp。经差异表达分析发现，共有832个基因在2个区域中的青海湖裸鲤鳃、肾脏中共表达。经GO功能注释分析，注释到结合(binding)、细胞过程(cellular process)、代谢过程(metabolic process)、单一生物过程(single-organism process)的DEGs占比较多。KEGG通路分析结果表明，与免疫、代谢、渗透相关的通路得到了富集。根据差异表达基因的GO注释和KEGG信号通路富集分析，实验初步筛选到了青海湖裸鲤渗透相关基因，主要包括钠/钾转运ATP酶(sodium/potassium-transporting, ATPase)、钙/钙调蛋白依赖性蛋白激酶(calcium/calmodulin-d... 相似文献
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性别异形在动物界广泛存在,长期以来一直是生物学中的热门话题。黄喉拟水龟性别分化属温度依赖型,其温度响应分子机制仍不清楚。为了进一步解析龟鳖动物性别分化的分子机制,本研究初步比较分析了黄喉拟水龟转录本中性别差异表达(different expressed, DE)的长链非编码RNA(long noncoding RNA, lncRNA)及其调控的靶基因。首先,运用Illumina深度测序平台,通过转录组测序(RNA-Seqs)对黄喉拟水龟的精巢和卵巢进行了比较转录组学分析并筛选鉴定出雌雄差异转录本,共筛选获得8 237个DE mRNA和9 573个DE lncRNA。通过GO功能注释及 KEGG通路富集分析发现,上述差异转录本主要参与龟鳖动物性别分化和性腺发育等相关信号通路。此外,通过顺式和反式作用分析,筛选获得了一系列与生殖发育相关的(性腺发育和性别分化)受DE lncRNAs调控的靶基因。本研究为进一步阐明黄喉拟水龟温度依赖型性别的分子机制提供了线索,特别是为进一步挖掘利用龟鳖动物性别决定因子,进行龟鳖动物性控育种技术研究奠定了基础。 相似文献
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大黄鱼雌雄性腺长链非编码RNA的挖掘与差异分析 总被引：2，自引：1，他引：1
为探究长链非编码RNA在大黄鱼性腺发育与分化中的作用,从雌雄各3尾大黄鱼(Larimichthys crocea)的性腺中提取总RNA,进行去除rRNA的链特异性转录组建库和二代测序。将测序数据比对到大黄鱼参考基因组,经比对、组装共得到来自31675个基因的66088个转录本,严格筛选得到来自3984个基因位点的5162条lncRNA。进一步分析获得了在大黄鱼雌雄性腺中差异表达的mRNA9341个,lncRNA2782个,高度相关的lncRNA-mRNA对1227个;有多个lncRNA靶向已知的性别分化和发育相关基因,其中lncRNA MSTRG.24346与大黄鱼的性别决定候选基因dmrt1距离相近,且相关性极显著。该研究表明lncRNA可能在大黄鱼性别分化中起到重要作用,值得深入研究阐明机制。 相似文献
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长吻鮠(Leiocassis longirostris)是淡水特色经济鱼类, 其雄性生长速度快于雌性, 培育全雄苗种可显著提高养殖效益。为加快长吻鮠全雄苗种培育进程, 需深入了解长吻鮠性别分化及性腺发育的调控机制。本研究通过 Illumina 高通量测序平台对长吻鮠卵巢和精巢进行转录组测序分析。结果显示, 共有 10872 个雌雄差异表达基因, 其中上调基因 9375 个, 下调基因 1497 个。通过功能注释, 筛选出 71 个与性别相关的重要候选基因, 包括 50 个精巢高表达基因(dmrt1、cyp17a1、samd7、wnt6、wt1 等)和 21 个卵巢高表达基因(foxl2、gdf9、zp3、zp1、figla、bmp15 等)。KEGG 通路富集分析发现, 差异表达基因显著富集到 16 条与性别决定与分化及性腺发育相关的信号通路, 包括 Wnt 信号通路、TGF-β 信号通路、MAPK 信号通路、卵巢类固醇通路、GnRH 信号通路等。本研究筛选出与长吻鮠性别决定和分化相关差异表达基因, 揭示参与其雌雄个体性腺发育的信号通路, 为今后长吻鮠性别决定和分化机制的研究积累重要数据, 从而为其全雄苗种的培育提供理论支撑。 相似文献
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为了探究阿维菌素胁迫对鲤机体的响应机制,在水温(22±2.0)℃,将体质量(150±30)g的鲤(Cyprinus carpio)分别暴露在阿维菌素浓度0μg·L-1(对照组)、1.5μg·L-1和3.0μg·L-1下5 d,采用转录组学测序分析方法,探究阿维菌素胁迫对鲤肝胰腺转录组学的影响,解析其对鲤的分子毒理机制。通过对所得基因的功能注释发现,被注释的差异基因主要与结合、催化和代谢等功能有关。KEGG通路富集分析结果显示,差异表达基因在药物代谢-细胞色素P450、药物代谢-其他酶、淀粉和蔗糖代谢等通路中显著富集,涉及药物代谢、氨基酸代谢、碳水化合物代谢、脂质代谢以及辅助因子和维生素的代谢等多个代谢过程。这些功能基因和预测通路为理解阿维菌素胁迫鲤体内解毒和免疫系统奠定了基础。本研究获得的转录组数据可为深入研究鱼类应对杀虫剂污染物的分子机制提供丰富的基因资源。 相似文献
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为探讨低盐胁迫对金乌贼影响的分子机制,通过转录组测序技术,测定了正常盐度(30)培养和低盐胁迫(15)6 h的孵出30 d、体质量(1.3±0.3)g金乌贼幼体的转录组数据。测序共获得87326026条序列,经过质量剪切和从头拼接得到575171条转录本和513053条Unigenes。分别在NR、Swiss-Prot、KEGG、String和Pfam数据库对Unigenes进行功能注释,共获得62485条注释结果。Unigenes包含数目较多的KEGG通路有嘌呤、嘧啶和碳代谢,PI3K-AKT、cAMP和Rap1信号通路,内吞作用,RNA转运,局灶性黏附,赖氨酸降解和泛素介导的蛋白水解等。低盐胁迫产生1923条差异表达基因,GO功能富集分析显示,一些可能与低盐胁迫相关的生物学过程如α-氨基酸、羧酸、氧乙酸、有机酸和RNA等代谢过程得到了显著富集。GO可视化分析发现,低盐胁迫对金属离子、阴离子及核苷酸结合,α-氨基酸代谢和水解酶活性等过程影响显著。KEGG通路富集分析显示,低盐胁迫6 h后差异表达基因主要富集到雌激素和心肌细胞肾上腺素信号通路,类固醇生物合成,抗原加工与表达,脂肪和蛋白质消化与吸收,甘油脂质、花生四烯酸和酪氨酸代谢等信号通路上。本研究中获得的通路及基因信息可为今后开展金乌贼低盐胁迫生理机制的探讨、分子标记的挖掘和关键基因的克隆等提供技术支撑。 相似文献
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MicroRNA(miRNAs)是一类长度为18-25nt的内源性非编码单链小RNA,参与细胞增殖与凋亡、免疫、脂肪代谢等过程。本试验以三组投喂不同类型饵料的鲤(Cyprinus carpio)肝脏为研究材料,通过HiSeq 2500深度测序技术和生物信息学分析miRNA,鉴定出235个已知miRNAs。三种饵料组共表达的差异miRNAs有13个,随机挑选5个miRNA并采用qPCR进行验证,表达趋势在qRT-PCR结果和RNA测序结果中高度相似;对13个共表达的差异表达miRNAs进行靶基因预测,共预测到靶基因530个。对预测靶基因进行KEGG通路分析,结果显示参与2-羰基羧酸代谢,糖基磷脂酰肌醇(GPI)-锚定生物合成,柠檬酸循环(TCA循环)等通路的调节。本研究首次了解鲤摄食不同种类饵料的miRNAs表达特征,可以为深入了解miRNA对鲤摄食不同种类饵料过程的调控作用奠定基础。 相似文献
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Improvement of flesh quality in rainbow trout (Oncorhynchus mykiss) fed supranutritional dietary selenium yeast is associated with the inhibited muscle protein degradation 
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下载免费PDF全文 L. Wang L. Wu Q. Liu D.F. Zhang J.J. Yin Z. Xu X.Z. Zhang 《Aquaculture Nutrition》2018,24(4):1351-1360
Supranutritional dietary selenium (Se) has been demonstrated beneficial for fish health, however, its effects on fish flesh quality remain unclear. This study investigated the effects of supranutritional dietary Se on the flesh quality of rainbow trout (Oncorhynchus mykiss) and their potential mechanism. Fish were fed a basal diet supplemented with or without graded Se yeast for 10 weeks. Results showed that Se supplementation significantly increased fillet crude protein and enhanced fillet water‐holding capacity as well as fillet firmness. Supplementing with both 2 and 4 mg/kg Se significantly downregulated the expressions of two autophagy–lysosome‐related genes (autophagy‐related 12‐like and gamma‐aminobutyric acid type A receptor‐associated protein‐like 1) in fish muscle, while supplementing with 4 mg/kg Se also significantly downregulated the expression of two ubiquitin–proteasome‐related genes (muscle RING finger 2 and F‐box protein 25). Correlation analysis indicated that the improved fillet quality parameters were closely correlated with the expressions of these differentially expressed genes. This study revealed that dietary Se was effective for the improvement of rainbow trout flesh quality, and the improved fish flesh quality was associated with the inhibited protein degradation in fish muscle. 相似文献
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As part of the investigation into cysteine metabolism in fish, sulfur amino acids and their derivatives were injected intraperitoneally to fingerling rainbow trout (Oncorhynchus mykiss) to examine how the doses of these compounds affect the hepatic cysteine dioxygenase [EC 1.12.11.20] in this species. A dose of 0.25 mmol L-cysteine per 100 g body weight induced the enzyme activity as much as 2.5 times that of the control fish within 4h after the injection. The activity increased proportionally to the increasing dose of cysteine up to the dose of 0.15 mmol per 100 g body weight. The induction was observed to be rather specific to L-cysteine. These findings suggested that the cysteine sulfinate pathway might play an important role in the metabolism of excess cysteine in rainbow trout. The dosage of L-cysteine larger than 0.50 mmol per 100g body weight led to mortality of the fish. The pathway of cysteine catabolism was considered to function to prevent toxic accumulation of cysteine in rainbow trout, as in the case of mammals. 相似文献
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Ccr-lncRNA172145靶向miR-206在锦鲤体色调控中的作用初探 总被引：1，自引：0，他引：1
基于前期对锦鲤皮肤组织的转录组测序数据,筛选到4条在3种皮肤（黑色、红色、白色）中显著差异表达的lncRNA;通过RNAhybrid和TargetScan靶基因软件,发现lncRNA172145与黑色素合成通路中miR-206之间存在靶向结合位点。基于CPC、CPAT及CNIT软件,对lncRNA172145进行编码能力分析,证实该序列为lncRNA,不具备编码蛋白能力。然后,利用qRT-PCR技术对该序列时空表达水平进行了检测,发现在眼睛、黑色皮肤、鳍条及血液中的表达量显著高于其他组织;自原肠胚时期表达量开始显著性上升,高水平趋势一直持续到孵化后20 d。借助双荧光素酶报告实验,进一步证实lncRNA172145与miR-206之间存在靶向调控关系。最后,通过合成miR-206拮抗剂,对miR-206进行了体内沉默,发现与注射阴性对照拮抗剂组和PBS组相比,miR-206拮抗剂组的lncRNA172145表达水平显著性升高。研究结果说明lncRNA172145可能通过靶向到miR-206,参与到黑色素合成通路的调控,这为后续深入挖掘二者在黑色素合成通路中具体的分子作用机制提供了基础资料。 相似文献
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Ken Overturf Roger L. Vallejo Yniv Palti Fredrick T. Barrows James E. Parsons 《Aquaculture International》2012,20(2):213-232
Microarray analysis was conducted using liver samples from two families of rainbow trout that differed in their growth responses
when compared between individuals fed a fishmeal or plant protein-based diet. Differential expression relating to dietary
utilization between the two families found significant changes in expression of 33 expressed sequence tags (ESTs). Eight of
the differentially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular
interactions and functions. Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes,
we were able to map gene pathways and process interactions. From this information, we were able to infer that the metabolic
changes associated with utilization of plant protein versus fishmeal were associated with differential regulation of genes
related to cell oxidative stress, proliferation, growth and survival. Furthermore, we inferred from the changes we observed
in immune response gene expression that ingestion of this plant-based diet upregulated the expression of genes involved in
immunoregulatory processes. 相似文献
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Whether it is better to use viable or non‐viable probionts in aquaculture is still a matter of debate. In this study, the molecular immunomodulation in rainbow trout Oncorhynchus mykiss induced by viable or killed forms of the probiont Lactobacillus rhamnosus JCM 1136 was investigated. Three forms of this probiont: (1) heat‐killed (HK), (2) live spray (LI) and (3) freeze‐dried (FD) were incorporated into a basal (control) diet for rainbow trout O. mykiss. The LI and FD diets are referred to as viable diets. A rearing trial, in triplicate, was conducted for 30 days, with the control and probiotic diets as treatments. The cytokine genes such as the tumour necrosis factor (TNF), transforming growth factor (TGF‐β), interferon (IFN) and immune gene Immunoglobulin (Ig) found in tissues from the kidney and spleen were assessed for their expression pattern by real‐time polymerase chain reaction. The tested immune genes were up‐regulated in the treatment groups, sometimes even in many folds like in the case of the Ig gene. The TNF gene was found to be highly (P<0.05) up‐regulated (5000‐fold) in groups fed both viable forms (LI, FD). With regard to the TGF‐β gene, the spleen of the HK and FD groups showed significant up‐regulation of 20‐ and 30‐folds respectively. The IFN gene was up‐regulated (P<0.05) in all treatments, but more in the viable diet treatments. Kidney and spleen tissues showed similar expression patterns, i.e. all of these genes were up‐regulated more with the viable diets that with the control, and in most cases, the viable diets induced a higher expression of the immune genes than the HK diet. 相似文献
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Hiromi Oku Masaharu Tokuda Hiroyuki Matsunari Hirofumi Furuita Koji Murashita Takeshi Yamamoto 《Fish physiology and biochemistry》2014,40(6):1757-1769
To characterize thermal-responsive genes in fish, firstly, juvenile rainbow trout were reared in four different temperature conditions (average temperatures were 10, 14, 18, and 22 °C, respectively) and differentially expressed genes were identified. Gene expression in the liver was analyzed by the differential display method, followed by validation using real-time PCR. Subsequently, to examine whether the identified genes show heritable differences, the gene expression levels were compared among juveniles of three genetically distinct lines of rainbow trout (a strain and two closed colonies) by rearing at two different temperature conditions (average 14 and 22 °C). By rearing at 22 °C, growth retardation was observed compared with fish reared at 14 and 18 °C, and six genes were identified as differentially expressed genes in response to the rearing temperature in the gene expression analyses. With the increase in rearing temperature, gene expressions of a complement C1q and two ribosomal proteins were significantly up-regulated. On the other hand, three metabolic genes (betaine homocysteine methyltransferase, triosephosphate isomerase, and glucose-6-phosphatase) were down-regulated, indicating a metabolic depression due to high temperature. In the subsequent analyses, in response to the rearing temperature (14 and 22 °C), there was a trend that the complement C1q and glucose-6-phosphatase genes showed different expression patterns among the three rainbow trout lines, suggesting heritable differences in these genes. Our study provides information on thermal-responsive genes in fish, and we anticipate it will facilitate further investigation in the thermal biology of fish. 相似文献