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Keywords = molecular markers, High Throughput Sequencing

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12 pages, 1076 KiB  
Article
Rapid Identification of the SNP Mutation in the ABCD4 Gene and Its Association with Multi-Vertebrae Phenotypes in Ujimqin Sheep Using TaqMan-MGB Technology
by Yue Zhang, Min Zhang, Hong Su, Jun Liu, Feifei Zhao, Yifan Zhao, Xiunan Li, Yanyan Yang, Guifang Cao and Yong Zhang
Animals 2025, 15(15), 2284; https://doi.org/10.3390/ani15152284 - 5 Aug 2025
Viewed by 46
Abstract
Ujimqin sheep, known for its distinctive multi-vertebrae phenotypes (T13L7, T14L6, and T14L7) and economic value, has garnered significant attention. However, conventional phenotypic detection methods suffer from low efficiency and high costs. In this study, based on a key SNP locus (ABCD4 gene, [...] Read more.
Ujimqin sheep, known for its distinctive multi-vertebrae phenotypes (T13L7, T14L6, and T14L7) and economic value, has garnered significant attention. However, conventional phenotypic detection methods suffer from low efficiency and high costs. In this study, based on a key SNP locus (ABCD4 gene, Chr7:89393414, C > T) identified through a genome-wide association study (GWAS), a TaqMan-MGB (minor groove binder) genotyping system was developed. the objective was to establish a high-throughput and efficient molecular marker-assisted selection (MAS) tool. Specific primers and dual fluorescent probes were designed to optimize the reaction system. Standard plasmids were adopted to validate genotyping accuracy. A total of 152 Ujimqin sheep were subjected to TaqMan-MGB genotyping, digital radiography (DR) imaging, and Sanger sequencing. the results showed complete concordance between TaqMan-MGB and Sanger sequencing, with an overall agreement rate of 83.6% with DR imaging. For individuals with T/T genotypes (127/139), the detection accuracy reached 91.4%. This method demonstrated high specificity, simplicity, and cost-efficiency, significantly reducing the time and financial burden associated with traditional imaging-based approaches. the findings indicate that the TaqMan-MGB technique can accurately identify the T/T genotype at the SNP site and its strong association with the multi-vertebrae phenotypes, offering an effective and reliable tool for molecular breeding of Ujimqin sheep. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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15 pages, 5560 KiB  
Article
Integrated Transcriptomic Analysis Reveals Molecular Mechanisms Underlying Albinism in Schima superba Seedlings
by Jie Jia, Mengdi Chen, Yuanheng Feng, Zhangqi Yang and Peidong Yan
Forests 2025, 16(8), 1201; https://doi.org/10.3390/f16081201 - 22 Jul 2025
Viewed by 253
Abstract
The main objective of this study was to reveal the molecular mechanism of the albinism in Schima superba and to identify the related functional genes to provide theoretical support for the optimization of S. superba seedling nursery technology. Combining third-generation SMRT sequencing with [...] Read more.
The main objective of this study was to reveal the molecular mechanism of the albinism in Schima superba and to identify the related functional genes to provide theoretical support for the optimization of S. superba seedling nursery technology. Combining third-generation SMRT sequencing with second-generation high-throughput sequencing technology, the transcriptomes of normal seedlings and albinism seedlings of S. superba were analyzed and the sequencing data were functionally annotated and deeply resolved. The results showed that 270 differentially expressed transcripts were screened by analyzing second-generation sequencing data. KEGG enrichment analysis of the annotation information revealed that, among the photosynthesis-antenna protein-related pathways, the expression of LHCA3 and LHCB6 was found to be down-regulated in S. superba albinism seedlings, suggesting that the down-regulation of photosynthesis-related proteins may affect the development of chloroplasts in leaves. Down-regulated expression of VDE in the carotenoid biosynthesis leads to impaired chlorophyll cycling. In addition, transcription factors (TFs), such as bHLH, MYB, GLK and NAC, were closely associated with chloroplast development in S. superba seedlings. In summary, the present study systematically explored the transcriptomic features of S. superba albinism seedlings, screened out key genes with significant differential expression and provide a reference for further localization and cloning of the key genes for S. superba albinism, in addition to laying an essential theoretical foundation for an in-depth understanding of the molecular mechanism of the S. superba albinism. The genes identified in this study that are associated with S. superba albinism will be important targets for genetic modification or molecular marker development, which is essential for improving the cultivation efficiency of S. superba. Full article
(This article belongs to the Special Issue Forest Tree Breeding: Genomics and Molecular Biology)
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20 pages, 1518 KiB  
Article
Research Trends and Hotspots in eDNA-Based Surveys of Macroinvertebrates: A Bibliometric Analysis
by Xinyu Ge, Junyu Zhang, Ziming Shao, Lu Chai, Jiaxin Nie, Dan Yin, Haoran Zhang, Wenbin Liu and Chuncai Yan
Diversity 2025, 17(6), 402; https://doi.org/10.3390/d17060402 - 6 Jun 2025
Viewed by 462
Abstract
Environmental DNA metabarcoding offers an efficient and non-invasive solution for aquatic biomonitoring surveys, particularly demonstrating remarkable potential in macroinvertebrate research. In this study, we systematically analyzed 322 articles in the Web of Science Core Collection from 2010 to 2024 using bibliometric methods to [...] Read more.
Environmental DNA metabarcoding offers an efficient and non-invasive solution for aquatic biomonitoring surveys, particularly demonstrating remarkable potential in macroinvertebrate research. In this study, we systematically analyzed 322 articles in the Web of Science Core Collection from 2010 to 2024 using bibliometric methods to reveal the research trends and technological advances in the field of macroinvertebrate surveys based on eDNA metabarcoding technology. The results showed that the number of annual publications has increased rapidly since 2012, with the United States (n = 58), France (n = 43), and Canada (n = 39) as the main contributing countries, and the most intensive collaboration network was observed among Europe countries. A keyword analysis shows that, in the past five years, the research direction has shifted to novel methodologies including multi-marker approaches, quantitative PCR, digital PCR, and other molecular detection platforms and high-throughput sequencing technology, with the integration of machine-learning and deep-learning architecture significantly improving the taxonomic resolution of data analysis. Despite the advantages of eDNA metabarcoding technology in terms of sensitivity and efficiency, persistent challenges including false positives/negatives in detection and incomplete reference databases are still the main challenges. This study provides methodological evidence for standardizing eDNA protocols in benthic assessments while identifying critical knowledge gaps. Full article
(This article belongs to the Section Animal Diversity)
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16 pages, 1159 KiB  
Review
Decoding Quantitative Traits in Yaks: Genomic Insights for Improved Breeding Strategies
by Yujiao Fu, Yuanyuan Yu, Xinjia Yan, Daoliang Lan and Jiabo Wang
Curr. Issues Mol. Biol. 2025, 47(5), 350; https://doi.org/10.3390/cimb47050350 - 12 May 2025
Viewed by 509
Abstract
The yak (Bos grunniens), the only large domesticated species endemic to the Qinghai–Tibet Plateau, is a vital resource for local livelihoods and regional economic sustainability. However, yak breeding faces significant challenges, including limited understanding of the genetic architecture underlying quantitative traits, [...] Read more.
The yak (Bos grunniens), the only large domesticated species endemic to the Qinghai–Tibet Plateau, is a vital resource for local livelihoods and regional economic sustainability. However, yak breeding faces significant challenges, including limited understanding of the genetic architecture underlying quantitative traits, inadequate advanced breeding strategies, and the sterility of hybrid offspring from yak–cattle crosses. These constraints have hindered genetic progress in key production traits. To address these issues, integrating modern genomic tools into yak breeding programs is imperative. This review explores the application and potential of molecular marker-assisted selection (MAS) and genomic prediction (GP) in yak genetic improvement. We systematically evaluate critical components of genomic breeding pipelines, including: (1) phenotypic trait assessment, (2) sample collection strategies, (3) reference population design, (4) high-throughput genotyping (via genome sequencing and SNP arrays), (5) predictive model development, and (6) heritability estimation. By synthesizing current advances and methodologies, this work aims to provide a framework for leveraging genomic technologies to enhance breeding efficiency, preserve genetic diversity, and accelerate genetic gains in yak populations. Full article
(This article belongs to the Section Bioinformatics and Systems Biology)
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16 pages, 1706 KiB  
Review
A Review of Cross-Species Transmission Mechanisms of Influenza Viruses
by Xianfeng Hui, Xiaowei Tian, Shihuan Ding, Ge Gao, Jiyan Cui, Chengguang Zhang, Tiesuo Zhao, Liangwei Duan and Hui Wang
Vet. Sci. 2025, 12(5), 447; https://doi.org/10.3390/vetsci12050447 - 7 May 2025
Viewed by 1712
Abstract
The cross-species transmission of influenza viruses represents a critical link in the pandemic of zoonotic diseases. This mechanism involves multi-level interactions, including viral genetic adaptability, host–receptor compatibility, and ecological drivers. Recent studies have highlighted the essential role of mutations in hemagglutinin and neuraminidase [...] Read more.
The cross-species transmission of influenza viruses represents a critical link in the pandemic of zoonotic diseases. This mechanism involves multi-level interactions, including viral genetic adaptability, host–receptor compatibility, and ecological drivers. Recent studies have highlighted the essential role of mutations in hemagglutinin and neuraminidase in overcoming host barriers, while elucidating the differences in the distribution of host sialic acid receptors. Furthermore, the “mixer” function of intermediate hosts, such as pigs, plays a significant role in viral redistribution. Advances in high-throughput sequencing and structural biology technologies have gradually resolved key molecular markers and host restriction factors associated with these viruses. However, challenges remain in understanding the dynamic evolutionary patterns of virus–host interaction networks, developing real-time early warning capabilities for cross-species transmission, and formulating broad-spectrum prevention and control strategies. Moving forward, it is essential to integrate multidisciplinary approaches to establish a multi-level defense system, leveraging the ‘One Health’ monitoring network, artificial intelligence prediction models, and new vaccine research and development to address the ongoing threat of cross-species transmission of influenza viruses. This paper systematically reviews the research progress and discusses bottlenecks in this field, providing a theoretical foundation for optimizing future prevention and control strategies. Full article
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19 pages, 6155 KiB  
Article
Complete Mitochondrial Genome of Two Amathusiini Species (Lepidoideae: Nymphalidae: Satyrinae): Characterization, Comparative Analyses, and Phylogenetic Implications
by Qinghui Shi, Xinyue Wang, Jianhong Xing, Xiaoyun Xu, Gang Sun and Juncheng Zhang
Genes 2025, 16(4), 447; https://doi.org/10.3390/genes16040447 - 12 Apr 2025
Cited by 1 | Viewed by 643
Abstract
Background: The Satyrinae subfamily represents a taxonomically critical group within Nymphalidae, characterized by its remarkable species diversity. Despite its evolutionary significance, the phylogenetic relationships among tribal and subtribal lineages remain poorly resolved. Although mitochondrial genomes have become crucial molecular markers in [...] Read more.
Background: The Satyrinae subfamily represents a taxonomically critical group within Nymphalidae, characterized by its remarkable species diversity. Despite its evolutionary significance, the phylogenetic relationships among tribal and subtribal lineages remain poorly resolved. Although mitochondrial genomes have become crucial molecular markers in Lepidoptera phylogenetics, their potential remains underutilized in the systematics of Satyrinae. Notably, Amathusiini exhibits a particular paucity, with only two congeneric representatives having been comprehensively sequenced to date. Methods: We employed high-throughput sequencing to assemble the complete mitochondrial genomes of two Amathusiini species, Discophora sondaica and Aemona amathusia. Our study revealed novel evolutionary insights through comparative genomics, which encompassed all available Satyrinae mitochondrial genomes. Additionally, we conducted phylogenetic reconstruction using maximum likelihood and Bayesian inference approaches, utilizing the most extensive dataset to date. Results: The closed, circular mitochondrial genomes measure 15,333 bp for D. sondaica and 15,423 bp for A. amathusia, maintaining the ancestral lepidopteran architecture: 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and an AT-rich control region. Comparative analyses of 71 mitochondrial genomes revealed strong evolutionary conservation across multiple parameters: nucleotide composition (AT content range: 77.9–81.8%), codon usage bias (ENC = 30.83–37.55), tRNA secondary structures, and control region organization. All PCGs showed purifying selection signals (Ka/Ks < 1.0), with atp8 exhibiting the highest evolutionary rate (Ka/Ks = 0.277). Phylogenetic reconstructions yielded congruent tribal-level topologies with strong nodal support: ((Satyrini + Melanitini) + (Amathusiini + Elymniini) + Zetherini), confirming a sister relationship between Amathusiini and Elymniini. Within Satyrini, five subtribes formed monophyletic groups: Ypthimina, Erebiina, Maniolina, Satyrina, and Melanargiina, arranged as ((Ypthimina + (Erebiina + Maniolina)) + (Satyrina + Melanargiina)). Mycalesina, Lethina, and Parargina comprised a well-supported clade (BS = 100%; PP = 1.0), though internal relationships required further resolution due to Lethina’s polyphyly. Conclusions: This study provides novel insights into mitochondrial genomic evolution within the Satyrinae subfamily while elucidating the efficacy of mitogenomic data for resolving deep phylogenetic relationships within this ecologically significant subfamily. Our findings establish critical genome baselines for further systematic research and underscore essential pathways for refining subtribal-level taxonomy through integrative molecular approaches. Full article
(This article belongs to the Special Issue Mitochondrial DNA Replication and Transcription)
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21 pages, 43593 KiB  
Article
Astilbin Alleviates Radiation-Induced Pulmonary Fibrosis via circPRKCE Targeting the TGF-β/Smad7 Pathway to Inhibit Epithelial–Mesenchymal Transition
by Zhiling Shi, Jing Liu, Jing Qin, Xian Liang, Xue Ou, Tingting Zhang, Xueting Yan, Qianxin Hu, Weimei Huang and Kai Hu
Biomedicines 2025, 13(3), 689; https://doi.org/10.3390/biomedicines13030689 - 11 Mar 2025
Viewed by 905
Abstract
Purpose: This study aimed to clarify the protective effect of astilbin (AST) on radiation-induced pulmonary fibrosis (RIPF) and explore its underlying molecular mechanism, focusing on non-coding RNAs. Methods: Mouse lung epithelial cells (MLE-12 and TC-1) and C57BL/6J mice were used to establish in [...] Read more.
Purpose: This study aimed to clarify the protective effect of astilbin (AST) on radiation-induced pulmonary fibrosis (RIPF) and explore its underlying molecular mechanism, focusing on non-coding RNAs. Methods: Mouse lung epithelial cells (MLE-12 and TC-1) and C57BL/6J mice were used to establish in vitro radiation injury models and in vivo RIPF models, respectively. Cell viability, apoptosis, the epithelial-to-mesenchymal transition (EMT), and fibrosis-related markers were assessed using cell-counting kit-8 assays, Western blotting, immunohistochemistry, and histological staining. High-throughput sequencing identified differentially expressed circRNAs. The mechanistic studies included RNA-FISH, a dual-luciferase reporter assay, an RNA immunoprecipitation (RIP) assay, and loss-of-function experiments. Results: AST significantly alleviated radiation-induced apoptosis and EMT in vitro, as well as RIPF in vivo. AST treatment reduced collagen deposition, fibrosis-related protein expression, and EMT marker changes. High-throughput sequencing revealed that AST upregulated circPRKCE, a non-coding RNA that functions through a ceRNA mechanism by binding to miR-15b-5p, thereby promoting Smad7 expression and suppressing the TGF-β/Smad7 pathway. Knockdown of circPRKCE abolished AST’s protective effects, confirming its pivotal role in mediating AST’s anti-fibrotic activity. Conclusions: This study demonstrates that Astilbin alleviates radiation-induced pulmonary fibrosis via circPRKCE targeting the TGF-β/Smad7 pathway to inhibit EMT, suggesting AST as a potential therapeutic agent for managing this severe complication of radiotherapy. Full article
(This article belongs to the Section Cell Biology and Pathology)
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16 pages, 11058 KiB  
Brief Report
Complete Mitochondrial Genome of Platygyra daedalea and Characteristics Analysis of the Mitochondrial Genome in Merulinidae
by Shuwen Jia, Tongtong Shen, Wenqi Cai, Jian Zhang and Shiquan Chen
Genes 2025, 16(3), 304; https://doi.org/10.3390/genes16030304 - 2 Mar 2025
Cited by 1 | Viewed by 919
Abstract
Background: The Merulinidae family belonging to the order Scleractinia is mainly distributed in the Indo-Pacific and Caribbean regions and often constitute the most dominant species of coral reefs. Mitochondrial genome is a key tool for studying the phylogeny and adaptation. Only a few [...] Read more.
Background: The Merulinidae family belonging to the order Scleractinia is mainly distributed in the Indo-Pacific and Caribbean regions and often constitute the most dominant species of coral reefs. Mitochondrial genome is a key tool for studying the phylogeny and adaptation. Only a few studies have conducted the characteristics analyses of mitochondrial genome in the Merulinidae family. Methods: Therefore, we used high-throughput sequencing technology to describe the mitochondrial genome of Platygyra daedalea, a member of this family. Bioinformatics was used to analyze the composition characteristics of the mitochondrial genome of 10 Merulinidae species. Results: The mitochondrial genome of P. daedalea had a total length of 16,462 bp and a GC content of 33.0%. Thirteen unique protein-coding genes (PCGs), two transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes were annotated. Each species of Merulinidae had 13 unique PCGs in the mitochondrial genome. In contrast, the number of tRNAs and rRNAs significantly varied in Merulinidae species. Collinearity and gene rearrangement analyses indicated that the mitochondrial evolution of species in the Merulinidae family was relatively conserved. Divergence time analysis indicated that Merulinidae originated in the Oligocene, whereas the Platygyra genus originated in the Miocene. The formation and intraspecific divergence of coral species were consistent with geological changes in the ocean. Conclusions: The results of this study help better understand the characteristics of the mitochondrial genome in the Merulinidae family and provide insights into the utility of mitochondrial genes as molecular markers of phylogeny. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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16 pages, 2458 KiB  
Article
Bridging the Gap Between Platforms: Comparing Grape Phylloxera Daktulosphaira vitifoliae (Fitch) Microsatellite Allele Size and DNA Sequence Variation
by Mark J. Blacket, Alexander M. Piper, Ary A. Hoffmann, John Paul Cunningham and Isabel Valenzuela
Insects 2025, 16(2), 230; https://doi.org/10.3390/insects16020230 - 19 Feb 2025
Viewed by 736
Abstract
Grape phylloxera, Daktulosphaira vitifoliae (Fitch), is an economically significant pest of grapevines. Identification of phylloxera genotypes is an important aspect of management as genotypes differ in virulence and susceptibility to control using resistant rootstocks. Microsatellite markers developed on polyacrylamide gel systems have been the [...] Read more.
Grape phylloxera, Daktulosphaira vitifoliae (Fitch), is an economically significant pest of grapevines. Identification of phylloxera genotypes is an important aspect of management as genotypes differ in virulence and susceptibility to control using resistant rootstocks. Microsatellite markers developed on polyacrylamide gel systems have been the most widely used molecular method for phylloxera genotype identification, but this approach has been superseded by fluorescent capillary-based genotyping. The current study presents new laboratory methods for amplifying a standard set of eight phylloxera microsatellite markers using PCR-incorporated fluorescently labelled primers, genotyped on an ABI capillary platform. Comparison of allele size data scored on (i) polyacrylamide, (ii) capillary, and (iii) high-throughput sequencing (HTS) platforms revealed that the capillary genotyping most closely matched the HTS allele sizes, while alleles of loci originally scored on a polyacrylamide platform differ in size by up to three base pairs, mostly due to the presence of previously uncharacterised DNA sequence indels. Seven common clonal lineages of phylloxera known from Australia are proposed as reference samples for use in calibrating genotyping systems between platforms and laboratories to ensure universal scoring of allele sizes, providing a critical link for accurately matching previous phylloxera genotype studies with current research. Full article
(This article belongs to the Special Issue Genetic Diversity of Insects)
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16 pages, 2547 KiB  
Article
Assessing the Influence of Selected Permeabilization Methods on Lymphocyte Single-Cell Multi-Omics
by Shifan Ding, Na Lu and Hassan Abolhassani
Antibodies 2025, 14(1), 15; https://doi.org/10.3390/antib14010015 - 10 Feb 2025
Viewed by 971
Abstract
(1) Background: Single-cell multi-omics is a powerful method for the dissection and detection of complicated immunologic functions and synapses. However, most currently available technologies merge datasets of different omics from separate portions of the same sample to generate combined multi-omics. This process is [...] Read more.
(1) Background: Single-cell multi-omics is a powerful method for the dissection and detection of complicated immunologic functions and synapses. However, most currently available technologies merge datasets of different omics from separate portions of the same sample to generate combined multi-omics. This process is a source of bias, mainly in the field of immunology on cells originating from pluripotent hematopoietic stem cells with high flexibility during maturation. (2) Methods: Although new multi-omics approaches have been developed to use the advantages of cellular and molecular barcoding and next-generation sequencing to solve this issue, one of the main current challenges is intracellular proteomics, which should be combined with other omics data with high importance for immune system studies. We designed this study to evaluate previously recommended minimal permeabilization and fixation methods on the quality and quantity of transcriptomics and proteomics data generated by the BD Rhapsody™ Single-Cell Analysis System. (3) Results: Our findings showed that high-throughput sequencing with advanced quality and read-out is required for the combination of multi-omics outcomes from a permeabilized single cell. Therefore, the HiseqX platform was selected for further analysis. The effect of immune stimulation was observed clearly as the separated clusters of helper and cytotoxic T cells using unsupervised clustering. Importantly, fixation and permeabilization did not affect the general expression profile of unstimulated cells. However, fixation and permeabilization were proved to negatively impact the detection of the whole transcriptome for single-cell assay. Nevertheless, about 60% of the transcriptomic signature of the stimulation was detected. If the measurement of combined surface and intracellular markers is required to be achieved, the modified fixation and permeabilization method is recommended because of a lower transcriptomic loss and more precise proteomic fingerprint detected. (4) Conclusions: The findings of this study support the potential possibility for integrating intracellular proteomics, which needs to be optimized and tested with newly designed oligonucleotide-tagged antibodies targeting intracellular proteins. Full article
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17 pages, 3837 KiB  
Article
Dynamic Immune Response Landscapes of Avian Peripheral Blood Post-Vaccination Against Infectious Bronchitis Virus Infection
by Xuefeng Li, Yumeng Liang, Yu Zhang, Zheyi Liu, Lu Cui, Miaomiao Xi, Shufeng Feng, Xiaoxiao Liu, Yongxin Zhu, Shengwang Liu and Hai Li
Vaccines 2025, 13(2), 146; https://doi.org/10.3390/vaccines13020146 - 30 Jan 2025
Viewed by 1347
Abstract
Background/Objectives: Despite decades of extensive vaccinations against avian infectious bronchitis virus (IBV) infection, outbreaks caused by constantly emerging variants due to genome recombination between different viral strains, including vaccine strains, occur annually worldwide. The development of novel vaccines with favorable safety and [...] Read more.
Background/Objectives: Despite decades of extensive vaccinations against avian infectious bronchitis virus (IBV) infection, outbreaks caused by constantly emerging variants due to genome recombination between different viral strains, including vaccine strains, occur annually worldwide. The development of novel vaccines with favorable safety and effectiveness is required but is hindered by a limited understanding of vaccination against IBV. Methods: Here, we performed a comprehensive analysis of the in vivo dynamics of peripheral blood mononuclear cells (PBMCs) in specific pathogen-free chickens inoculated with the widely used live attenuated IBV vaccine strain H120 at single-cell level, using high-throughput single-cell transcriptome sequencing (scRNA-seq). Results: High-quality sequencing dataset for four scRNA-seq data containing the transcriptomes of 29,846 individual chicken PBMCs were obtained, defining 22 populations and 7 cell types based on distinct molecular signatures and known markers. Further integrative analysis constructed the time series dynamic cell transition and immune response landscapes within the two weeks post-prime vaccination against IBV. Enhanced crosstalk between antigen-presenting cells and T lymphocytes was revealed as early as four days post-vaccination. The specific immune cell populations and their comprehensive cellular and molecular networks involved in the initiation phase of antiviral adaptive immune responses were elucidated in details. Conclusions: Our study provides a comprehensive view of the dynamic initiation of immune responses in chickens against IBV infection at the cellular and molecular levels, which provides theoretical support and potential solutions for the future rational design of safe and effective vaccines, the augmentation of the efficacy of current vaccines, and the optimization of immune programs. Full article
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28 pages, 10072 KiB  
Article
Chloroplast Genome Diversity and Molecular Evolution in Hypericaceae: New Insights from Three Hypericum Species
by Kan Yan, Xin Lu, Wandi Li, Chao Sun, Xueqiong Zhou and Youyou Wang
Int. J. Mol. Sci. 2025, 26(1), 323; https://doi.org/10.3390/ijms26010323 - 2 Jan 2025
Cited by 3 | Viewed by 1631
Abstract
The Hypericaceae family, comprising nine genera and over seven hundred species, includes Hypericum plants traditionally used for medicinal purposes. In this study, we performed high-throughput sequencing on three Hypericum species: Hypericum acmosepalum, Hypericum addingtonii, and Hypericum beanii, and conducted comparative [...] Read more.
The Hypericaceae family, comprising nine genera and over seven hundred species, includes Hypericum plants traditionally used for medicinal purposes. In this study, we performed high-throughput sequencing on three Hypericum species: Hypericum acmosepalum, Hypericum addingtonii, and Hypericum beanii, and conducted comparative genomic analyses with related species. The chloroplast genome sizes were 152,654 bp, 122,570 bp, and 137,652 bp, respectively, with an average GC content of 37.9%. All genomes showed a quadripartite structure, with significant variations in IR regions (3231–26,846 bp). The total number of genes ranged from 91 to 129. SSRs were predominantly located in the LSC region, with mononucleotide repeats being dominant. Comparative analysis identified several hotspot regions, including accD, rpoC2, rpoB, and rpl22 in the LSC region and matK, rpl32, rpl33, and rps4 in the SSC region. Nucleotide polymorphism analysis revealed eight highly variable regions and eleven gene loci, providing potential molecular markers for species identification. Phylogenetic analysis indicated that Triadenum and Cratoxylum are closely related to Hypericum, with H. acmosepalum and H. beanii being closest relatives and Hypericum hookerianum as their sister species. These findings provide molecular tools for species identification and insights for conservation strategies of medicinal Hypericum species. Full article
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18 pages, 2505 KiB  
Review
From Species to Varieties: How Modern Sequencing Technologies Are Shaping Medicinal Plant Identification
by Mingcheng Wang, Haifeng Lin, Hongqiang Lin, Panyue Du and Shuqiao Zhang
Genes 2025, 16(1), 16; https://doi.org/10.3390/genes16010016 - 26 Dec 2024
Cited by 20 | Viewed by 1981
Abstract
Background/Objectives: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing [...] Read more.
Background/Objectives: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing the accuracy and reliability of plant identification. Additionally, the integration of multi-omics approaches is examined to provide a comprehensive understanding of medicinal plant identity. Methods: The literature search for this review was conducted across databases such as Google Scholar, Web of Science, and PubMed, using keywords related to plant taxonomy, genomics, and biotechnology. Inclusion criteria focused on peer-reviewed studies closely related to plant identification methods and techniques that contribute significantly to the field. Results: The review highlights that while sequencing technologies offer substantial improvements, challenges such as high costs, technical expertise, and the lack of standardized protocols remain barriers to widespread adoption. Potential solutions, including AI-driven data analysis and portable sequencers, are discussed. Conclusions: This review provides a comprehensive overview of molecular techniques, their transformative impact, and future perspectives for more accurate and efficient medicinal plant identification. Full article
(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants: 2nd Edition)
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16 pages, 2518 KiB  
Article
Application of Environmental DNA Metabarcoding to Differentiate Algal Communities by Littoral Zonation and Detect Unreported Algal Species
by Sergei Bombin, Andrei Bombin, Brian Wysor and Juan M. Lopez-Bautista
Phycology 2024, 4(4), 605-620; https://doi.org/10.3390/phycology4040033 - 18 Dec 2024
Viewed by 1553
Abstract
Coastal areas are the most biologically productive and undoubtedly among the most complex ecosystems. Algae are responsible for most of the gross primary production in these coastal regions. However, despite the critical importance of algae for the global ecosystem, the biodiversity of many [...] Read more.
Coastal areas are the most biologically productive and undoubtedly among the most complex ecosystems. Algae are responsible for most of the gross primary production in these coastal regions. However, despite the critical importance of algae for the global ecosystem, the biodiversity of many algal groups is understudied, partially due to the high complexity of morphologically identifying algal species. The current study aimed to take advantage of the recently developed technology for biotic community assessment through the high-throughput sequencing (HTS) of environmental DNA (eDNA), known as the “eDNA metabarcoding”, to characterize littoral algal communities in the Northern Gulf of Mexico (NGoM). This study demonstrated that eDNA metabarcoding, based on the universal plastid amplicon (UPA) and part of the large nuclear ribosomal subunit (LSU) molecular markers, could successfully differentiate coastal biotic communities among littoral zones and geographical locations along the shoreline of the NGoM. The statistical significance of separation between biotic communities was partially dependent on the dissimilarity calculation metric; thus, the differentiation of algal community structure according to littoral zones was more distinct when phylogenetic distances were incorporated into the diversity analysis. Current work demonstrated that the relative abundance of algal species obtained with eDNA metabarcoding matches previously established zonation patterns for these species. In addition, the present study detected molecular signals of 44 algal species without previous reports for the Gulf of Mexico, thus providing an important, molecular-validated baseline of species richness for this region. Full article
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26 pages, 12100 KiB  
Article
Molecular Profiling of A549 Cell-Derived Exosomes: Proteomic, miRNA, and Interactome Analysis for Identifying Potential Key Regulators in Lung Cancer
by Alexandros Giannopoulos-Dimitriou, Aikaterini Saiti, Andigoni Malousi, Athanasios K. Anagnostopoulos, Giannis Vatsellas, Passant M. Al-Maghrabi, Anette Müllertz, Dimitrios G. Fatouros and Ioannis S. Vizirianakis
Cancers 2024, 16(24), 4123; https://doi.org/10.3390/cancers16244123 - 10 Dec 2024
Cited by 1 | Viewed by 2345
Abstract
Background/Objectives: Exosomes, nano-sized extracellular vesicles released by all cells, play a key role in intercellular communication and carry tumorigenic properties that impact surrounding or distant cells. The complexity of the exosomal molecular interactome and its effects on recipient cells still remain unclear. This [...] Read more.
Background/Objectives: Exosomes, nano-sized extracellular vesicles released by all cells, play a key role in intercellular communication and carry tumorigenic properties that impact surrounding or distant cells. The complexity of the exosomal molecular interactome and its effects on recipient cells still remain unclear. This study aims to decipher the molecular profile and interactome of lung adenocarcinoma A549 cell-derived exosomes using multi-omics and bioinformatics approaches. Methods: We performed comprehensive morphological and physicochemical characterization of exosomes isolated from cell culture supernatant of A549 cells in vitro, using DLS, cryo-TEM, Western blot, and flow cytometry. Proteomic and miRNA high-throughput profiling, coupled with bioinformatics network analysis, were applied to elucidate the exosome molecular cargo. A comparative miRNA analysis was also conducted with exosomes derived from normal lung fibroblast MRC-5 cells. Results: Exosomes exhibited an average size of ~40 nm and disk-shaped lipid bilayer structures, with tetraspanins CD9 and CD63 validated as exosomal markers. Proteomic analysis identified 68 proteins, primarily linked to the extracellular matrix organization and metabolic processes. miRNA sequencing revealed 72 miRNAs, notably hsa-miR-619-5p, hsa-miR-122-5p, hsa-miR-9901, hsa-miR-7704, and hsa-miR-151a-3p, which are involved in regulating metabolic processes, gene expression, and tumorigenic pathways. Th integration of proteomic and miRNA data through a proteogenomics approach identified dually affected genes including ERBB2, CD44, and APOE, impacted by both exosomal miRNA targeting and protein interactions through synergistic or antagonistic interactions. Differential analysis revealed a distinct miRNA profile in A549 exosomes, associated with cancer-related biological processes, compared to MRC-5 exosomes; notably, hsa-miR-619-5p emerged as a promising candidate for future clinical biomarker studies. The network analysis also revealed genes targeted by multiple upregulated tumor-associated miRNAs in potential exosome-recipient cells. Conclusions: This integrative study provides insights into the molecular interactome of lung adenocarcinoma A549 cell-derived exosomes, providing a foundation for future research on exosomal cargo and its role in tumor cell communication, growth, and progression. Full article
(This article belongs to the Special Issue Lung Cancer Proteogenomics: New Era, New Insights)
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