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Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies. 利用 10x Genomics 和 Parse scRNA-seq 技术对胸腺细胞进行转录组比较分析。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-11 DOI: 10.1186/s12864-024-10976-x
Igor Filippov, Chinna Susan Philip, Leif Schauser, Pärt Peterson

Background: Single-cell RNA sequencing experiments commonly use 10x Genomics (10x) kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences (Parse) introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. Parse enables the analysis of more cells from multiple samples in a single run without the need for additional reagents or specialized microfluidics equipment. To evaluate the performance of both platforms, we conducted a benchmark study using biological and technical replicates of mouse thymus as a complex immune tissue.

Results: We found that Parse detected nearly twice the number of genes compared to 10x, with each platform detecting a distinct set of genes. The comparison of multiplexed samples generated from 10x and Parse techniques showed 10x data to have lower technical variability and more precise annotation of biological states in the thymus compared to Parse.

Conclusion: Our results provide a comprehensive comparison of the suitability of both single-cell platforms for immunological studies.

背景:单细胞 RNA 测序实验通常使用 10x Genomics(10x)试剂盒,因为它们具有高通量能力和标准化方案。最近,Parse Biosciences(Parse)推出了一种替代技术,在标准 96 孔板中使用多轮原位条形码。Parse 可在一次运行中分析来自多个样本的更多细胞,而无需额外的试剂或专门的微流体设备。为了评估这两种平台的性能,我们使用作为复杂免疫组织的小鼠胸腺的生物和技术重复样本进行了一项基准研究:结果:我们发现 Parse 检测到的基因数量几乎是 10x 的两倍,每个平台都能检测到一组不同的基因。对 10x 和 Parse 技术产生的多重样本进行比较后发现,10x 数据与 Parse 相比,技术变异性更低,对胸腺生物状态的注释更精确:我们的研究结果全面比较了两种单细胞平台在免疫学研究中的适用性。
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引用次数: 0
Genome-wide analysis of the HSF family in Allium sativum L. and AsHSFB1 overexpression in Arabidopsis under heat stress. 薤白中 HSF 家族的全基因组分析以及拟南芥在热胁迫下 AsHSFB1 的过表达。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-11 DOI: 10.1186/s12864-024-11002-w
Qing-Qing Yang, Feng Yang, Can-Yu Liu, Yong-Qiang Zhao, Xin-Juan Lu, Jie Ge, Bi-Wei Zhang, Meng-Qian Li, Yan Yang, Ji-De Fan

The heat shock transcription factor (HSF) family is one of the most widely studied transcription factor families in plants; HSFs can participate in the response to various stressors, such as heat stress, high salt, and drought stress. Based on garlic transcriptome data, we screened and identified 22 garlic HSFs. The HSF proteins of garlic and Arabidopsis can be divided into three (A, B, C) subfamilies. The phylogenetic relationship, chromosome localization, sequence characteristics, conserved motifs, and promoter analysis of the HSF family were analyzed through bioinformatics methods. RT-qPCR analysis showed that the nine selected genes had different degrees of response to heat stress. In addition, we isolated and identified a class B HSF gene, AsHSFB1, from garlic variety 'Xusuan No.6'. Subsequently, the AsHSFB1 gene was overexpressed in Arabidopsis thaliana. Under heat stress, the germination rate and growth of wild-type plants were better than that of transgenic plants. Moreover, after heat treatment, the contents of peroxidase, catalase, and chlorophyll a and b of transgenic plants were lower, but the contents of malondialdehyde (MDA) and leaf conductivity were higher. Nitroblue tetrazolium (NBT) staining showed that the stained area of transgenic plant leaves was larger than that of the wild type. Further studies showed that AsHSFB1 overexpression inhibited the expression of related reverse resistance genes. These results indicate that AsHSFB1 might play a negative regulatory role in garlic resistance under high stress. Altogether, these findings provide valuable data for revealing the function of HSF genes and lay a foundation for the subsequent selection of heat-resistant garlic varieties.

热休克转录因子(HSF)家族是研究最广泛的植物转录因子家族之一;HSFs 可参与对各种胁迫(如热胁迫、高盐胁迫和干旱胁迫)的响应。基于大蒜转录组数据,我们筛选并鉴定了 22 个大蒜 HSFs。大蒜和拟南芥的 HSF 蛋白可分为三个(A、B、C)亚家族。通过生物信息学方法分析了HSF家族的系统发育关系、染色体定位、序列特征、保守基序和启动子分析。RT-qPCR 分析表明,所选的九个基因对热胁迫有不同程度的响应。此外,我们还从大蒜品种 "旭轩6号 "中分离鉴定出了一个B类HSF基因AsHSFB1。随后,我们在拟南芥中过表达了AsHSFB1基因。在热胁迫条件下,野生型植株的发芽率和生长情况均优于转基因植株。此外,热处理后,转基因植株的过氧化物酶、过氧化氢酶、叶绿素 a 和叶绿素 b 的含量较低,但丙二醛(MDA)含量和叶电导率较高。硝基蓝四氮唑(NBT)染色显示,转基因植物叶片的染色面积比野生型大。进一步的研究表明,AsHSFB1 的过表达抑制了相关抗逆基因的表达。这些结果表明,AsHSFB1 可能对大蒜在高胁迫下的抗性起到负调控作用。总之,这些研究结果为揭示 HSF 基因的功能提供了宝贵的数据,为后续抗热大蒜品种的选育奠定了基础。
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引用次数: 0
Multi-omics approaches define novel aphid effector candidates associated with virulence and avirulence phenotypes. 多组学方法确定了与毒力和无毒表型相关的新型蚜虫效应子候选体。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-11 DOI: 10.1186/s12864-024-10984-x
Peter Thorpe, Simone Altmann, Rosa Lopez-Cobollo, Nadine Douglas, Javaid Iqbal, Sadia Kanvil, Jean-Christophe Simon, James C Carolan, Jorunn Bos, Colin Turnbull

Background: Compatibility between plant parasites and their hosts is genetically determined {Citation}both interacting organisms. For example, plants may carry resistance (R) genes or deploy chemical defences. Aphid saliva contains many proteins that are secreted into host tissues. Subsets of these proteins are predicted to act as effectors, either subverting or triggering host immunity. However, associating particular effectors with virulence or avirulence outcomes presents challenges due to the combinatorial complexity. Here we use defined aphid and host genetics to test for co-segregation of expressed aphid transcripts and proteins with virulent or avirulent phenotypes.

Results: We compared virulent and avirulent pea aphid parental genotypes, and their bulk segregant F1 progeny on Medicago truncatula genotypes carrying or lacking the RAP1 (Resistance to Acyrthosiphon pisum 1) resistance quantitative trait locus. Differential gene expression analysis of whole body and head samples, in combination with proteomics of saliva and salivary glands, enabled us to pinpoint proteins associated with virulence or avirulence phenotypes. There was relatively little impact of host genotype, whereas large numbers of transcripts and proteins were differentially expressed between parental aphids, likely a reflection of their classification as divergent biotypes within the pea aphid species complex. Many fewer transcripts intersected with the equivalent differential expression patterns in the bulked F1 progeny, providing an effective filter for removing genomic background effects. Overall, there were more upregulated genes detected in the F1 avirulent dataset compared with the virulent one. Some genes were differentially expressed both in the transcriptome and in the proteome datasets, with aminopeptidase N proteins being the most frequent differentially expressed family. In addition, a substantial proportion (27%) of salivary proteins lack annotations, suggesting that many novel functions remain to be discovered.

Conclusions: Especially when combined with tightly controlled genetics of both insect and host plant, multi-omics approaches are powerful tools for revealing and filtering candidate lists down to plausible genes for further functional analysis as putative aphid effectors.

背景:植物寄生虫与其宿主之间的相容性是由{引文}两种相互作用生物的基因决定的。例如,植物可能携带抗性(R)基因或采取化学防御措施。蚜虫唾液中含有许多分泌到寄主组织中的蛋白质。据预测,这些蛋白质的子集可作为效应物,颠覆或触发宿主免疫。然而,由于组合的复杂性,将特定效应蛋白与毒力或无毒结果联系起来是一项挑战。在这里,我们利用定义的蚜虫和宿主遗传学来检验表达的蚜虫转录本和蛋白质与毒力或无毒表型的共分离:我们比较了带毒和不带毒的豌豆蚜亲本基因型及其在携带或缺乏RAP1(Resistance to Acyrthosiphon pisum 1)抗性数量性状基因座的Medicago truncatula基因型上的大量分离F1后代。结合唾液和唾液腺的蛋白质组学,我们对全身和头部样本进行了差异基因表达分析,从而确定了与毒力或无毒表型相关的蛋白质。宿主基因型的影响相对较小,而大量转录本和蛋白质在亲蚜之间有不同表达,这可能反映了它们在豌豆蚜种群中被划分为不同的生物型。在批量 F1 后代中,与等效差异表达模式交叉的转录本数量较少,这为消除基因组背景效应提供了有效的过滤器。总体而言,在 F1 无毒性数据集中检测到的上调基因多于有毒性数据集。一些基因在转录组和蛋白质组数据集中都有差异表达,其中氨肽酶 N 蛋白是最常见的差异表达家族。此外,相当一部分(27%)唾液蛋白缺乏注释,这表明许多新功能仍有待发现:结论:多组学方法是揭示和筛选候选基因列表的强大工具,尤其是当与昆虫和寄主植物的严格控制遗传学相结合时,这些候选基因可作为推定的蚜虫效应因子进行进一步的功能分析。
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引用次数: 0
Transcriptome-wide methylated RNA immunoprecipitation sequencing profiling reveals m6A modification involved in response to heat stress in Apostichopus japonicus. 全转录组甲基化 RNA 免疫沉淀测序分析揭示了日本狎鸥鸥对热胁迫反应中涉及的 m6A 修饰。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-11 DOI: 10.1186/s12864-024-10972-1
Yanan Sun, Youmei Sun, Xiaohua He, Siyi Li, Xiaohui Xu, Yanwei Feng, Jianmin Yang, Rubiao Xie, Guohua Sun

Background: Global warming-induced environmental stresses have diverse effects on gene expression and regulation in the life processes of various aquatic organisms. N6 adenylate methylation (m6A) modifications are known to influence mRNA transcription, localization, translation, stability, splicing, and nuclear export, which are pivotal in mediating stress responses. Apostichopus japonicus is a significant species in aquaculture and a representative of benthic organisms in ecosystems, thus there is a growing need for research on its heat stress mechanism.

Results: In this study, m6A-modified whole transcriptome profiles of the respiratory tree tissues of A. japonicus in the control (T18) and high-temperature stress (T32) groups were obtained using MeRIP-seq technology. The results showed that 7,211 common m6A peaks, and 9,459 genes containing common m6A were identified in three replicates T18 and T32 groups. The m6A peaks were found to be highly enriched in the 3' untranslated region, and the common sequence of the m6A peak was also enriched, which was shown as RRACH (R = G or A; H = A, C, or U). A total of 1,200 peaks were identified as significantly differentially enriched in the T32 group compared with the T18 group. Among them, 245 peaks were upregulated and 955 were downregulated, which indicated that high temperature stress significantly altered the methylation pattern of m6A, and there were more demethylation sites in the T32 group. Conjoint analysis of the m6A methylation modification and the transcript expression level (the MeRIP-seq and RNA-seq data) showed co-differentiated 395 genes were identified, which were subsequently divided into four groups with a predominant pattern that more genes with decreased m6A modification and up-regulated expression, including HSP70IV, EIF2AK1, etc. GO enrichment and KEGG analyses of differential m6A peak related genes and co-differentiated genes showed the genes were significantly associated with transcription process and pathways such as protein processing in the endoplasmic reticulum, Wnt signaling pathway, and mTOR signaling pathway, etc. CONCLUSION: The comparisons of m6A modification patterns and conjoint analyses of m6A modification and gene expression profiles suggest that m6A modification was involved in the regulation of heat stress-responsive genes and important functional pathways in A. japonicus in response to high-temperature stress. The study will contribute to elucidate the regulatory mechanism of m6A modification in the response of A. japonicus to environmental stress, as well as the conservation and utilization of sea cucumber resources in the context of environmental changes.

背景:全球变暖引起的环境胁迫对各种水生生物生命过程中的基因表达和调控产生了不同的影响。众所周知,N6腺苷酸甲基化(m6A)修饰可影响mRNA的转录、定位、翻译、稳定性、剪接和核输出,在介导应激反应中起着关键作用。日本芹菜是水产养殖中的重要物种,也是生态系统中底栖生物的代表,因此对其热应激机制的研究需求越来越大:结果:本研究利用 MeRIP-seq 技术获得了对照组(T18)和高温胁迫组(T32)日本竹节虫呼吸树组织的 m6A修饰全转录组图谱。结果表明,在三个重复的 T18 和 T32 组中,共鉴定出 7,211 个常见 m6A 峰和 9,459 个含有常见 m6A 的基因。结果发现,m6A峰高度富集于3'非翻译区,m6A峰的共同序列也被富集,显示为RRACH(R = G或A;H = A、C或U)。与 T18 组相比,共有 1,200 个峰在 T32 组中明显富集。其中,245个峰上调,955个峰下调,这表明高温胁迫明显改变了m6A的甲基化模式,T32组的去甲基化位点较多。对m6A甲基化修饰和转录表达水平(MeRIP-seq和RNA-seq数据)的联合分析表明,共发现了395个共同分化的基因,随后将其分为4组,主要模式是m6A修饰减少而表达上调的基因较多,包括HSP70IV、EIF2AK1等。对差异m6A峰相关基因和共分化基因的GO富集和KEGG分析表明,这些基因与内质网蛋白加工、Wnt信号通路、mTOR信号通路等转录过程和通路显著相关。结论:m6A修饰模式的比较以及m6A修饰和基因表达谱的联合分析表明,m6A修饰参与了日本箭毒对高温胁迫响应基因和重要功能通路的调控。该研究将有助于阐明m6A修饰在日本刺参对环境胁迫响应中的调控机制,以及环境变化背景下海参资源的保护和利用。
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引用次数: 0
Sustained applicability of SARS-CoV-2 variants identification by Sanger Sequencing Strategy on emerging various SARS-CoV-2 Omicron variants in Hiroshima, Japan. 针对日本广岛出现的各种 SARS-CoV-2 Omicron 变异株,采用 Sanger 测序策略持续鉴定 SARS-CoV-2 变异株。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-11 DOI: 10.1186/s12864-024-10973-0
Chanroth Chhoung, Ko Ko, Serge Ouoba, Zayar Phyo, Golda Ataa Akuffo, Aya Sugiyama, Tomoyuki Akita, Hiroshi Sasaki, Tadashi Yamamoto, Kazuaki Takahashi, Junko Tanaka

Background: The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) persists, giving rise to new variants characterized by mutations in the spike protein. However, public data regarding the virus's evolutionary trend is not widely available after the downgrade of coronavirus disease 2019(COVID-19). Therefore, this study aimed to investigate the applicability of an in-house Sanger-based method for identifying SARS-CoV-2 variants, particularly focusing on newly emerged Omicron variants, and updating the epidemiology of COVID-19 during the 8th wave in Hiroshima Prefecture.

Results: A total of 639 saliva samples of individuals who had tested positive for COVID-19, received from Hiroshima City Medical Association Clinical Laboratory Center between February 01, 2023, and March 12, 2024, were included in the study. SARS-CoV-2 variants were identified in 69.3% (443/639) with the mean viral titer 2 × 106 copies/mL, and high viral titer in Omicron variant XBC.1.6* (5 × 108 copies/mL) using RT-qPCR. By partial Spike gene-based sequencing using the Sanger Sequencing strategy, Omicron sub-lineages XXB.1, BA.5, and EG.1 were identified during different periods. A comprehensive phylogenetic analysis of 7383 SARS-CoV-2 strains retrieved from GISAID, collected in Hiroshima from the onset of the COVID-19 pandemic in early 2020 until July 2024, revealed the dynamic evolution of SARS-CoV-2 variants over time. The study found a similar pattern of variant distribution between the full genomes from GISAID, and the partial genomes obtained from our screening strategy during the same period.

Conclusions: Our study revealed that all SARS-CoV-2 viruses circulated in Hiroshima were Omicron variants and their sub-lineages during the 8th wave outbreak in Hiroshima. Persistent molecular surveillance of SARS-CoV-2 is needed for the decision-making and strategic planning of the public promptly. Our study added evidence for the usefulness of SARS-CoV-2 spike gene partial sequencing-based SARS-CoV-2 variant identification strategy for mass screening and molecular surveillance even though the evolution of newly emerged various SARS-CoV-2 Omicron variants.

背景:严重急性呼吸系统综合征冠状病毒2(SARS-CoV-2)持续进化,产生了以尖峰蛋白突变为特征的新变种。然而,在冠状病毒病 2019(COVID-19)降级后,有关该病毒进化趋势的公开数据并不广泛。因此,本研究旨在调查一种基于 Sanger 的内部方法是否适用于识别 SARS-CoV-2 变异体,特别是新出现的 Omicron 变异体,并更新广岛县第 8 次流行期间 COVID-19 的流行病学:研究共纳入了广岛市医学会临床检验中心在 2023 年 2 月 1 日至 2024 年 3 月 12 日期间采集的 639 份 COVID-19 检测呈阳性者的唾液样本。通过 RT-qPCR,在 69.3%(443/639)的患者中发现了 SARS-CoV-2 变异株,平均病毒滴度为 2 × 106 copies/mL,其中 Omicron 变异株 XBC.1.6* 的病毒滴度较高(5 × 108 copies/mL)。通过使用桑格测序策略进行基于 Spike 基因的部分测序,确定了不同时期的 Omicron 亚系 XXB.1、BA.5 和 EG.1。对从 GISAID 中检索到的 7383 株 SARS-CoV-2 株系进行了全面的系统发育分析,这些株系是从 2020 年初 COVID-19 大流行开始到 2024 年 7 月在广岛收集的,分析结果显示了 SARS-CoV-2 变体随时间的动态演变。研究发现,在同一时期,来自 GISAID 的全基因组和通过我们的筛选策略获得的部分基因组之间存在相似的变异分布模式:我们的研究表明,在广岛第 8 次疫情爆发期间,广岛流行的所有 SARS-CoV-2 病毒都是 Omicron 变种及其亚系。需要对 SARS-CoV-2 进行持续的分子监测,以便及时做出公共决策和战略规划。我们的研究为基于 SARS-CoV-2 棘波基因部分测序的 SARS-CoV-2 变异识别策略在大规模筛查和分子监测中的实用性提供了证据,即使新出现的各种 SARS-CoV-2 Omicron 变异也是如此。
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引用次数: 0
Comparative ultrastructural and transcriptomic profile analysis of skin tissues from indigenous, improved meat, and dairy goat breeds. 本土山羊、改良肉羊和奶山羊皮肤组织的超微结构和转录组图谱比较分析。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-11 DOI: 10.1186/s12864-024-10995-8
Xiling Hou, Xianwei Wang, Shuang Hou, Jiangyang Dang, Xinyu Zhang, Jianxiang Tang, Yinghua Shi, Sen Ma, Zejun Xu

Background: High-quality goatskins are valuable byproducts usually produced by indigenous goat breeds with poorer production performance in Asia and Africa. However, the genetic and molecular mechanisms underpinning goatskin's biomechanical properties (e.g., tensile strength) remain elusive. Mechanistic exploration of these traits could greatly aid the genetic improvement and genetic resource conservation of native breeds in these regions. To fulfill this purpose, we collected skin tissues from three goat breeds: Huai goat (HG), a Chinese native variety producing high-quality goatskins; Yudong meat goat (YDMG), a crossbreed of HG and Boer goat; Henan dairy goat (HNDG), a dairy goat breed.

Results: Scanning electronic microscopy analysis of skin tissues found that the collagen fiber diameters, collagen fibril diameters, and crimps significantly differed among the three goat breeds; however, collagen fibril diameters are similar in HG and HNDG. A sum of 230, 775, and 86 differentially expressed genes (DEGs) were identified from YDMG versus HNDG, HG versus HNDG, and YDMG versus HG, respectively. Functional enrichment analysis suggested that signaling pathways involved in fatty acid, retinol, steroid metabolisms, and GO items related to the physical properties of the skin (e.g., collagen-containing extracellular matrix) are significantly overrepresented in DEGs identified from meat versus dairy goats. Furthermore, 106 DEGs (e.g., COL1A1, COL1A2, and SPARC) showed specific expression patterns in HG and YDMG versus HNDG. Items about biophysical features of skin (e.g., extracellular matrix organization and ECM proteoglycans) are markedly enriched. Protein-protein interaction analysis suggested that two growth factors (IGF1 and PDGFD) are latent collagen and other ECM protein expression modulators.

Conclusion: Ultrastructural analysis of goat skin tissues suggested that collagen fibril diameter is not a major factor affecting goatskin quality. Transcriptomic profiles unveiled core genes and associated biological processes potentially involved in regulating goatskin quality. These discoveries shined new light on deeper understanding the mechanisms of hide-related traits in goat and other livestock.

背景:优质山羊皮是一种宝贵的副产品,通常由亚洲和非洲生产性能较差的本土山羊品种生产。然而,山羊皮生物力学特性(如抗张强度)的遗传和分子机制仍然难以捉摸。对这些特性的机理探索将大大有助于这些地区本土品种的遗传改良和遗传资源保护。为此,我们收集了三个山羊品种的皮肤组织:淮山羊(HG)是中国本土品种,生产优质山羊皮;豫东肉用山羊(YDMG)是淮山羊和波尔山羊的杂交品种;河南奶山羊(HNDG)是奶山羊品种:结果:对皮肤组织的扫描电子显微镜分析发现,三个山羊品种的胶原纤维直径、胶原蛋白纤维直径和卷曲度存在显著差异;但HG和HNDG的胶原纤维直径相似。在 YDMG 与 HNDG、HG 与 HNDG 和 YDMG 与 HG 中分别发现了 230、775 和 86 个差异表达基因(DEGs)。功能富集分析表明,涉及脂肪酸、视黄醇、类固醇代谢的信号通路以及与皮肤物理特性(如含胶原的细胞外基质)相关的 GO 项目在肉用山羊与奶用山羊的 DEGs 中的代表性明显偏高。此外,106 个 DEGs(如 COL1A1、COL1A2 和 SPARC)在 HG 和 YDMG 与 HNDG 中显示出特定的表达模式。有关皮肤生物物理特征的项目(如细胞外基质组织和 ECM 蛋白多糖)明显富集。蛋白质-蛋白质相互作用分析表明,两种生长因子(IGF1 和 PDGFD)是潜在的胶原蛋白和其他 ECM 蛋白表达调节因子:山羊皮组织的超微结构分析表明,胶原纤维直径不是影响山羊皮质量的主要因素。转录组图谱揭示了可能参与调节山羊皮质量的核心基因和相关生物过程。这些发现为深入了解山羊和其他家畜兽皮相关性状的机制提供了新的启示。
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引用次数: 0
Insights into the structural features and phylogenetic implications of the complete mitochondrial genome of Fasin rainbow fish (Melanotaenia fasinensis). 洞察法新彩虹鱼(Melanotaenia fasinensis)完整线粒体基因组的结构特征和系统发育意义。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-11 DOI: 10.1186/s12864-024-10996-7
Huria Marnis, Khairul Syahputra, Kadarusman, Jadmiko Darmawan, Imam Civi Cartealy, Sekar Larashati, Wahyu Endra Kusuma, Erma Primanita Hayuningtyas, Bambang Iswanto, Ruzkiah Asaf, Admi Athirah, Arsad Tirta Subangkit, Dwi Wahyudha Wira, Sularto, Indrawati

The Fasin rainbow fish, scientifically named Melanotaenia fasinensis, is highly prized by aquarium enthusiasts for its vibrant colors and adaptability to artificial aquatic environments. This species is endemic to the karst landscape of the Bird's Head region in Papua, Indonesia, and belongs to the family Melanotaeniidae. Discovered relatively recently in 2010, this species was designated as endangered by the International Union for Conservation of Nature (IUCN) in 2021. However, there is currently insufficient data regarding its phylogenetic position. To address this gap, our study employed next-generation sequencing (NGS) to analyze the entire mitochondrial genome of M. fasinensis. The mitochondrial genome comprises 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with a total length of 16,731 base pairs. The base composition of the mitogenome revealed percentages of 27.76% adenine (A), 27.34% thymine (T), 16.15% guanine (G), and 28.75% cytosine (C) residues. Our phylogenetic analysis based on sequence data indicated that all species of the Melanotaeniidae family clustered together on the same branch. Furthermore, the intergeneric and interspecific taxonomic positions were explicit and clear. Phylogenetically, Melanotaeniidae were more closely related to the family Isonidae than to the family Atherinomorus. The phylogenetic position of M. fasinensis was relatively basal within the genus Melanotaenia. This study provides valuable molecular insights for further exploration of the phylogeography and evolutionary history of M. fasinensis and other members of the genus Melanotaenia.

法辛彩虹鱼学名 Melanotaenia fasinensis,因其鲜艳的色彩和对人工水生环境的适应性而备受水族爱好者的青睐。该物种是印尼巴布亚鸟头地区喀斯特地貌的特有物种,属于 Melanotaeniidae 科。该物种最近于 2010 年被发现,并于 2021 年被世界自然保护联盟(IUCN)列为濒危物种。然而,目前有关其系统发育位置的数据不足。为了填补这一空白,我们的研究采用了新一代测序技术(NGS)分析了M. fasinensis的整个线粒体基因组。线粒体基因组包括 13 个蛋白质编码基因、22 个转运 RNA 基因和 2 个核糖体 RNA 基因,总长度为 16,731 碱基对。有丝分裂基因组的碱基组成显示,腺嘌呤(A)占 27.76%,胸腺嘧啶(T)占 27.34%,鸟嘌呤(G)占 16.15%,胞嘧啶(C)占 28.75%。基于序列数据的系统进化分析表明,Melanotaeniidae 家族的所有物种都聚集在同一分支上。此外,属间和种间的分类位置清晰明确。在系统发育上,Melanotaeniidae 与 Isonidae 科的亲缘关系比与 Atherinomorus 科的亲缘关系更为密切。M.fasinensis在Melanotaenia属中的系统发育位置相对较低。这项研究为进一步探讨M. fasinensis和Melanotaenia属其他成员的系统地理学和进化历史提供了宝贵的分子见解。
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引用次数: 0
Mechanism of vitamin C alleviating the immunotoxicity of 17α-methyltestosterone in Carassius auratus. 维生素 C 减轻鲫鱼体内 17α- 甲基睾酮免疫毒性的机制
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-11 DOI: 10.1186/s12864-024-10967-y
Tongyao Li, Zijun Xiong, Yan Liu, Haiyan Zhao, Weiya Rong, Yue Chen, Gen Chen, Lu Cao, Qing Liu, Jing Song, Weiwei Wang, Yu Liu, Xian-Zong Wang, Shao-Zhen Liu

Background: In recent years, the use of endocrine-disrupting chemicals (EDCs) has become increasingly common, leading to severe environmental pollution and harm to aquatic organisms. 17α-Methyltestosterone (MT) is a synthetic androgen that can cause immunotoxicity in aquaculture, affecting fish health. To address this issue, this study aimed to investigate the effect of Vitamin C (VC) on MT-induced immunotoxicity and determine the optimal VC supplementation.

Results: Carassius auratus was exposed to 50 ng/L MT and treated with 25, 50, and 150 mg/kg VC for 7, 14, and 21 d. Morphological indicators, histological characteristics, hepatic antioxidant capacity, and immune-related gene expression were analyzed. Additionally, RNA-seq was performed on the liver tissues of the control, MT, and MT + 25 mg/kg VC groups after 21 d. Results showed that, MT treatment significantly increased liver malondialdehyde content and inhibited immune-related gene expression (TNF-α, IL-8, INF-γ, IL-10, Caspase-9, and IGF-I), causing oxidative stress and immunotoxicity, leading to hepatic steatosis. However, supplementation with 25-50 mg/kg VC effectively alleviated the MT-induced damage to the hepatic structure and immune system. RNA-seq revealed significant enrichment of differentially expressed genes in multiple signaling pathways, including the mTOR, MAPK, and Wnt pathways.

Conclusions: In summary, 25-50 mg/kg VC alleviated inhibitory effect of MT on immune-related genes in C. auratus liver, reducing MT-induced tissue damage. VC not only alleviated inflammation, oxidative stress, and immunotoxicity induced by MT through the regulation of the mTOR, MAPK, and Wnt signaling pathways, but also indirectly enhanced cellular antioxidant defense mechanisms by regulating the NRF2 pathway. This provides a theoretical basis for VC application in aquaculture, improving fish health and increasing efficiency.

背景:近年来,干扰内分泌的化学品(EDCs)的使用越来越普遍,导致了严重的环境污染和对水生生物的危害。17α-甲基睾酮(17α-Methyltestosterone,MT)是一种人工合成的雄性激素,在水产养殖中可引起免疫毒性,影响鱼类健康。针对这一问题,本研究旨在探讨维生素 C(VC)对 MT 诱导的免疫毒性的影响,并确定最佳的 VC 补充量:结果:研究人员将鲫鱼暴露于 50 ng/L MT,并分别用 25、50 和 150 mg/kg VC 处理 7、14 和 21 d。结果表明,MT能显著增加肝脏丙二醛含量,抑制免疫相关基因(TNF-α、IL-8、INF-γ、IL-10、Caspase-9和IGF-I)的表达,从而引起氧化应激和免疫毒性,导致肝脏脂肪变性。然而,补充 25-50 mg/kg VC 能有效缓解 MT 诱导的肝结构和免疫系统损伤。RNA-seq揭示了多种信号通路中差异表达基因的显著富集,包括mTOR、MAPK和Wnt通路:综上所述,25-50 毫克/千克 VC 可减轻 MT 对乌龟肝脏免疫相关基因的抑制作用,减少 MT 引起的组织损伤。VC不仅能通过调节mTOR、MAPK和Wnt信号通路缓解MT诱导的炎症、氧化应激和免疫毒性,还能通过调节NRF2通路间接增强细胞的抗氧化防御机制。这为将 VC 应用于水产养殖、改善鱼类健康和提高效率提供了理论依据。
{"title":"Mechanism of vitamin C alleviating the immunotoxicity of 17α-methyltestosterone in Carassius auratus.","authors":"Tongyao Li, Zijun Xiong, Yan Liu, Haiyan Zhao, Weiya Rong, Yue Chen, Gen Chen, Lu Cao, Qing Liu, Jing Song, Weiwei Wang, Yu Liu, Xian-Zong Wang, Shao-Zhen Liu","doi":"10.1186/s12864-024-10967-y","DOIUrl":"10.1186/s12864-024-10967-y","url":null,"abstract":"<p><strong>Background: </strong>In recent years, the use of endocrine-disrupting chemicals (EDCs) has become increasingly common, leading to severe environmental pollution and harm to aquatic organisms. 17α-Methyltestosterone (MT) is a synthetic androgen that can cause immunotoxicity in aquaculture, affecting fish health. To address this issue, this study aimed to investigate the effect of Vitamin C (VC) on MT-induced immunotoxicity and determine the optimal VC supplementation.</p><p><strong>Results: </strong>Carassius auratus was exposed to 50 ng/L MT and treated with 25, 50, and 150 mg/kg VC for 7, 14, and 21 d. Morphological indicators, histological characteristics, hepatic antioxidant capacity, and immune-related gene expression were analyzed. Additionally, RNA-seq was performed on the liver tissues of the control, MT, and MT + 25 mg/kg VC groups after 21 d. Results showed that, MT treatment significantly increased liver malondialdehyde content and inhibited immune-related gene expression (TNF-α, IL-8, INF-γ, IL-10, Caspase-9, and IGF-I), causing oxidative stress and immunotoxicity, leading to hepatic steatosis. However, supplementation with 25-50 mg/kg VC effectively alleviated the MT-induced damage to the hepatic structure and immune system. RNA-seq revealed significant enrichment of differentially expressed genes in multiple signaling pathways, including the mTOR, MAPK, and Wnt pathways.</p><p><strong>Conclusions: </strong>In summary, 25-50 mg/kg VC alleviated inhibitory effect of MT on immune-related genes in C. auratus liver, reducing MT-induced tissue damage. VC not only alleviated inflammation, oxidative stress, and immunotoxicity induced by MT through the regulation of the mTOR, MAPK, and Wnt signaling pathways, but also indirectly enhanced cellular antioxidant defense mechanisms by regulating the NRF2 pathway. This provides a theoretical basis for VC application in aquaculture, improving fish health and increasing efficiency.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"25 1","pages":"1068"},"PeriodicalIF":3.5,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11552423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142614342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Targeting splicing for hematological malignancies therapy. 以剪接为靶点,治疗血液恶性肿瘤。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-11 DOI: 10.1186/s12864-024-10975-y
Monika Szelest, Krzysztof Giannopoulos

Alterations in splicing patterns of leukemic cells have a functional impact and influence most cellular processes since aberrantly spliced isoforms can provide a proliferative advantage, enable to evade apoptosis, induce metabolic reprogramming, change cell signaling and antitumor immune response, or develop drug resistance. In this Review, we first characterize the general mechanism of mRNA processing regulation with a focus on the role of splicing factors, which are commonly mutated in blood neoplasms. Next, we provide a comprehensive summary on the current understanding of alternative splicing events, which confer resistance to targeted treatment strategies and immunotherapy. We introduce the functional consequences of mis-spliced variants (CD19-∆ex2, CD22-∆ex2, CD22-∆ex5-6, CD33-∆ex2, PIK3CD-S, BCR-ABL35INS, BIM-γ, FPGS-8PR, dCK-∆ex2-3, and SLC29A1-∆ex13) production in leukemic cells. Of therapeutic relevance, we summarize novel strategies focused on pharmacological correction of aberrant splicing, including small-molecule splicing modulators and splice-switching oligonucleotides. We also include the findings of recent preclinical investigation of the antisense strategies based on modified oligonucleotides. Finally, we discuss the potential of emerging combination therapies for the treatment of hematological disorders with disrupted splicing.

白血病细胞剪接模式的改变会产生功能性影响,并对大多数细胞过程产生影响,因为剪接异常的异构体可提供增殖优势,使细胞逃避凋亡,诱导代谢重编程,改变细胞信号传导和抗肿瘤免疫反应,或产生耐药性。在这篇综述中,我们首先描述了 mRNA 加工调控的一般机制,重点是血液肿瘤中常见的剪接因子的作用。接下来,我们全面总结了目前对替代剪接事件的理解,这些事件会使患者对靶向治疗策略和免疫疗法产生耐药性。我们介绍了白血病细胞中错误剪接变体(CD19-Δex2、CD22-Δex2、CD22-Δex5-6、CD33-Δex2、PIK3CD-S、BCR-ABL35INS、BIM-γ、FPGS-8PR、dCK-Δex2-3 和 SLC29A1-Δex13)产生的功能性后果。在治疗方面,我们总结了以药物纠正剪接异常为重点的新策略,包括小分子剪接调节剂和剪接转换寡核苷酸。我们还介绍了基于修饰寡核苷酸的反义策略的最新临床前研究结果。最后,我们讨论了新出现的联合疗法在治疗剪接紊乱的血液病方面的潜力。
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引用次数: 0
The complete mitochondrial genome assembly of Capsicum pubescens reveals key evolutionary characteristics of mitochondrial genes of two Capsicum subspecies. 短辣椒线粒体基因组的完整组装揭示了两个辣椒亚种线粒体基因的关键进化特征。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-11-11 DOI: 10.1186/s12864-024-10985-w
Lin Li, Huizhen Fu, Muhammad Ahsan Altaf, Zhiwei Wang, Xu Lu

Background: Pepper (Capsicum pubescens), one of five domesticated pepper species, has unique characteristics, such as numerous hairs on the epidermis of its leaves and stems, black seeds, and vibrant purple flowers. To date, no studies have reported on the complete assembly of the mitochondrial genome (mitogenome) of C. pubescens. Understanding the mitogenome is crucial for further research on C. pubescens.

Results: In our study, we successfully assembled the first mitogenome of C. pubescens, which was assigned the GenBank accession number OP957066. This mitogenome has a length of 454,165 bp and exhibits the typical circular structure observed in most mitogenomes. We annotated a total of 70 genes, including 35 protein-coding genes (PCGs), 30 tRNA genes, 3 rRNA genes, and 2 pseudogenes. Compared to the other three pepper mitogenomes (KJ865409, KJ865410, and MN196478), C. pubescens OP957066 exhibited four unique PCGs (atp4, atp8, mttB, and rps1), while two PCGs (rpl10 and rps3) were absent. Notably, each of the three pepper mitogenomes from C. annuum (KJ865409, KJ865410, and MN196478) experienced the loss of four PCGs (atp4, atp8, mttB, and rps1). To further explore the evolutionary relationships, we reconstructed a phylogenetic tree using the mitogenomes of C. pubescens and fourteen other species. Structural comparison and synteny analysis of the above four pepper mitogenomes revealed that C. pubescens shares high sequence similarity with KJ865409 and that C. pubescens has rearranged with the other three pepper mitogenomes. Interestingly, we observed 72 similar sequences between the mitochondrial and chloroplast genomes, which accounted for 12.60% of the mitogenome, with a total length of 57,207 bp. These sequences encompassed 12 tRNA genes and the rRNA gene (rrn18). Remarkably, selective pressure analysis suggested that the nad5 gene underwent obvious positive selection. Furthermore, a single-base mutation in three genes (nad1, nad2, and nad4) resulted in an amino acid change.

Conclusion: This study provides a high-quality mitogenome of pepper, providing valuable molecular data for future investigations into the exchange of genetic information between pepper organelle genomes.

背景:辣椒(Capsicum pubescens)是五种驯化的辣椒品种之一,具有独特的特征,如叶和茎的表皮上有许多毛、黑色的种子和鲜艳的紫色花朵。迄今为止,还没有任何研究报告完整地组装了 C. pubescens 的线粒体基因组(有丝分裂基因组)。了解有丝分裂基因组对进一步研究 C. pubescens 至关重要:在我们的研究中,我们成功地组装了 C. pubescens 的第一个有丝分裂基因组,该基因组的 GenBank 登录号为 OP957066。该有丝分裂基因组长度为 454,165 bp,具有大多数有丝分裂基因组的典型环状结构。我们共注释了 70 个基因,包括 35 个蛋白质编码基因(PCGs)、30 个 tRNA 基因、3 个 rRNA 基因和 2 个假基因。与其他三个辣椒有丝分裂基因组(KJ865409、KJ865410 和 MN196478)相比,C. pubescens OP957066 表现出四个独特的 PCG(atp4、atp8、mttB 和 rps1),而两个 PCG(rpl10 和 rps3)则不存在。值得注意的是,来自 C. annuum 的三个辣椒有丝分裂基因组(KJ865409、KJ865410 和 MN196478)中的每一个都经历了四个 PCG(atp4、atp8、mttB 和 rps1)的缺失。为了进一步探索其进化关系,我们利用 C. pubescens 和其他 14 个物种的有丝分裂基因组重建了一棵系统发生树。对上述四个辣椒有丝分裂基因组的结构比较和同源关系分析表明,C. pubescens与KJ865409具有高度的序列相似性,并且C. pubescens与其他三个辣椒有丝分裂基因组发生了重排。有趣的是,我们在线粒体基因组和叶绿体基因组之间观察到 72 个相似序列,占有丝分裂基因组的 12.60%,总长度为 57,207 bp。这些序列包括 12 个 tRNA 基因和 rRNA 基因(rrn18)。值得注意的是,选择压力分析表明,nad5 基因经历了明显的正选择。此外,三个基因(nad1、nad2 和 nad4)的单碱基突变导致了氨基酸的改变:本研究提供了高质量的辣椒有丝分裂基因组,为今后研究辣椒细胞器基因组之间的遗传信息交流提供了宝贵的分子数据。
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引用次数: 0
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BMC Genomics
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