Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献_第9页

Transcriptome analysis reveals the immune response mechanism of golden cuttlefish (Sepia esculenta) larvae exposed to ink 转录组分析揭示了金乌贼（Sepia esculenta）幼体接触墨水后的免疫反应机制。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2024-11-07 DOI: 10.1016/j.cbd.2024.101355

Deyuan Chang , Yancheng Zhao , Ziwen Ren , Xueyu Zhu , Xiaokai Bao , Yongjie Wang , Weijun Wang , Cuiju Cui , Xiumei Liu , Zan Li , Yuan Shan , Jianmin Yang

The golden cuttlefish (Sepia esculenta), a significant cephalopod in the Yellow and Bohai Seas of China, is highly esteemed for its exceptional medicinal and commercial value. The natural resources of the S. esculenta are currently facing depletion due to the ongoing environmental degradation and overfishing. Secreted by the ink sac of the S. esculenta, the ink contains a diverse array of nutrients and active ingredients, which can exert a substantial impact on biological immune cells' proliferation and differentiation, the occurrence of inflammation, autophagy, along with other processes pertaining to immune response, and thus affects their survival. In the actual production, the high-density artificial cultivation and transportation process of S. esculenta often leads to large-scale inkjet phenomenon, posing a significant threat to the survival of this species. The present study employed RNA-seq as the basis to investigate the mechanisms of immune response in S. esculenta larvae when exposed to ink. Conduct functional enrichment analysis (GO and KEGG) as well as protein-protein interaction (PPI) network analysis for the 1951 differentially expressed genes (DEGs). In addition, this study is the pioneering attempt to employ a combined analysis of KEGG and PPI network construction and further reveal a set of 20 key genes associated with immunity, which have higher numbers of PPI or KEGG pathway participation. It is evident that the ink exposure has an impact on the inflammatory response, immune cell propagation and specialization, transmission of signals in the immune system, and autophagy in S. esculenta larvae. Through the enrichment analysis of genes and pathway functions, we understood the impact of ink exposure on the larvae of S. esculenta exhibit immune resistance, further improved our overall comprehension regarding the immune functionality exhibited by mollusks, and contributed to improving the survival rate of S. esculenta in factory farming.

金乌贼（Sepia esculenta）是中国黄海和渤海的一种重要头足类动物，因其卓越的药用和商业价值而备受推崇。由于环境持续恶化和过度捕捞，金眼鲷的自然资源目前正面临枯竭。蚕蛹墨囊分泌的墨汁中含有多种营养物质和活性成分，可对生物免疫细胞的增殖和分化、炎症的发生、自噬以及与免疫反应相关的其他过程产生重大影响，从而影响其存活。在实际生产中，S. esculenta 的高密度人工栽培和运输过程往往会导致大规模的喷墨现象，对该物种的生存构成重大威胁。本研究以RNA-seq为基础，研究S. esculenta幼虫暴露于墨汁时的免疫反应机制。对 1951 个差异表达基因（DEGs）进行功能富集分析（GO 和 KEGG）以及蛋白质相互作用（PPI）网络分析。此外，本研究还开创性地采用了 KEGG 和 PPI 网络构建相结合的分析方法，进一步揭示了一组与免疫相关的 20 个关键基因，这些基因有较多的 PPI 或 KEGG 通路参与。结果表明，油墨接触对幼虫的炎症反应、免疫细胞的繁殖和特化、免疫系统的信号传递以及自噬都有影响。通过对基因和通路功能的富集分析，我们了解了油墨暴露对虾虎鱼幼体表现出免疫抵抗力的影响，进一步提高了我们对软体动物免疫功能的整体认识，有助于提高虾虎鱼在工厂化养殖中的存活率。

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引用次数: 0

Study of carbonate alkalinity-induced hepatic tissue damage in Hefang crucian carp (Carassius auratus) based on transcriptomic analysis 基于转录组分析的碳酸盐碱度诱导的河坊鲫肝组织损伤研究

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2024-11-06 DOI: 10.1016/j.cbd.2024.101351

Xinyu Lei , Xue Cao , Faye Zhang , Qifang Lai , Pengcheng Gao , Yue-hong Li

This study investigated the effects of different sodium bicarbonate (NaHCO₃) concentrations (0 g/L, 1 g/L, and 3 g/L) on Hefang crucian carp (12.0 ± 1.1 g) over a 96-hour period. The experiment is divided into three groups, each with three replicates, and each replicate contains 30 fish. We employed a comprehensive approach integrating histology, physiological and biochemical assays, transcriptomics, as well as artificial intelligence (AI)-assisted analysis. This multifaceted method allowed us to examine changes in gill and liver morphology, osmoregulation, antioxidant capacity, immune response, and physiological metabolism. Results showed that gill and liver tissue damage increased with rising water alkalinity. Serum sodium (Na⁺), potassium (K⁺), blood ammonia, and gill Na⁺/K⁺-ATPase (NKA) levels increased significantly (p < 0.05). Hepatic antioxidant enzymes initially increased, then decreased with prolonged stress. Serum and liver immunoenzyme indices were higher in bicarbonate-treated groups compared to controls. Carbonate treatment altered lipid and glucose metabolism in both serum and liver. Transcriptome analysis, enhanced by large language models (LLMs), revealed differentially expressed genes (DEGs) significantly associated with ion binding, transport, apoptosis, and metabolism. In conclusion, excessive carbonate intake in fish alters serum physiological functions and affects hepatic metabolic functions. Crucian carp primarily regulate hepatic antioxidant systems, utilize carbohydrate breakdown for energy requirements, and employ lipids in osmoregulation. This study provides insights into fish adaptation to saline-alkaline environments and offers support for the development of aquaculture in saline-alkaline waters.

本研究调查了不同碳酸氢钠（NaHCO3）浓度（0 g/L、1 g/L 和 3 g/L）对河坊鲫（12.0 ± 1.1 g）在 96 小时内的影响。实验分为三组，每组三个重复，每个重复包含 30 条鱼。我们采用了一种综合方法，将组织学、生理生化测定、转录组学以及人工智能（AI）辅助分析融为一体。这种多方面的方法使我们能够研究鱼鳃和肝脏形态、渗透调节、抗氧化能力、免疫反应和生理代谢的变化。结果表明，鳃和肝组织的损伤随着水碱度的升高而增加。血清钠（Na+）、钾（K+）、血氨和鳃Na+/K+-ATP酶（NKA）水平显著上升（p

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引用次数: 0

Understanding the spleen response of Russian sturgeon (Acipenser gueldenstaedtii) dealing with chronic heat stress and Aeromonas hydrophila challenge 了解俄罗斯鲟鱼（Acipenser gueldenstaedtii）对慢性热应激和嗜水气单胞菌挑战的脾脏反应。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2024-11-05 DOI: 10.1016/j.cbd.2024.101352

Alicia Costábile , Gonzalo Paredes , Marcio Aversa-Marnai , Carmen Lorenzo , Diana Pérez Etcheverry , Mauricio Castellano , Ignacio Quartiani , Daniel Conijeski , Alejandro Perretta , Andrea Villarino , Ana María Ferreira , Valeria Silva-Álvarez

Sturgeon aquaculture has grown in recent years, driven by increasing global demand for its highly valued products. Russian sturgeon (Acipenser gueldenstaedtii), recognised as one of the most valuable species for caviar production, is farmed in several warm-temperate regions. However, the substantial temperature increase due to global warming represents a challenge for developing sturgeon aquaculture. Previously we demonstrated that Russian sturgeon under chronic heat stress (CHS) exhibited a liver metabolic reprogramming to meet energy demands, weakening their innate defences and leading to increased mortality and economic losses. Here, we used RNA-seq technology to analyse regulated genes in the spleen of Russian sturgeons exposed to CHS and challenged with Aeromonas hydrophila. The assembly gave 253,415 unigenes, with 13.7 % having at least one reliable functional annotation. We found that CHS caused mild splenitis and upregulated genes related to protein folding, heat shock response, apoptosis and autophagy while downregulated genes associated with the cell cycle. The cell cycle arrest was maintained upon A. hydrophila challenge in heat-stressed fish, potentially inducing cell senescence. Surprisingly, immunoglobulin heavy and light chains were upregulated in the spleen of stressed sturgeons but not in those maintained at tolerable temperatures; however, no changes in IgM serum levels were observed in any condition. Our findings indicate that long-term exposure to non-tolerable temperatures induced a heat shock response and activated apoptosis and autophagy processes in the spleen. These mechanisms may enable the control of tissue damage and facilitate the recycling of cell components in a condition where the nutrient supply by the liver might be insufficient. Stressed sturgeons challenged with A. hydrophila maintain these mechanisms, which could culminate in cellular senescence.

近年来，由于全球对鲟鱼高价值产品的需求不断增长，鲟鱼养殖业也随之增长。俄罗斯鲟鱼（Acipenser gueldenstaedtii）是公认的最有价值的鱼子酱生产物种之一，在几个暖温带地区都有养殖。然而，全球变暖导致气温大幅升高，给鲟鱼养殖业的发展带来了挑战。以前我们曾证实，俄罗斯鲟鱼在慢性热应激（CHS）下表现出肝脏代谢重编程以满足能量需求，削弱了其先天防御能力，导致死亡率上升和经济损失。在这里，我们利用 RNA-seq 技术分析了暴露于 CHS 并受到嗜水气单胞菌挑战的俄罗斯鲟鱼脾脏中的调控基因。组装结果显示有 253,415 个单个基因，其中 13.7% 至少有一个可靠的功能注释。我们发现，CHS 会导致轻度脾炎，并上调与蛋白质折叠、热休克反应、细胞凋亡和自噬相关的基因，同时下调与细胞周期相关的基因。当热应激鱼受到蚜蝇疫病挑战时，细胞周期的停滞仍会持续，这可能会诱导细胞衰老。令人惊讶的是，受热应激的鲟鱼脾脏中免疫球蛋白重链和轻链上调，而在可耐受温度下的鲟鱼脾脏中则没有上调；但是，在任何条件下都没有观察到 IgM 血清水平的变化。我们的研究结果表明，长期暴露在非耐受温度下会诱发热休克反应，并激活脾脏中的细胞凋亡和自噬过程。在肝脏营养供应不足的情况下，这些机制可控制组织损伤并促进细胞成分的循环。受刺激的鲟鱼在嗜水鲱鱼的挑战下会维持这些机制，最终导致细胞衰老。

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引用次数: 0

Transcriptome analysis of the moso bamboo pest, Hippotiscus dorsalis, reveals differentially expressed unigenes across various tissues 毛竹害虫 Hippotiscus dorsalis 的转录组分析揭示了不同组织中差异表达的单基因。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2024-11-05 DOI: 10.1016/j.cbd.2024.101354

Mingzhen Zhao , MengJiao Chen , Hong Qiu , Jieyu Wu , Lulu Dai , Shaoyong Zhang

Hippotiscus dorsalis (Hemiptera: Pentatomidae) is a common pest that feeds on the stems of Moso bamboo. Therefore, investigating the molecular processes related to its fundamental physiology is important. In this study, transcriptome sequencing was employed to compare gene expression in different tissues of male and female adults. A total of 36,238 annotated unigenes were identified through the NR database and compared with those of other known species. Among these, Halyomorpha halys and Nezara viridula showed the highest homology with H. dorsalis, with a total similarity exceeding 86 %. The top significant differentially expressed genes were mainly associated with protein digestion, carbohydrates metabolism, as well as reproduce regulation between sexes. The Gene Ontology enrichment analysis across three different segments of each sex revealed some terms associated with detoxification such like IMP biosynthetic process and acetyl-CoA metabolic process. Additionally, Kyoto Encyclopedia of Genes and Genomes enrichment analysis highlighted significant pathways related to glucose metabolism and pancreatic secretion. Further investigation of these DEGs, particularly in the calcium signaling pathway and glycan biosynthesis and metabolism, is essential for understanding sugar metabolism and transport in phytophagous insects.

Hippotiscus dorsalis（半翅目：五蠹科）是一种常见害虫，以毛竹的茎为食。因此，研究与其基本生理相关的分子过程非常重要。本研究采用转录组测序比较了雌雄成虫不同组织的基因表达。通过 NR 数据库共鉴定出 36 238 个注释的单基因，并与其他已知物种的单基因进行了比较。其中，Halyomorpha halys 和 Nezara viridula 与 H. dorsalis 的同源性最高，总相似度超过 86%。差异表达最高的基因主要与蛋白质消化、碳水化合物代谢以及两性繁殖调节有关。对每种性别的三个不同区段进行的基因本体富集分析发现了一些与解毒有关的术语，如 IMP 生物合成过程和乙酰-CoA 代谢过程。此外，《京都基因和基因组百科全书》的富集分析突出了与葡萄糖代谢和胰腺分泌有关的重要通路。进一步研究这些 DEGs，特别是钙信号通路和糖生物合成与代谢中的 DEGs，对于了解植食性昆虫的糖代谢和转运至关重要。

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引用次数: 0

Remodeling of the epigenetic landscape in rainbow trout, Oncorhynchus mykiss, offspring in response to maternal choline intake 母体胆碱摄入量对虹鳟后代表观遗传景观的重塑。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2024-10-31 DOI: 10.1016/j.cbd.2024.101348

Khalid Freij , Beth Cleveland , Peggy Biga

This project focused on evaluating the effects of maternal dietary choline intake on global DNA methylation profiles and related transcriptional changes in rainbow trout offspring. Three experimental diets were formulated to test different levels of choline intake: (a) 2065 ppm choline (Low Choline, 0 % supplementation), (b) 5657 ppm choline (Medium Choline, 0.6 % supplementation), and (c) 9248 ppm choline (High Choline, 1.2 % choline supplementation). Six rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning; their offspring were fed a commercial diet. Reduced representation bisulfite sequencing (RRBS) was utilized to measure genome-wide methylation in offspring immediately after hatching. When comparing to the Medium Choline offspring, differential DNA methylation occurred more in the Low Choline offspring than High Choline, especially in genic features like promoters. The differentially methylated CpGs (q ≤ 0.01) were identified evenly between CpG islands and shores in the genome, mostly found in the introns of genes. Genes such as fabp2 and leap2B associated with protein binding, fatty acid binding, DNA binding, and response to bacteria were differentially methylated and detected as differentially regulated genes by previous RNA-seq analysis. Although these findings indicate that levels of dietary choline available in broodstock diets alter offspring DNA methylation;, most differentially expressed genes were not associated with differential DNA methylation, suggesting additional mechanisms playing a role in regulating gene expression in response to maternal choline intake.

本项目重点评估母体膳食胆碱摄入量对虹鳟后代全局 DNA 甲基化图谱及相关转录变化的影响。为了测试不同水平的胆碱摄入量，我们配制了三种实验日粮：（a）2065 ppm 胆碱（低胆碱，补充 0%）；（b）5657 ppm 胆碱（中胆碱，补充 0.6%）；（c）9248 ppm 胆碱（高胆碱，补充 1.2%）。六个虹鳟鱼家庭从孵化后 18 个月开始喂食实验饲料，直到产卵；它们的后代喂食商业饲料。利用还原表征亚硫酸氢盐测序（RRBS）测量孵化后代的全基因组甲基化。与中胆碱后代相比，低胆碱后代的DNA甲基化差异比高胆碱后代更大，尤其是在启动子等基因特征中。差异甲基化的 CpGs（q ≤ 0.01）在基因组中的 CpG 岛和 CpG 海岸之间均匀分布，主要存在于基因的内含子中。与蛋白质结合、脂肪酸结合、DNA结合和对细菌的反应有关的基因（如fabp2和leap2B）被不同程度地甲基化，并被先前的RNA-seq分析检测为不同程度调控的基因。尽管这些研究结果表明，鱼苗膳食中的胆碱水平会改变后代的DNA甲基化水平，但大多数差异表达基因与DNA甲基化差异无关，这表明还有其他机制在调节基因表达以应对母体胆碱摄入量。

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引用次数: 0

Construction and integrative analysis of miRNA-mRNA response to salinity stress in Oreochromis mossambicus cells 构建并综合分析大口鲈细胞中 miRNA-mRNA 对盐度胁迫的响应

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2024-10-31 DOI: 10.1016/j.cbd.2024.101350

Zhi Luo , Yuxing Huang , Jinquan Fan, Erchao Li, Liqiao Chen, Xiaodan Wang

This study investigated the genetic response of tilapia (Oreochromis mossambicus) brain cells to hypertonic stress, focusing on miRNAs regulation. Three hundred and thirty-one known miRNAs and 163 novel miRNAs which responded to hypertonic stress were identified by high-throughput sequencing in tilapia brain cells. Differential expression analysis revealed that 16 miRNAs were significantly upregulated, while 11 miRNAs were significantly downregulated. These differentially expressed miRNAs are closely related to metabolism, immune response, and neural regulation. The target genes of these miRNAs are implicated in neurotrophic and synaptic signaling pathways, potentially affecting metabolic and apoptotic processes. GO and KEGG enrichment analyses provided insights into the biological processes and pathways affected by hypertonic stress. Furthermore, correlation analysis between mRNA and miRNA highlighted miRNA-mRNA interactions related to cell cycle and apoptosis regulation. These results indicated significant changes of miRNA expression under hypertonic stress and their crucial role in osmotic pressure regulation. This study offers a basis for further exploration of miRNA functions and molecular mechanisms in tilapia, potentially informing practices for aquaculture in challenging environments such as saline-alkaline waters.

本研究以miRNAs调控为重点，研究了罗非鱼（Oreochromis mossambicus）脑细胞对高渗应激的遗传响应。通过高通量测序鉴定了罗非鱼脑细胞中331个已知的miRNA和163个对高渗胁迫有反应的新型miRNA。差异表达分析表明，16 个 miRNA 显著上调，而 11 个 miRNA 则显著下调。这些差异表达的 miRNA 与新陈代谢、免疫反应和神经调控密切相关。这些 miRNA 的靶基因与神经营养和突触信号通路有关，可能影响新陈代谢和细胞凋亡过程。GO 和 KEGG 富集分析有助于深入了解受高渗应激影响的生物过程和途径。此外，mRNA 和 miRNA 之间的相关性分析突显了与细胞周期和细胞凋亡调控有关的 miRNA-mRNA 相互作用。这些结果表明，在高渗胁迫下，miRNA的表达发生了重大变化，并在渗透压调节中发挥了关键作用。这项研究为进一步探索罗非鱼体内 miRNA 的功能和分子机制奠定了基础，有可能为在盐碱水域等具有挑战性的环境中进行水产养殖提供参考。

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引用次数: 0

Revealing the adaptation mechanism of different color morphs of sea cucumber Apostichopus japonicus to light intensities from the perspective of metabolomics 从代谢组学角度揭示日本刺参不同颜色形态对光照强度的适应机制

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2024-10-29 DOI: 10.1016/j.cbd.2024.101346

Bohong Liu , Shilin Liu , Lina Sun , Lili Xing

Global warming has multi-dimensional and complex impacts on the Earth's system, among which changes in light intensities cannot be overlooked. Sea cucumbers are a marine biological resource with significant economic and ecological value. Their presence and activity help maintain the balance and stability of marine ecosystems. The variation in light intensities have important ecological effects on sea cucumbers. Light intensities can alter the synthesis and degradation of metabolic substances within the bodies of Apostichopus japonicus by changing their body color. Their changes affect the production of microorganisms in the environment, thereby achieving the goal of bioremediation. This study investigated metabolic variations in green, purple, and white sea cucumber Apostichopus japonicus under different light conditions (0 lx and 910 lx) with a 12-h light and 12-h dark photoperiod. The findings indicated that the sea cucumbers displayed more diverse metabolic alterations under 910 lx illumination compared to 0 lx. Specifically, these color morphs primarily responded to changes in light intensities through “tryptophan metabolism” and “biosynthesis of steroid hormones”. Additionally, high light intensities environment exacerbated the consumption of fatty acids by sea cucumbers. Different color morphs of sea cucumbers have differences in key metabolites in response to changes in light intensities. Green and white sea cucumbers primarily adapt to environment through phospholipids, while purple sea cucumbers mainly utilize fatty acids. These results enhance our comprehension of how sea cucumbers adapt ecologically to varying light intensities, and they offer valuable insights for systematically uncovering the regulatory processes that marine animals employ in response to environmental changes.

全球变暖对地球系统产生了多方面的复杂影响，其中光照强度的变化不容忽视。海参是一种具有重要经济和生态价值的海洋生物资源。它们的存在和活动有助于维持海洋生态系统的平衡和稳定。光照强度的变化对海参有重要的生态影响。光照强度可以通过改变日本海参的体色来改变其体内代谢物质的合成和降解。它们的变化会影响环境中微生物的产生，从而达到生物修复的目的。本研究调查了绿色、紫色和白色海参在不同光照条件（0 lx 和 910 lx）和 12 小时光照和 12 小时黑暗光照周期下的代谢变化。研究结果表明，与 0 lx 光照相比，910 lx 光照下的海参表现出更多样的新陈代谢变化。具体来说，这些颜色形态主要通过 "色氨酸代谢 "和 "类固醇激素的生物合成 "对光照强度的变化做出反应。此外，高光照强度环境加剧了海参对脂肪酸的消耗。不同颜色形态的海参对光照强度变化的关键代谢物的反应也不同。绿色和白色海参主要通过磷脂来适应环境，而紫色海参则主要利用脂肪酸。这些结果加深了我们对海参如何在生态学上适应不同光照强度的理解，并为系统揭示海洋动物应对环境变化的调控过程提供了宝贵的见解。

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引用次数: 0

Impact of gonadotropin on certain testis-related genes identified through testicular transcriptome analysis in the Asian and the African catfish 通过对亚洲和非洲鲶鱼睾丸转录组的分析，确定了促性腺激素对某些睾丸相关基因的影响。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2024-10-29 DOI: 10.1016/j.cbd.2024.101349

Sonika Kar , Swathi Tenugu , Akanksha Pranoty , Narlagiri Anusha , Uday Kumar Udit , Prabhaker Sangem , Balasubramanian Senthilkumaran

Induction of spawning in catfish is well demonstrated in females while stimulation of spermiation in males seems difficult. This has led to least understanding of gene profile changes during testicular maturation. Expression of the factors after hormonal induction that control reproductive processes has become an intense research area in fish endocrinology. In view of this, de novo assemblies of testicular transcriptomes of the Asian catfish, Clarias batrachus and the African catfish, C. gariepinus, were performed to identify genes/factors involved in testicular maturation. For testicular induction, human chorionic gonadotropin (hCG) was administered in vivo to both the catfish species during active phase of reproduction. 1,68,071 and 1,26,232 assembled transcripts were obtained from C. batrachus and C. gariepinus testicular transcriptomes and were annotated using different databases. Further, in silico analysis suggested the presence of several transcripts that were involved in steroidogenesis and male reproduction. Comparison of transcriptomes of both species revealed the presence of certain unique genes related to reproduction differentially. Expression profiles after hCG induction in testis showed higher expression of certain steroidogenesis related genes such as star, cyp11b1, cyp17a and cyp21a in both the species. Further, expression levels of crucial factors related to testis, such as dmrt1/2/3, were also found to be significantly higher after gonadotropin induction. However, amh, tgfα and dmrt4/5 expression levels were significantly low. Factors related to male reproduction i.e., tekt1, tekt2, sox9, spag1, spata2 and spata7 were found to be differentially upregulated in hCG treated testicular tissues of both the species. Histology analysis indicated that the gonadotropin induction either short or long term is a better strategy to highlight expression profile changes during testicular maturation in teleost.

雌性鲶鱼的产卵诱导已得到充分证明，而雄性鲶鱼的精子生成刺激似乎很难。这使得人们对睾丸成熟过程中的基因变化了解甚少。激素诱导后控制生殖过程的因子表达已成为鱼类内分泌学的一个重要研究领域。有鉴于此，我们对亚洲鲶鱼（Clarias batrachus）和非洲鲶鱼（C. gariepinus）的睾丸转录组进行了重新组装，以确定参与睾丸成熟的基因/因子。为了诱导睾丸，在两种鲶鱼的生殖活跃期给它们体内注射了人绒毛膜促性腺激素（hCG）。利用不同的数据库，分别从蝙蝠鲶和加里鲶的睾丸转录组中获得了 1,68,071 和 1,26,232 个组装转录本并进行了注释。此外，硅学分析表明存在几种参与类固醇生成和雄性繁殖的转录本。比较这两个物种的转录组发现，存在某些与生殖有关的独特基因。hCG诱导睾丸后的表达谱显示，某些与类固醇生成相关的基因，如star、cyp11b1、cyp17a和cyp21a，在两个物种中的表达量都较高。此外，在促性腺激素诱导后，与睾丸有关的关键因子（如 dmrt1/2/3）的表达水平也明显升高。然而，amh、tgfα和dmrt4/5的表达水平明显偏低。与雄性繁殖有关的因子，即 tekt1、tekt2、sox9、spag1、spata2 和 spata7，在两种动物经 hCG 处理的睾丸组织中都出现了不同程度的上调。组织学分析表明，促性腺激素短期或长期诱导是突显远洋鱼类睾丸成熟过程中表达谱变化的更好策略。

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引用次数: 0

Transcriptome analysis uncovers the expression of genes associated with growth in the gills and muscles of white shrimp (Litopenaeus vannamei) with different growth rates 转录组分析揭示了不同生长速度的南美白对虾（Litopenaeus vannamei）鳃和肌肉中与生长相关的基因的表达情况

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2024-10-28 DOI: 10.1016/j.cbd.2024.101347

Wenhao Wang , Junrou Huang , Wenyu Fang , Hongyun Zhang , Zhiqiang Chen , Jianguo Lu

Litopenaeus vannamei is a crucial species in aquaculture. The gene expression patterns associated with distinct growth rates are not well understood. To investigate this, we used RNA-seq to study the underlying growth mechanism of L. vannamei with varying growth rates. Individuals of higher growth performance (HG), middle growth performance (MG), and lower growth performance (LG) were examined. A total of 8422 and 4560 differentially expressed genes (DEGs) were identified in gill and muscle samples, respectively. Genes related to growth were significantly up-regulated in HG gills, such as cuticle protein, chitin synthase, pupal cuticle protein, titin myosin G heavy chain, and myosin heavy chain 10. The GO enrichment analysis revealed that the DEGs of HG gills were significantly enriched in “structural constituent of cuticle”, “primary metabolic process” and “chitin binding”. The growth-related genes were highly expressed in HG muscle, such as myosin heavy chain, myosin heavy chain type A and myosin 3. The GO enrichment analysis revealed that the DEGs of HG muscle were significantly enriched in “myosin filament”, “myosin complex” and “myofibril”. These findings provide insights into mechanisms underlying the growth performance of superior L. vannamei, and identify candidate genes for genetic improvement programs aimed at enhancing this trait.

凡纳滨对虾是水产养殖中的重要物种。与不同生长率相关的基因表达模式尚不十分清楚。为了研究这个问题，我们使用 RNA-seq 研究了不同生长率的凡纳滨对虾的潜在生长机制。我们研究了生长性能较高（HG）、生长性能中等（MG）和生长性能较低（LG）的个体。在鳃和肌肉样本中分别发现了 8422 个和 4560 个差异表达基因（DEG）。与生长相关的基因在HG鳃中明显上调，如角质层蛋白、几丁质合成酶、蛹角质层蛋白、titin肌球蛋白G重链和肌球蛋白重链10。GO富集分析表明，HG鳃的DEGs在 "角质层结构成分"、"初级代谢过程 "和 "几丁质结合 "中显著富集。GO富集分析表明，HG肌肉中的DEGs在 "肌球蛋白丝"、"肌球蛋白复合物 "和 "肌原纤维 "中明显富集。这些发现有助于深入了解优质凡纳米鱼生长性能的内在机制，并为旨在提高该性状的遗传改良计划确定候选基因。

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引用次数: 0

Effects of high-protein feeds on growth, free amino acid metabolism and protein metabolism-related genes in larvae and juveniles of rice flower carp (Procypris merus) 高蛋白饲料对稻花鲤幼鱼和幼鱼生长、游离氨基酸代谢和蛋白质代谢相关基因的影响

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2024-10-18 DOI: 10.1016/j.cbd.2024.101345

Ruijie Guo , Kai Huang , Kai Yu , Fei Xue , Yixin Liang , Xuhong Yang , Jiao Huang , Yaoting Wu , Dandan Wang

The effect of dietary protein on fish is widely studied. However, the high-protein diet effects and mechanisms on growth and amino acid metabolism in Procypris merus remain unclear. In this study, we investigated the effect of dietary protein levels (38 %, 44 %, 50 %) on the growth performance and amino acid contents in larvae and juveniles of P. merus. Transcriptome sequencing was used to study the adaptation mechanism of P. merus to a high-protein diet. The final length, specific growth rate, and protein efficiency ratio were remarkably decreased with increasing dietary protein levels, while the amino acid content of the body was significantly increased. In addition, 370,513,858 reads were obtained and assembled into 278,939 unigenes, with an average length of 559 bp. KEGG analysis revealed that differentially expressed genes were mainly involved in protein digestion and absorption, carbohydrate digestion and absorption, starch and sucrose metabolism, and pancreatic secretion. Moreover, high-protein increased the expression of genes involved in trypsin (prss, ctrl, cpa, cpb), peptide transporter (pept), amino acid transporter (b0at1), and gluconeogenesis (g6pase), which could digest and absorb the dietary protein, and converse amino acids into energy, resulting in adaption to a high-protein diet.

膳食蛋白质对鱼类的影响已被广泛研究。然而，高蛋白日粮对梅氏原鲤生长和氨基酸代谢的影响及其机制仍不清楚。本研究探讨了日粮蛋白质水平（38%、44%、50%）对梅花鱼幼体和幼鱼生长性能和氨基酸含量的影响。转录组测序被用来研究梅花鱼对高蛋白食物的适应机制。结果表明，随着日粮蛋白质水平的增加，美罗鱼的最终体长、特定生长率和蛋白质效率比明显下降，而体内氨基酸含量则显著增加。此外，研究人员还获得了 370,513,858 个读数，并将其组装成 278,939 个平均长度为 559 bp 的单基因。KEGG 分析显示，差异表达基因主要涉及蛋白质消化吸收、碳水化合物消化吸收、淀粉和蔗糖代谢以及胰腺分泌。此外，高蛋白增加了参与胰蛋白酶（prss、ctrl、cca、ccb）、肽转运体（pept）、氨基酸转运体（b0at1）和糖元生成（g6pase）的基因的表达，这些基因可以消化吸收食物中的蛋白质，并将氨基酸转化为能量，从而适应高蛋白饮食。

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引用次数: 0