Ecological Genetics and Genomics最新文献_第2页

Evaluation of genetic diversity and population structure of the medicinal plant Justicia adhatoda L. from North India using ISSR markers

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-08 DOI: 10.1016/j.egg.2025.100326

Diksha Chaudhary , Vikas Sharma

Justicia adhatoda L. is an important medicinal plant found in the form of shrub across the country up to an altitude of 1300 masl. It is used in treatment of respirartory diseases. In the present study, 32 pooled samples representing 140 accessions of J. Adhatoda from seven states of North India were analyzed for genetic diversity and structure using inter-simple sequence repeat (ISSR) markers. For this analysis, 23 ISSR markers were screened, and finally 15 ISSR primers were selected for analysis. Overall, these 15 polymorphic primers amplified 96 fragments with an average of 6.4 fragments per primer. The size range of amplified fragments was 300–2000 bp. Primers UBC834 and UBC846 amplified highest (9) number of fragments while UBC850 amplified lowest (3) fragments. Primer UBC855 exhibited highest (0.499) Polymorphism Information Content (PIC) value while UBC850 showed lowest (0.136) PIC value. Similarly, highest (3.906) Marker Index (MI) was shown by UBC834 and lowest (0.408) MI was shown by UBC850. Dendrogram showed that there were two major groups and one minor group with three samples in it. Although dendrogram was largely in concordance with geographical locations, some samples were placed exceptionally. Interestingly, samples from hilly regions grouped in one cluster except one sample. Factorial and structure results were in agreement to the results of dendrogram. STRUCTURE detected three clusters with some admixed individuals. The results of present study can be helpful in identifying unique accessions, devising conservation plans and strategic utilization methods of J. Adhatoda prevailing in the North Indian states.

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引用次数: 0

The evolutionary landscape of mitogenomes: Insights from Elsholtzia blanda and comparative analysis of ten related species

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-07 DOI: 10.1016/j.egg.2025.100328

Bimal K. Chetri , S.S. Sonu , Rahul G. Shelke , Nicolas Dierckxsens , Sudip Mitra , Latha Rangan

We investigated the mitogenomes of 11 Lamiaceae species, including the newly sequenced Elsholtzia blanda mitogenome (304,466 bp), which identified 58 genes. The analysis revealed a negative correlation between genome size and GC content, as well as between gene length and GC content. A positive correlation was also observed between GC content, gene length, and the total number of amino acids. Gene lengths varied across species, with genes like cox2, nad6, ccmC, matR, nad1, and nad2 showing high standard deviations, suggesting selective pressures. Conversely, genes like atp1, atp4, atp6, atp8, and ccmB displayed conserved lengths, potentially indicating crucial roles in mitochondrial function. SSR analysis revealed moderate repeats in nad1 and nad2, suggesting hotspots for genomic variability. Nucleotide diversity and Ka/Ks ratios indicated high variability and adaptive evolution, with genes like atp9 and atp6 exhibiting higher Pi values, while nad1 and nad5 are under purifying selection. Codon usage analysis revealed non-random patterns, with optimal codons showing mean RSCU values between 1.146 and 1.726 and ΔRSCU values ranging from 0.146 to 0.726. The RSCU heatmap and dendrogram corroborated phylogenetic data, situating E. blanda within the Lamiaceae family and indicating close relationships with Pogostemon heyneanus and Salvia splendens. E. blanda possesses 6310 RNA editing sites, with 445 exhibiting scores >0.90, predominantly C-to-U conversions in genes like nad4 and ccmC, reflecting adaptive mechanisms. These findings provide insights into mitochondrial evolution and phylogeny, supporting functional genomics research and conservation strategies for E. blanda and other Lamiaceae species.

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引用次数: 0

Metagenomics study reveals altered composition of Avispirillum, Phocaeicola, Bacteroides, and Faecalibacterium in the gut of patients suffering with Alzheimer's disease

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-04 DOI: 10.1016/j.egg.2025.100322

Jahvnavi, Prekshi Garg, Prachi Srivastava

Alzheimer's disease (AD) is a chronic neurodegenerative disorder that is characterized by memory loss and changes in behaviours, associated with the presence of amyloid-beta and tau proteins in the brain, which interferes with the normal functioning of the brain. Recent studies have tried to establish the structural relationship between the gut microbiota and the brain referred to as the Microbiota–Gut–Brain Axis. The present study aims to investigate a 16S rRNA gene sequencing sample, to analyze the differences in gut microbiota between 116 AD patients and 60 healthy controls retrieved from NCBI ((PRJNA770746, PRJNA533610, and PRJNA811324). Each sample was retrieved, demuxed and denoised to remove low-quality and chimeric sequences. The feature table was then constructed to determine the alpha diversity. The Kruskal-Wallis test done for prediction of alpha diversity calculated in patients with AD had a p-value of 0.0592. The bacterial features calculated through the Adonis test had a f-test value of 2.724 indicating huge microbial dysbiosis in the patient sample. Further ANCOM statistical test identified increased composition of Phocaeicola (clr 3.585), Bacteroides (clr 3.411) and Faecalibacterium (clr 3.3165) while Avispirillum (clr −1.0804) were found in reduced composition in patients with AD. The increasing microbes in Alzheimer's disease patients could be attributed to alterations in diet, immune system changes, and metabolic disturbances that create a gut environment conducive to the growth of these specific bacterial communities. Therefore, it can be an essential research area for neurodegenerative diseases, advancing our knowledge of potential biomarkers and therapeutic targets for minimizing the burden of AD.

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引用次数: 0

GGE biplot analysis for yield performance and stability of faba bean (Vicia faba L.) genotypes under multi environmental condition

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-03 DOI: 10.1016/j.egg.2025.100325

Gizachew Yilma Kebede, Kedir Yimam Assen, Aliyi Robsa Shuro

The presence of genotype × environment interactions (GEI) remains a major issue for crop improvement. The study was conducted to identify best performing, high yielding, and stable faba bean genotypes across different growing environments. Thirteen advanced faba bean genotypes were evaluated using RCBD with four replications at six environments in Ethiopia. The results of combined analysis of variance indicated that highly significant (p < 0.01) differences observed among environments, and genotype × environment interaction, but non-significant genotypic difference for grain yield. The results revealed that faba bean genotypes performed differently in different environmental conditions, and the interaction was crossover in nature. The GGE biplot analysis showed that PC1 and PC2 accounted for 31.8 % and 22.0 % of the genotype × environment sum of squares respectively. The accessions that performed best in each environment based on the “mean vs stability”, are genotypes Gora, EH 08035-1, EH 08035-3 and EH 09031-4; however, based on the “which-won-where” polygon, G8 (EH 06007-4), G3 (EK 05037-4), G11 (EH 08035-1), G2 (EH 010010-1), and G9 (EH 09031-4) are desirable genotypes. In terms of discriminating and representativeness of the environments, Env-1, and Env-6 considered as the most superior environment, while Env-4 and Env-5 were consistently non-discriminating environments they give little information. The result gives more information on the stability and genotype × environment interactions of faba bean genotypes for future breeding programs. Thus, the selected accessions are recommended as parental lines in future breeding programs for faba bean yield improvement in different agro-ecological zones of Ethiopia.

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引用次数: 0

Metagenomic analysis of microbial physiological consortia in Iko River estuary impacted by petroleum products pollution

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-03 DOI: 10.1016/j.egg.2025.100323

Augustine A. Unimke , Abiye A. Ibiene , Phillip O. Okerentugba

The application of genomics in microbial ecological research is of great importance especially in the marine environment with high anthropogenic impacts. Four functional analysis tools (NCBI CDD, PANNZER, and KEGG KOfamKOALA) were used to reveal the functional properties of each of the metagenome in relation to hydrocarbons biodegradation in Iko River estuary. From the 16S rRNA metagenomics result, in the phylum classification, the read counts obtained were; Proteobacteria 178.0, Actinobacteria 28.0, Firmicutes 8.0 and Bacteroidetes 3.0 at 82.03 %, 12.90 %, 3.69 %, and 1.38 % occurrence respectively. Various Classes to genera were all revealed. Nineteen top species were identified, these were Sphingomonas sp154.0 (70.97 %), Unknown¹ 23.0 (10.60 %), Unknown² 17.0 (7.83 %), Sphingomonas_asaccharolytica 5.0 (2.30 %), Mycobacterium sp 2.0 (0.92 %), Patulibacter sp 2.0 (0.92 %), Nocardioides_insulae 2.0 (0.92 %), Porphyromonas sp 1.0 (0.46 %), Knoellia_subterranea 1.0 (0.46 %), Hylemonella sp 1.0 (0.46 %), Tetrasphaera sp 1.0 (0.46 %), Sphingomonas_mali 1.0 (0.46 %), Robiginitalea sp 1.0 (0.46 %) and Prevotella_ruminicola 1.0 (0.46 %). Functional prediction showed the presence of genes and enzymes such as monooxygenase activity (GO:0004497), describing enzymes that incorporate one atom of oxygen into substrates, critical for the breakdown of hydrocarbons, dioxygenase activity (GO:0016706) describing enzymes that incorporate two atoms of oxygen, often involved in aromatic compound degradation, hydrolase activity (GO:0016787) describing enzymes that catalyze the hydrolysis of various bonds, playing a role in the breakdown of complex hydrocarbons as well as transferase activity (GO:0016740) describing enzymes that transfer functional groups from one substrate to another, relevant in modifying hydrocarbon compounds. This could help towards developing new bioremediation strategies in Iko River estuary.

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引用次数: 0

Genomic synergy in food traceability: Enhancing global food safety and security

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-02 DOI: 10.1016/j.egg.2025.100324

Jacob Tizhe Liberty

The global food system faces unprecedented challenges from foodborne diseases, contamination, fraud, and climate change-induced disruptions, threatening public health and food security. Traditional traceability systems, reliant on barcodes and manual records, are increasingly inadequate in managing complex supply chains and ensuring food safety. This review explores how the integration of genomic technologies—DNA barcoding, next-generation sequencing, and CRISPR diagnostics—with digital platforms such as blockchain, IoT, and AI can transform food traceability systems. These technologies offer unparalleled accuracy in pathogen detection, species verification, and fraud prevention, enabling real-time monitoring and predictive capabilities across supply chains. The paper highlights the critical role of interdisciplinary collaboration in advancing genomic traceability, incorporating insights from molecular biology, law, sociology, and economics to address technical, ethical, and societal challenges. Key policy recommendations include harmonizing global standards, promoting equitable access in low-income regions, and strengthening data privacy regulations. Case studies demonstrate the transformative potential of genomic traceability, from combating seafood fraud in Southeast Asia to enabling rapid outbreak responses in high-income countries. Future research should focus on improving the scalability, affordability, and accessibility of genomic tools, particularly for resource-limited regions. By fostering international collaboration and aligning genomic innovations with sustainability goals, these technologies can strengthen global food security and public health. This paper contributes to the growing discourse on the integration of genomics in food systems, offering a pathway toward a resilient, transparent, and equitable global food supply chain.

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引用次数: 0

Exploration of uncultivable actinobacteria from pristine mangrove sediments of Palk Strait, India – A metagenomic approach

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2024-12-27 DOI: 10.1016/j.egg.2024.100321

Madhu Subramani, K. Suthindhiran

Marine actinobacteria are ubiquitous and polyextremophilic microbes vastly studied from terrestrial and coastal ecosystems, leaving mangroves unexplored due to their uncultivable nature and complex media requirements. This study aims to explore the microbial diversity from the pristine mangrove ecosystems – Pathanendal (PN), Muthukuda (MK), and Karankadu (KK) from the coast of Tamil Nadu, India. The sediment geochemical analysis of these sites revealed moderate to high salinity with overall neutral pH, and lower to higher fluctuating levels of soil macro and micro-nutrients, which defines extreme environment conditions. The α-diversity analysis of the Shannon, Simpsons, Fischer, and Chao1 index revealed higher species richness, evenness, and diversity observed from the MK sampling site, followed by the KK and PN samples. The β-diversity analysis showcased the presence of 26 phyla and 108 families in MK, 21 phyla and 179 families from KK, and 19 phyla and 128 families in PN mangroves. In addition, the diversity analysis showed the dominance of Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria, and Spirochaetes among all the sampling sites. Several rare microbes, such as Ignavibacteriae (0.005 %) and Calditrichaeota (0.006 %) from KK, Verrucomicrobia (0.0009 %) and Gemmatimonadetes (0.0006 %) from MK, and finally Deinococcus-Thermus and Elusimicrobia phyla were identified from PN mangroves. In addition, the Actinobacteria phyla were dominant in MK (MK1 – 2.09 % and MK_M − 0.02 %), followed by KK (KK_MR – 1.21 % and KK_M − 1.25 %) and PN (PAN_MR – 0.8 % and PAN_M − 0.49 %), with the presence of Microbacteriaceae, Micrococcaceae, Actinomycetaceae, and Bifidobacteriaceae as dominant families. These data could aid in deciphering the growth of media development and identifying natural products.

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引用次数: 0

Growth performance, survival rate and expression of MHC-I gene in Clarias gariepinus at post Vagococcus carniphilus challenge period

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2024-12-19 DOI: 10.1016/j.egg.2024.100319

O.O. Oyebola , E.O. Babaoye , O.R. Anifowose

The emergence of Vagococcus carniphilus in Nigeria's catfish farming sparked an investigation into its lethal concentration, effect on growth, and the possible interplay of a genetic factor (MHC-1 gene) in the survival of farmed Clarias gariepinus.

Juvenile C. gariepinus (average weight = 41.04 g; n = 10/tank.) was immersed into a liter of water containing different concentrations of 1, 2, 3, 4, and 5 mL of V. carniphilus isolates in different tanks. Intraperitoneal injection at 1, 2, 3, 4, and 5 mL concentration of V. carniphilus during 96 h was carried out. Time at first mortality and LC₅₀ across different routes were documented and utilized to select the fastest mortality-inflicting route (FMIR). C. gariepinus subsamples (n = 28/tank in triplicate) were challenged with the selected FMIR for 24 h. The challenged and controlled fish were fed to satiation once daily for 28 days. Liver samples of the control, challenged dead and challenged survived specimens were assessed for MHC-1 gene expression.

First occurrence of mortality, mortality rate, and LC₅₀ occurred in respective immersion (p < 0.05) and intraperitoneal injection(p > 0.05) treatments at 3.33 ± 1.52hr (5 mL) to 17.33 ± 3.51hr (1 mL); 11.00 ± 3.60hr (5 mL) to 14.66 ± 4.04hr (1 mL) concentrations. The 5 mL immersion (FMIR) challenged fish had significantly higher FCR (8.12 ± 5.79; 1.69 ± 0.14), but lower feed intake, feed efficiency ratio, weight gained, average daily growth, and relative growth rate. Relative percentage survival ranged from 33.3 (challenged) to 100.00 % (control). The MHC-1 gene expressed at ΔΔCT 5.22 ± 1.54 (dead) and −1.27 ± 0.52 (survivors).

Differential expression of MHC-1 gene across the dead and survived C. gariepinus indicates its relevance as a genetic factor for survival.

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引用次数: 0

Characterization and genome sequence of chitinase-producing Chitiniphilus shinanonensis

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2024-12-18 DOI: 10.1016/j.egg.2024.100320

Dinh Minh Tran , To Uyen Huynh , Tu Oanh Do , Le Nguyen Tieu Ngoc , Iuliia Pentekhina

Chitinolytic bacteria play a crucial role in the degradation of chitin and have been widely applied for green crop production. In this work, 4 chitinase-producing strains were isolated from chitin flakes placed in the water of Suoi Hong Lake, Yok Don National Park, Vietnam, and identified as Chitiniphilus shinanonensis by 16S rDNA phylogeny. Experimental characterization demonstrated that all strains produced cellulases, amylases, biofilms, siderophores, IAA, GA3, and zeatin, and solubilized inorganic phosphate and potassium sources. The genome sequence of the most potent bacterium, C. shinanonensis YWS-5.2, contained 4302709 bp with 66.3 % GC content, 3874 coding sequences, 60 tRNAs, and 3 rRNAs. It displayed 98.45 % ANI and 86.5 % dDDH to those of the C. shinanonensis NBRC 104970 genome. Of the coding sequences, KEGG assigned 2058, and COG clarified 3249. The genome possessed 29 sequences concerning plant growth promotion and 122 carbohydrate-active enzymes. The chitinolytic system of the strain contained 28 enzymes, among them, 9 was not present in the reported C. shinanonensis. Furthermore, it harbored 9 BGCs responsible for antibiotic metabolites, with 2 being novel clusters. These results implied that 4 chitinolytic bacteria have great potential as plant growth promoters, and strain YWS-5.2 is a promising candidate as a novel chitinase and antibiotic producer. This is the first report demonstrating plant growth-promoting traits and BGCs of C. shinanonensis.

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引用次数: 0

Innovative approaches to food traceability with DNA barcoding: Beyond traditional labels and certifications

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2024-12-10 DOI: 10.1016/j.egg.2024.100317

Jacob Tizhe Liberty , Haijiao Lin , Christopher Kucha , Shangpeng Sun , Fatemah B. Alsalman

The increasing difficulty of global food supply chains has heightened the dangers of food fraud, including species substitution, geographic origin misrepresentation, and adulteration. Traditional labeling and certification systems often fail to prevent these fraudulent practices, necessitating the development of more reliable authentication methods. DNA barcoding has surfaced as a potent molecular tool for verifying food authenticity, offering enhanced species identification and traceability across various food sectors. This work explores the application of DNA barcoding in food authentication, providing a comparative analysis of DNA barcoding with other molecular techniques such as PCR, LAMP, and next-generation sequencing. We examine key case studies across the seafood, meat, and herbal supplement industries, and discuss the integration of DNA barcoding with blockchain, IoT sensors, and AI technologies. The review also addresses ethical, regulatory, and technical challenges, particularly in relation to processed foods. DNA barcoding has proven highly effective in detecting food fraud, with case studies demonstrating its ability to identify species mislabeling and adulteration. While other molecular techniques offer specific advantages, DNA barcoding stands out for its accuracy and applicability in highly processed foods when combined with emerging technologies like blockchain and IoT. However, limitations such as the difficulty of handling degraded DNA in some processed products remain. Upcoming investigation should focus on the expansion of DNA reference databases and the integration of AI to further enhance species detection. DNA barcoding is perched to become a gold-standard tool in food authentication, promoting transparency, consumer trust, and food integrity.

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引用次数: 0