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Sequence Flow: interactive web application for visualizing partial order alignments. 序列流:可视化偏序排列的交互式网络应用程序。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-16 DOI: 10.1186/s12864-024-10886-y
Krzysztof Zdąbłasz, Anna Lisiecka, Norbert Dojer

Background: Multiple sequence alignment (MSA) has proven extremely useful in computational biology, especially in inferring evolutionary relationships via phylogenetic analysis and providing insight into protein structure and function. An alternative to the standard MSA model is partial order alignment (POA), in which aligned sequences are represented as paths in a graph rather than rows in a matrix. While the POA model has proven useful in several applications (e.g. sequencing reads assembly and pangenome structure exploration), we lack efficient visualization tools that could highlight its advantages.

Results: We propose Sequence Flow - a web application designed to address the above problem. Sequence Flow presents the POA as a Sankey diagram, a kind of graph visualisation typically used for graphs representing flowcharts. Sequence Flow enables interactive alignment exploration, including fragment selection, highlighting a selected group of sequences, modification of the position of graph nodes, structure simplification etc. After adjustment, the visualization can be saved as a high-quality graphic file. Thanks to the use of SanKEY.js - a JavaScript library for creating Sankey diagrams, designed specifically to visualize POAs, Sequence Flow provides satisfactory performance even with large alignments.

Conclusions: We provide Sankey diagram-based POA visualization tools for both end users (Sequence Flow) and bioinformatic software developers (SanKEY.js). Sequence Flow webservice is available at https://sequenceflow.mimuw.edu.pl/ . The source code for SanKEY.js is available at https://github.com/Krzysiekzd/SanKEY.js and for Sequence Flow at https://github.com/Krzysiekzd/SequenceFlow .

背景:事实证明,多序列比对(MSA)在计算生物学中非常有用,尤其是在通过系统发育分析推断进化关系以及深入了解蛋白质结构和功能方面。标准 MSA 模型的另一种选择是偏序比对(POA),其中比对的序列表示为图中的路径而不是矩阵中的行。虽然 POA 模型已在多个应用中被证明非常有用(如测序读数组装和庞基因组结构探索),但我们缺乏能突出其优势的高效可视化工具:结果:我们提出了 "序列流"(Sequence Flow)--一个旨在解决上述问题的网络应用程序。Sequence Flow将POA呈现为Sankey图,这是一种图形可视化,通常用于表示流程图的图形。Sequence Flow 可以进行交互式比对探索,包括片段选择、突出显示一组选定的序列、修改图节点的位置、简化结构等。调整后,可视化效果可以保存为高质量的图形文件。由于使用了 SanKEY.js(一个用于创建 Sankey 图的 JavaScript 库,专为 POA 可视化而设计),Sequence Flow 即使在处理大型排列时也能提供令人满意的性能:我们为终端用户(Sequence Flow)和生物信息软件开发人员(SanKEY.js)提供了基于桑基图的 POA 可视化工具。Sequence Flow 网络服务可在 https://sequenceflow.mimuw.edu.pl/ 上获取。SanKEY.js 的源代码见 https://github.com/Krzysiekzd/SanKEY.js,Sequence Flow 的源代码见 https://github.com/Krzysiekzd/SequenceFlow。
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引用次数: 0
Comprehensive evaluation and guidance of structural variation detection tools in chicken whole genome sequence data. 鸡全基因组序列数据中结构变异检测工具的综合评估与指导。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-16 DOI: 10.1186/s12864-024-10875-1
Cheng Ma, Xian Shi, Xuzhen Li, Ya-Ping Zhang, Min-Sheng Peng

Background: Structural variations (SVs) are widespread across genome and have a great impact on evolution, disease, and phenotypic diversity. Despite the development of numerous bioinformatic tools, commonly referred to as SV callers, tailored for detecting SVs using whole genome sequence (WGS) data and employing diverse algorithms, their performance necessitates rigorous evaluation with real data and validated SVs. Moreover, a considerable proportion of these tools have been primarily designed and optimized using human genome data. Consequently, their applicability and performance in Avian species, characterized by smaller genomes and distinct genomic architectures, remain inadequately assessed.

Results: We performed a comprehensive assessment of the performance of ten widely used SV callers using population-level real genomic data with the validated five common types of SVs. The performance of SV callers varies with the types and sizes of SVs. As compared with other tools, GRIDSS, Lumpy, Wham, and Manta present better detection accuracy. Pindel can detect more small SVs than others. CNVnator and CNVkit can detect more medium and large copy number variations. Given the poor consistency among different SV callers, the combination calling strategy is not recommended. All tools show poor ability in the detection of insertions (especially with size > 150 bp). At least 50× read depth is required to detect more than 80% of the SVs for most tools.

Conclusions: This study highlights the importance and necessity of using real sequencing data, rather than simulated data only, with validated SVs for SV caller evaluation. Some practical guidance and suggestions are provided for SV detection in future researches.

背景:结构变异(SV)广泛存在于基因组中,对进化、疾病和表型多样性有很大影响。尽管开发出了许多生物信息学工具(通常称为 SV 调用器),这些工具专为利用全基因组序列(WGS)数据检测 SV 而设计,并采用了多种算法,但它们的性能仍需要利用真实数据和经过验证的 SV 进行严格评估。此外,这些工具中有相当一部分主要是利用人类基因组数据设计和优化的。因此,它们在禽类物种中的适用性和性能仍未得到充分评估,而禽类物种的特点是基因组较小,基因组结构独特:结果:我们利用经过验证的五种常见 SV 的群体级真实基因组数据,对十种广泛使用的 SV 调用器的性能进行了全面评估。SV 调用器的性能随 SV 的类型和大小而变化。与其他工具相比,GRIDSS、Lumpy、Wham 和 Manta 的检测准确率更高。与其他工具相比,Pindel 能检测到更多的小 SV。CNVnator 和 CNVkit 能检测到更多的中型和大型拷贝数变异。鉴于不同 SV 调用器之间的一致性较差,因此不建议采用组合调用策略。所有工具在检测插入因子(尤其是大小大于 150 bp 的插入因子)方面的能力都很差。大多数工具至少需要 50 倍的读取深度才能检测到 80% 以上的 SV:本研究强调了使用真实测序数据(而非模拟数据)和经过验证的 SV 进行 SV 调用评估的重要性和必要性。为今后的研究提供了一些 SV 检测的实用指导和建议。
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引用次数: 0
Transcriptome sequencing analysis of overexpressed SikCDPK1 in tobacco reveals mechanisms of cold stress response. 烟草中过表达的 SikCDPK1 的转录组测序分析揭示了冷胁迫响应机制。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-16 DOI: 10.1186/s12864-024-10801-5
Guangzhen Shi, Xinxia Zhu

Background: Cold is a significant limiting factor in productivity, particularly in northwestern and eastern China. Calcium-Dependent Protein Kinases (CDPKs), a primary calcium signaling sensor in plants, play an important role in their response to cold. Snow lotus (Sasussured involucrata Kar L) is a plant that thrives in harsh climates and grows in northwest China. However, there were no reports on the transcriptome of OE-SikCDPK1 transgenic tobacco in response to cold.

Results: When exposed to cold stress, OE-SikCDPK1 plants displayed a cold-tolerant phenotype compared to non-transgenic tobacco. Under cold conditions, relative water content reduced, relative conductivity increased, malondialdehyde levels rose, and cold-responsive gene expression increased. The OE-SikCDPK1 gene and non-transgenic tobacco were employed for research purposes. The transcriptome of leaves was sequenced using the HISAT2 sequencing platform, and the data were used to examine gene function annotation and differentially expressed genes (DEGs). 53,022 DEGs in tobacco leaves under cold treatment were obtained. The GO enrichment results revealed that it was enriched for biological-process, defense response and other processes under cold stress. The KEGG pathway enrichment analysis revealed that the metabolic pathways of significant enrichment of DEGs under cold stress mainly involved MAPK signaling pathway transduction. The transcription factor identification results showed that the transcription factors with the largest number of differential expressions under cold treatment were mainly from WRKY, AP2, MYB, bHLH, NAC and other transcription factor families.

Conclusion: The cold tolerance mechanism of snow lotus SikCDPK1 was comprehensively analyzed at the transcriptional level for the first time using RNA-seq technology. This study demonstrates that SikCDPK1 can respond to cold by participating in the MAPK signaling pathway and regulating the expression levels of transcription factors, including WRKY, AP2, MYB, bHLH, and NAC. These results offer valuable insights for further exploration of the cold tolerance mechanism associated with SikCDPK1.

背景:寒冷是限制生产力的一个重要因素,尤其是在中国西北部和东部地区。钙依赖蛋白激酶(CDPKs)是植物体内主要的钙信号传感器,在植物对寒冷的反应中发挥着重要作用。雪莲(Sasussured involucrata Kar L)是一种在恶劣气候条件下生长的植物,生长在中国西北地区。然而,目前还没有关于 OE-SikCDPK1 转基因烟草对寒冷反应的转录组的报道:结果:与非转基因烟草相比,OE-SikCDPK1植株在遭受冷胁迫时表现出耐寒表型。在寒冷条件下,相对含水量降低,相对电导率升高,丙二醛水平升高,冷响应基因表达增加。研究采用了 OE-SikCDPK1 基因和非转基因烟草。利用 HISAT2 测序平台对叶片转录组进行了测序,并利用这些数据研究了基因功能注释和差异表达基因(DEGs)。结果表明,在冷处理条件下,烟草叶片中有 53022 个 DEGs。GO富集结果显示,烟草叶片在冷胁迫下富集了生物过程、防御反应和其他过程。KEGG通路富集分析表明,冷胁迫下DEGs显著富集的代谢通路主要涉及MAPK信号通路的转导。转录因子鉴定结果表明,冷处理下差异表达最多的转录因子主要来自WRKY、AP2、MYB、bHLH、NAC等转录因子家族:结论:利用 RNA-seq 技术首次在转录水平上全面分析了雪莲花 SikCDPK1 的耐寒机制。该研究表明,SikCDPK1可通过参与MAPK信号通路和调节转录因子(包括WRKY、AP2、MYB、bHLH和NAC)的表达水平来应对寒冷。这些结果为进一步探索与 SikCDPK1 相关的耐寒机制提供了宝贵的见解。
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引用次数: 0
Genomic epidemiology of ceftriaxone-resistant non-typhoidal Salmonella enterica strain in China. 中国耐头孢曲松非伤寒沙门氏菌肠道菌株的基因组流行病学。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-16 DOI: 10.1186/s12864-024-10890-2
Danni Bao, Lei Chen, Weiwei Shen, Xiaohong Xu, Lifei Zhu, Yizhang Wang, Yanhong Wu, Xianhong He, Fengjiao Zhu, Hongzhang Li

Non-typhoidal Salmonella (NTS) is one of the top causes of diarrhea worldwide. Ceftriaxone is commonly recommended as the initial treatment option for Salmonella infections due to its antibacterial effectiveness. The objective of this study was to investigate the molecular epidemiological characteristics of NTS and to compare the phenotypic and genotypic profiles of antimicrobial resistance in multidrug-resistant Salmonella strains by sequencing 329 NTS strains collected from a county-level hospital between 2018 and 2021. Multi-locus sequence typing (MLST), antimicrobial resistance genes and plasmid types were identified by BacWGSTdb 2.0 webserver. Phylogenetic analysis of all NTS strains was carried out using Snippy and Gubbins software. The transferability of ceftriaxone resistant plasmids was confirmed through plasmid conjugation assays, and verified by S1-PFGE-Southern blot assays. The predominant serotypes among all NTS strains were Typhimurium (161/329), Enteritidis (49/329) and London (45/329). The most common sequence type observed was ST34 (86/329), followed by ST19 (72/329) and ST11 (47/329). The antimicrobial resistance of Salmonella to a wide range of antimicrobials showed an overall increase. Out of these 37 (11.24%) ceftriaxone-resistant strains, with the majority of them (33/37) being blaCTX-M. The predominant plasmid types identified were IncHI2 (14/21) and IncI1 (6/21), ranging in size from 70 kb to 360 kb. The conjugation efficiency was calculated with the high conjugation efficiency of 1.1 × 10- 5 to 9.3 × 10- 2. The strains varied widely, ranging from 3 to 45,024 single nucleotide polymorphisms (SNPs). There are close linkages observed among the predominant lineage, with an average of 78 SNPs between each pair of ST34 strains. The findings contribute to our understanding of the transmission and resistance mechanisms of multidrug-resistant Salmonella, thereby facilitating the development of effective control strategies.

非伤寒沙门氏菌(NTS)是导致全球腹泻的主要原因之一。头孢曲松因其抗菌效果显著,通常被推荐作为沙门氏菌感染的初始治疗方案。本研究旨在调查NTS的分子流行病学特征,并通过对2018年至2021年期间从一家县级医院收集的329株NTS菌株进行测序,比较多重耐药沙门氏菌菌株抗菌药耐药性的表型和基因型特征。多焦点序列分型(MLST)、抗菌药耐药基因和质粒类型由BacWGSTdb 2.0网络服务器鉴定。使用 Snippy 和 Gubbins 软件对所有 NTS 菌株进行了系统发育分析。通过质粒连接试验确认了耐头孢曲松质粒的可转移性,并通过 S1-PFGE-Southern 印迹试验进行了验证。在所有 NTS 菌株中,最主要的血清型是 Typhimurium(161/329)、Enteritidis(49/329)和 London(45/329)。最常见的序列类型是 ST34(86/329),其次是 ST19(72/329)和 ST11(47/329)。沙门氏菌对多种抗菌药物的耐药性总体呈上升趋势。其中 37 株(11.24%)对头孢曲松耐药,大部分(33/37)为 blaCTX-M。鉴定出的主要质粒类型为 IncHI2(14/21)和 IncI1(6/21),大小从 70 kb 到 360 kb 不等。计算出的共轭效率为 1.1 × 10- 5 至 9.3 × 10- 2。菌株差异很大,单核苷酸多态性(SNPs)从 3 个到 45 024 个不等。在主要菌系之间观察到了密切的联系,每对 ST34 菌株之间平均有 78 个 SNPs。这些发现有助于我们了解耐多药沙门氏菌的传播和耐药机制,从而促进有效控制策略的制定。
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引用次数: 0
HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences. HiCDiffusion - 基于扩散增强的变压器,根据 DNA 序列预测染色质相互作用。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-15 DOI: 10.1186/s12864-024-10885-z
Mateusz Chiliński, Dariusz Plewczynski

Prediction of chromatin interactions from DNA sequence has been a significant research challenge in the last couple of years. Several solutions have been proposed, most of which are based on encoder-decoder architecture, where 1D sequence is convoluted, encoded into the latent representation, and then decoded using 2D convolutions into the Hi-C pairwise chromatin spatial proximity matrix. Those methods, while obtaining high correlation scores and improved metrics, produce Hi-C matrices that are artificial - they are blurred due to the deep learning model architecture. In our study, we propose the HiCDiffusion, sequence-only model that addresses this problem. We first train the encoder-decoder neural network and then use it as a component of the diffusion model - where we guide the diffusion using a latent representation of the sequence, as well as the final output from the encoder-decoder. That way, we obtain the high-resolution Hi-C matrices that not only better resemble the experimental results - improving the Fréchet inception distance by an average of 11 times, with the highest improvement of 56 times - but also obtain similar classic metrics to current state-of-the-art encoder-decoder architectures used for the task.

根据 DNA 序列预测染色质相互作用是过去几年中的一项重大研究挑战。目前已经提出了几种解决方案,其中大多数都是基于编码器-解码器架构,即先对一维序列进行卷积,然后编码成潜在表示,再利用二维卷积解码成染色质空间邻近度 Hi-C 成对矩阵。这些方法虽然能获得较高的相关性得分和改进的指标,但产生的 Hi-C 矩阵是人为的--由于深度学习模型架构的原因,它们是模糊的。在我们的研究中,我们提出了纯序列模型 HiCDiffusion 来解决这一问题。我们首先训练编码器-解码器神经网络,然后将其作为扩散模型的一个组成部分--在此模型中,我们使用序列的潜在表示以及编码器-解码器的最终输出来引导扩散。这样,我们得到的高分辨率 Hi-C 矩阵不仅更接近实验结果--弗雷谢特阈值距离平均提高了 11 倍,最高提高了 56 倍--而且还获得了与当前用于该任务的最先进编码器-解码器架构相似的经典指标。
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引用次数: 0
Evidence of true seed transmissible nature of turnip mosaic virus in mustard species. 证明萝卜花叶病毒在芥菜品种中具有真正的种子传播特性。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-15 DOI: 10.1186/s12864-024-10866-2
Pankhuri Singhal, Damini Diksha, Virendra Kumar Baranwal, Naveen Singh, Amalendu Ghosh

Mustard is a commercial oilseed crop worldwide infected by a highly infectious turnip mosaic virus (TuMV). In the experimental field at ICAR-IARI, New Delhi, in 2022, a 100% incidence of TuMV infection was observed in brown, black and yellow mustard. A very low aphid population suggested the possibility of seed transmission. Earlier, the virus genome was characterized by high throughput sequencing and it was a recombinant of World-B and Asian-BR isolates. The presence of TuMV in immature seeds was confirmed in eight field-grown genotypes via RT-PCR using CP-specific primers designed from the same genome sequence. TuMV was found to be localized in embryo and cotyledon, indicating its true seed-borne nature. Presence of TuMV was also confirmed by RT-PCR in the grow out plants from seeds of field grown eight infected genotypes and 9 genotypes collected from seed stock, that were grown in an aphid-free growth chamber. Further, out of 24 seedlings of Pusa Gold (seed stock) and Pusa Karishma (seeds from field grown plants), 20 and 17 seedlings were found infected with TuMV, respectively. The internally seed-borne nature of the virus leads to its early establishment at the seedling stage, leading to stunting and leaf-puckering symptoms in the progeny plants. This study is the first evidence of seed embryo infection and seedling transmission of TuMV of all the three species of mustard plants (brown, black and yellow mustard). Seed transmission of TuMV in mustard genotypes have implications for the seed exchange programme of mustard seeds.

芥菜是世界上受高传染性芜菁花叶病毒(TuMV)感染的一种商业油籽作物。2022 年,在新德里 ICAR-IARI 的试验田里,棕色、黑色和黄色芥菜的 TuMV 感染率均为 100%。蚜虫数量极少,这表明病毒有可能通过种子传播。早些时候,通过高通量测序确定了病毒基因组的特征,它是世界-B 和亚洲-BR 分离物的重组体。使用根据相同基因组序列设计的 CP 特异引物,通过 RT-PCR 在八个田间种植的基因型中证实了未成熟种子中存在 TuMV。结果发现,TuMV 定位于胚和子叶中,这表明它是真正的种子传播病毒。在无蚜虫生长室中生长的 8 个田间种植的受感染基因型和 9 个从种子库中收集的基因型的种子中,通过 RT-PCR 也证实了 TuMV 的存在。此外,在 Pusa Gold(种子库)和 Pusa Karishma(田间种植的种子)的 24 株幼苗中,分别发现 20 株和 17 株幼苗感染了 TuMV。该病毒的内部种子传播特性导致其在幼苗期就已形成,并导致后代植株出现发育不良和叶片皱缩症状。这项研究首次证明了 TuMV 在三种芥菜植物(褐芥、黑芥和黄芥)中的种胚感染和幼苗传播。芥菜基因型中 TuMV 的种子传播对芥菜种子交换计划具有重要意义。
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引用次数: 0
Dynamic chromatin accessibility and transcriptome changes following PDGF-BB treatment of bone-marrow derived mesenchymal stem cells. 骨髓间充质干细胞经 PDGF-BB 处理后染色质可及性和转录组的动态变化。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-15 DOI: 10.1186/s12864-024-10861-7
Sheng Liu, Xiaona Chu, Jill L Reiter, Xuhong Yu, Fang Fang, Patrick McGuire, Hongyu Gao, Yunlong Liu, Jun Wan, Yue Wang

Background: Mesenchymal stem cells (MSCs) are multipotent stem cells that are under investigation for use in clinical trials because they are capable of self-renewal and differentiating into different cell types under defined conditions. Nonetheless, the therapeutic effects of MSCs have been constrained by low engraftment rates, cell fusion, and cell survival. Various strategies have been explored to improve the therapeutic efficacy of MSCs, with platelet-derived growth factor (PDGF)-BB emerging as a promising candidate. To enhance our comprehension of the impact of PDGF-BB on the gene expression profile and chromosomal accessibility of MSCs, RNA-sequencing and analysis of chromatin accessibility profiles were conducted on three human primary MSCs in culture, both with and without stimulation by PDGF-BB.

Results: Integrative analysis of gene expression and chromatin accessibility demonstrated that PDGF-BB treatment modified the chromatin accessibility landscape, marking regions for activation or repression through the AP-1 family transcription factors TEAD, CEBP, and RUNX2. These changes in AP-1 transcription factor expression, in turn, led to cell proliferation and differentiation potential towards osteoblasts, adipocytes, or chondrocytes. The degree of MSC differentiation varies among cells isolated from different donors. The presence of an enrichment of exosome-related genes is also noted among all the differentially expressed genes.

Conclusions: In conclusion, the observed changes in AP-1 transcription factor expression not only induced cellular proliferation and differentiation, but also revealed variations in the degree of MSC differentiation based on donor-specific differences. Moreover, the enrichment of exosome-related genes among differentially expressed genes suggests a potential significant role for PDGF-BB in facilitating intercellular communication.

背景:间充质干细胞(MSCs)是一种多能干细胞,能够自我更新并在特定条件下分化成不同类型的细胞,因此正被研究用于临床试验。然而,间充质干细胞的治疗效果一直受到接种率、细胞融合和细胞存活率低的制约。为了提高间充质干细胞的治疗效果,人们探索了各种策略,其中血小板衍生生长因子(PDGF)-BB 是一种很有前景的候选药物。为了进一步了解 PDGF-BB 对间叶干细胞基因表达谱和染色体可及性的影响,我们对培养中的三种人类原代间叶干细胞进行了 RNA 测序和染色质可及性谱分析,包括有 PDGF-BB 刺激和无 PDGF-BB 刺激的情况:基因表达和染色质可及性的综合分析表明,PDGF-BB 处理改变了染色质的可及性,通过 AP-1 家族转录因子 TEAD、CEBP 和 RUNX2 标记了激活或抑制区域。AP-1转录因子表达的这些变化反过来又导致了细胞的增殖和向成骨细胞、脂肪细胞或软骨细胞分化的潜力。从不同供体分离的间充质干细胞的分化程度各不相同。在所有差异表达的基因中,还发现了外泌体相关基因的富集:总之,观察到的 AP-1 转录因子表达变化不仅诱导了细胞增殖和分化,还揭示了间充质干细胞分化程度因供体特异性差异而不同。此外,外泌体相关基因在差异表达基因中的富集表明,PDGF-BB 在促进细胞间通讯方面可能起着重要作用。
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引用次数: 0
Identification of sex-specific markers using genome re-sequencing in the blunt snout bream (Megalobrama amblycephala). 利用基因组重测序鉴定钝口鳊(Megalobrama amblycephala)的性别特异性标记。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-15 DOI: 10.1186/s12864-024-10884-0
Yuye Fu, Lifei Luo, Shilong Wang, Yue Yu, Yao Wang, Zexia Gao

Background: The blunt snout bream (Megalobrama amblycephala) is an important economic freshwater fish in China with tender flesh and high nutritional value. With the cultivation of superior new varieties and the expansion of breeding scale, it becomes imperative to employ sex-control technology to cultivate monosexual populations of M. amblycephala, thereby preventing the deterioration of desirable traits. The development of specific markers capable of accurately identifying the sex of M. amblycephala would facilitate the determination of the genetic sex of the breeding population before gonad maturation, thereby expediting the processes of sex-controlled breeding of M. amblycephala.

Results: A whole-genome re-sequencing was performed for 116 females and 141 males M. amblycephala collected from nine populations. Seven candidate male-specific sequences were identified through comparative analysis of male and female genomes, which were further compared with the sequencing data of 257 individuals, and finally three male-specific sequences were generated. These three sequences were further validated by PCR amplification in 32 males and 32 females to confirm their potential as male-specific molecular markers for M. amblycephala. One of these markers showed potential applicability in M. pellegrini as well, enabling males to be identified using this specific molecular marker.

Conclusions: The study provides a high-efficiency and cost-effective approach for the genetic sex identification in two species of Megalobrama. The developed markers in this study have great potential in facilitating sex-controlled breeding of M. amblycephala and M. pellegrini, while also contributing valuable insights into the underlying mechanisms of fish sex determination.

背景:钝口鳊(Megalobrama amblycephala)是中国重要的经济淡水鱼类,肉质细嫩,营养价值高。随着优良新品种的培育和养殖规模的扩大,采用性控技术培育钝口鳊的单性种群,从而防止其优良性状的退化已成为当务之急。开发能准确识别伏牛花性别的特异性标记,有助于在性腺成熟前确定育种群体的遗传性别,从而加快伏牛花性别控制育种的进程:结果:对从九个种群中收集到的116条雌性和141条雄性伏尾蜥进行了全基因组重测序。通过对雌雄基因组的比较分析,确定了七个候选雄性特异性序列,并与 257 个个体的测序数据进行了进一步比较,最终产生了三个雄性特异性序列。通过在 32 个雄性个体和 32 个雌性个体中进行 PCR 扩增,进一步验证了这三个序列作为雄性特异性分子标记的潜力。其中一个标记也显示了在 M. pellegrini 中的潜在适用性,从而可以使用该特异性分子标记来鉴定雄性:本研究为两种巨蜥的性别遗传鉴定提供了一种高效、经济的方法。本研究中开发的标记物在促进M. amblycephala和M. pellegrini的性别控制育种方面具有巨大潜力,同时也有助于深入了解鱼类性别决定的基本机制。
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引用次数: 0
Integrated miRNA-mRNA analysis uncovers immediate-early response to salinity stress in gill-derived cell line of Gymnocypris przewalskii. miRNA-mRNA综合分析揭示了Gymnocypris przewalskii鳃源细胞系对盐度胁迫的早期反应。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-15 DOI: 10.1186/s12864-024-10869-z
Fulei Wei, Xianzhi Zuo, Faxin Jin, Qiangdong Yang, Yanrong Cui, Mingyang Zhao, Mingming Cui, Jian Liang

Salinity adaptation is an important issue in aquaculture. Understanding the immediate-early response to salinity stress helps in comprehending this process. In vitro experiments using cell lines can explain cell-independent reactions without the involvement of hormones in vivo. In this study, salinity stress experiments were conducted using cell line derived from the gills of Gymnocypris przewalskii (GPG cell line) to isolate immediate-early response-related genes and miRNAs using transcriptomics, followed by bioinformatics analysis. The results showed that intracellular free Ca2+ appeared to be a key factor in cell sensing and initiating downstream cell signaling in response to external salinity. Additionally, cell apoptosis was the most common feature of salinity stress, with multiple signaling pathways involved in salinity-induced cell apoptosis. Furthermore, MiRNAs played a crucial role in the rapid response to salinity stress by selectively inhibiting the expression of specific genes. Additionally, for the first time in the G. przewalskii genome, Tf2 and TY3 families of transposons were found to have responsive roles to the external salinity stress. This study contributes to a better understanding of osmotic sensing in G. przewalskii and provides theoretical assistance for improving salinity adaptation in aquaculture fish species.

盐度适应是水产养殖中的一个重要问题。了解对盐度胁迫的早期即时反应有助于理解这一过程。利用细胞系进行体外实验可以解释不依赖于细胞的反应,而不需要体内激素的参与。在这项研究中,我们利用从鲤鱼鳃中提取的细胞系(GPG 细胞系)进行了盐度胁迫实验,并利用转录组学分离了与早期反应相关的基因和 miRNA,随后进行了生物信息学分析。结果表明,细胞内游离 Ca2+ 似乎是细胞感知外部盐度并启动下游细胞信号传导的关键因素。此外,细胞凋亡是盐度胁迫最常见的特征,多种信号通路参与了盐度诱导的细胞凋亡。此外,MiRNAs 通过选择性地抑制特定基因的表达,在快速应对盐胁迫方面发挥了关键作用。此外,研究还首次在 G. przewalskii 基因组中发现 Tf2 和 TY3 家族转座子对外部盐度胁迫具有响应作用。这项研究有助于更好地理解przewalskii的渗透感应,并为提高水产养殖鱼类的盐度适应性提供理论帮助。
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引用次数: 0
The molecular anatomy of cashmere goat hair follicle during cytodifferentiation stage. 羊绒山羊毛囊细胞分化阶段的分子解剖。
IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-15 DOI: 10.1186/s12864-024-10820-2
Minghao Li, Xuxu Hao, Zixi Cheng, Jiamian Du, Xinmiao Wang, Niu Wang, Tongtong Zhang, Zhenyu Zhong, Xin Wang

Background: Cashmere, named as "soft gold", derives from the secondary hair follicles (SHFs) of cashmere goat which is vital to Northwest China's economy. The cytodifferentiation stage (E120), mirroring the complete hair follicle (HF) structure of adult goats and marking a critical phase in SHF development. Therefore, this study aims to enhance the understanding of SHF development and its impact on fiber quality, informing breeding strategies.

Results: From the scRNA-seq data analysis, the intricate processes and transcriptional dynamics of inner layer cell differentiation of HFs were unveiled in this study. we identified nine cell populations during cytodifferentiation and key structures such as the hair shaft and inner root sheath. And we discovered three main inner layer lineages and seven subpopulations, clarifying their roles in specialization and signaling. Pseudotime mapping analysis showed cell evolution from early stage to mature stages marked by unique gene expressions, and the intermediate stage on the differentiation of each lineage was revealed. The identification and spatial localization of specific transcription factors, such as GATA3, LEF1 and PRDM1, as well as keratin genes highlight regulatory pathways involved in HF development, which was further validated by immunofluorescence. These findings suggested the potential strategies to improve fiber quality, and the discovery of diverse cell types and their developmental molecular mechanisms, particularly in this species-specific context, offered a nuanced view of the regulatory mechanisms driving HF development in cashmere goats.

Conclusion: Overall, these findings provide a systematic molecular atlas of skin, defining three major branches and cell states of inner layer cells of HF, and determining how the branch-specific transcription factors, keratins, and signals coordinate HF morphogenesis during cytodifferentiation stage. This research not only advances skin tissue research in goats but also holds broader implications for the understanding of HF regeneration and development across various species.

背景:羊绒被称为 "软黄金",源自对中国西北地区经济至关重要的羊绒山羊的次级毛囊(SHFs)。细胞分化阶段(E120)反映了成年山羊完整的毛囊(HF)结构,是SHF发育的关键阶段。因此,本研究旨在加强对 SHF 发育及其对纤维质量影响的了解,为育种策略提供参考:通过 scRNA-seq 数据分析,本研究揭示了高频内层细胞分化的复杂过程和转录动态。我们确定了细胞分化过程中的九个细胞群以及毛轴和内根鞘等关键结构。我们还发现了三个主要的内层细胞系和七个亚群,明确了它们在特化和信号传导中的作用。伪时间图谱分析表明了细胞从早期阶段到成熟阶段的进化,并以独特的基因表达为标志,揭示了各系分化的中间阶段。特定转录因子(如 GATA3、LEF1 和 PRDM1)以及角蛋白基因的鉴定和空间定位突显了高频发育过程中的调控通路,免疫荧光进一步验证了这一点。这些发现提出了提高纤维质量的潜在策略,而对不同细胞类型及其发育分子机制的发现,尤其是在这一物种特异性背景下的发现,提供了对驱动羊绒山羊高频发育的调控机制的细致观察:总之,这些发现提供了一个系统的皮肤分子图谱,定义了高频内层细胞的三个主要分支和细胞状态,并确定了细胞分化阶段分支特异性转录因子、角蛋白和信号如何协调高频形态发生。这项研究不仅推动了山羊皮肤组织的研究,而且对理解不同物种的高频再生和发育具有更广泛的意义。
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