Pub Date : 2025-11-02DOI: 10.1016/j.egg.2025.100422
Amir Hasan Taghiloofar, Gülsüm Boztaş, Emine Bayram
Saffron (Crocus sativus L.) is a high-value crop known for its unique aroma, coloring properties, and medicinal uses. This study assessed agro-morphological and yield-related traits of Turkish and Iranian saffron populations under Mediterranean climatic conditions over two years (2013–2014). Fourteen quantitative traits, including floral organ dimensions, biomass components, and flower number, were analysed to explore phenotypic variation and genotype × environment (G × E) interactions. Significant year and population effects were observed. The Iranian genotype showed greater stability and performance under warmer, drier conditions, whereas the Turkish population was more productive in cooler, wetter climates. Principal component analysis (PCA) revealed that style length, stigma length, fresh stigma weight, and flower number were key contributors to trait variation, explaining 56.4 % of the total variance. A trade-off between flower abundance and stigma biomass indicated differing resource allocation strategies. Climatic variables, particularly rainfall and temperature during flowering, had a substantial impact on trait expression. These results support population-specific selection strategies to optimize saffron cultivation under shifting climatic conditions.
{"title":"Morpho-agronomic diversity and population-environment interactions in Crocus sativus L. revealed by multivariate analysis","authors":"Amir Hasan Taghiloofar, Gülsüm Boztaş, Emine Bayram","doi":"10.1016/j.egg.2025.100422","DOIUrl":"10.1016/j.egg.2025.100422","url":null,"abstract":"<div><div>Saffron (<em>Crocus sativus</em> L.) is a high-value crop known for its unique aroma, coloring properties, and medicinal uses. This study assessed agro-morphological and yield-related traits of Turkish and Iranian saffron populations under Mediterranean climatic conditions over two years (2013–2014). Fourteen quantitative traits, including floral organ dimensions, biomass components, and flower number, were analysed to explore phenotypic variation and genotype × environment (G × E) interactions. Significant year and population effects were observed. The Iranian genotype showed greater stability and performance under warmer, drier conditions, whereas the Turkish population was more productive in cooler, wetter climates. Principal component analysis (PCA) revealed that style length, stigma length, fresh stigma weight, and flower number were key contributors to trait variation, explaining 56.4 % of the total variance. A trade-off between flower abundance and stigma biomass indicated differing resource allocation strategies. Climatic variables, particularly rainfall and temperature during flowering, had a substantial impact on trait expression. These results support population-specific selection strategies to optimize saffron cultivation under shifting climatic conditions.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100422"},"PeriodicalIF":0.0,"publicationDate":"2025-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-31DOI: 10.1016/j.egg.2025.100423
Supreet Kaur, Shazia Shareef, P. Hariprasad
Lignin, a complex and recalcitrant component of plant biomass, remains a major bottleneck in agricultural waste valorization and bioprocessing, highlighting the importance of microbial degradation as a sustainable solution. In this study, 112 lignin-degrading bacterial strains were isolated from 24 diverse soil samples collected across the ecologically rich Western Ghats region of Karnataka, India. Their growth on lignin-containing substrates, including paddy straw, poplar wood, and Kraft lignin (KL) with or without nutrient supplementation, revealed substantial variability in ligninolytic potential. The isolates also exhibited lignin-mimicking dye decolorization activity against Azure B, Methylene Blue, Toluidine Blue O, Congo Red, and Remazol Brilliant Blue R, with efficiencies ranging from 0 % to 100 %. Notably, 24 strains showed superior KL degradation efficiency (50–60 %). GC-MS and LC-MS analyses confirmed lignin depolymerization, detecting low molecular weight aromatic intermediates and organic acids such as caffeic acid, sinapyl alcohol, coniferyl alcohol, cinnamic acid, eugenol, oxalic acid, benzoic acid, and butyric acid. The most efficient strains were identified as Streptomyces griseorubens CRDT-EB-21.6, Ochrobactrum ciceri CRDT-EB-22.2, Streptomyces mangrovi CRDT-EB-18.4, Streptomyces sp. CRDT-EB-19.7, and Streptomyces sp. CRDT-EB-21.12. Whole-genome sequencing of S. griseorubens CRDT-EB-21.6 revealed the presence of key genes associated with lignin degradation and aromatics assimilation pathways, including the β-ketoadipate, phenol catabolism, and gentisate routes, alongside glutathione peroxidase genes supporting extracellular peroxidase production. These data collectively emphasize that these lignolytic bacterial isolates from the Western Ghats are effective lignin degraders, possessing considerable potential for use in biorefineries, bioremediation, and sustainable biomass valorization.
{"title":"Evaluating the ligninolytic potential of soil bacteria isolated from Western Ghats, India","authors":"Supreet Kaur, Shazia Shareef, P. Hariprasad","doi":"10.1016/j.egg.2025.100423","DOIUrl":"10.1016/j.egg.2025.100423","url":null,"abstract":"<div><div>Lignin, a complex and recalcitrant component of plant biomass, remains a major bottleneck in agricultural waste valorization and bioprocessing, highlighting the importance of microbial degradation as a sustainable solution. In this study, 112 lignin-degrading bacterial strains were isolated from 24 diverse soil samples collected across the ecologically rich Western Ghats region of Karnataka, India. Their growth on lignin-containing substrates, including paddy straw, poplar wood, and Kraft lignin (KL) with or without nutrient supplementation, revealed substantial variability in ligninolytic potential. The isolates also exhibited lignin-mimicking dye decolorization activity against Azure B, Methylene Blue, Toluidine Blue O, Congo Red, and Remazol Brilliant Blue R, with efficiencies ranging from 0 % to 100 %. Notably, 24 strains showed superior KL degradation efficiency (50–60 %). GC-MS and LC-MS analyses confirmed lignin depolymerization, detecting low molecular weight aromatic intermediates and organic acids such as caffeic acid, sinapyl alcohol, coniferyl alcohol, cinnamic acid, eugenol, oxalic acid, benzoic acid, and butyric acid. The most efficient strains were identified as <em>Streptomyces griseorubens</em> CRDT-EB-21.6, <em>Ochrobactrum ciceri</em> CRDT-EB-22.2, <em>Streptomyces mangrovi</em> CRDT-EB-18.4, <em>Streptomyces</em> sp. CRDT-EB-19.7, and <em>Streptomyces</em> sp. CRDT-EB-21.12. Whole-genome sequencing of <em>S. griseorubens</em> CRDT-EB-21.6 revealed the presence of key genes associated with lignin degradation and aromatics assimilation pathways, including the β-ketoadipate, phenol catabolism, and gentisate routes, alongside glutathione peroxidase genes supporting extracellular peroxidase production. These data collectively emphasize that these lignolytic bacterial isolates from the Western Ghats are effective lignin degraders, possessing considerable potential for use in biorefineries, bioremediation, and sustainable biomass valorization.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100423"},"PeriodicalIF":0.0,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant-microbe interactions underpin plant health, ecosystem functioning and agricultural sustainability, yet their complexity demands approaches that move beyond single-layer analysis. Over the past decade omics technologies-spanning genomics, transcriptomics, proteomics, metabolomics and meta-omics have revolutionized our capacity to characterize microbial communities and their functional roles. While prior reviews have largely focused on individual omics layers, this review uniquely emphasizes the integration of multi-omics datasets with systems biology, artificial intelligence and gene-editing innovations to provide a holistic framework for understanding plant-microbe dynamics. By synthesizing insights across symbiosis, pathogen interactions, signaling pathways and environmental microbiomes, we highlight how cross-disciplinary integration refines mechanistic models and accelerates translation from laboratory discovery to field-level application. In doing so, we underscore underexplored opportunities such as the role of epigenomics, spatial omics and in situ mobile sequencing, while critically addressing challenges of data integration, reproducibility and standardization. This review therefore contributes not only a synthesis of current knowledge but also a forward looking perspective that positions multi-omics integration, empowered by AI and systems biology, as a transformative paradigm for developing resilient crops, advancing sustainable agriculture and fostering environmental stewardship.
{"title":"Genomic insights into plant-microbe interactions","authors":"Pushpa Gehlot, Jyoti Yadav, Poonam Meena, Priya Soni, Tripta Jain","doi":"10.1016/j.egg.2025.100421","DOIUrl":"10.1016/j.egg.2025.100421","url":null,"abstract":"<div><div>Plant-microbe interactions underpin plant health, ecosystem functioning and agricultural sustainability, yet their complexity demands approaches that move beyond single-layer analysis. Over the past decade omics technologies-spanning genomics, transcriptomics, proteomics, metabolomics and meta-omics have revolutionized our capacity to characterize microbial communities and their functional roles. While prior reviews have largely focused on individual omics layers, this review uniquely emphasizes the integration of multi-omics datasets with systems biology, artificial intelligence and gene-editing innovations to provide a holistic framework for understanding plant-microbe dynamics. By synthesizing insights across symbiosis, pathogen interactions, signaling pathways and environmental microbiomes, we highlight how cross-disciplinary integration refines mechanistic models and accelerates translation from laboratory discovery to field-level application. In doing so, we underscore underexplored opportunities such as the role of epigenomics, spatial omics and in situ mobile sequencing, while critically addressing challenges of data integration, reproducibility and standardization. This review therefore contributes not only a synthesis of current knowledge but also a forward looking perspective that positions multi-omics integration, empowered by AI and systems biology, as a transformative paradigm for developing resilient crops, advancing sustainable agriculture and fostering environmental stewardship.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100421"},"PeriodicalIF":0.0,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Soybean production in Indonesia is constrained by land competition, yet coastal sandy soils planted with high-value chili offer a niche for soybean via relay cropping. We evaluated five varieties (Anjasmoro, Dena 1, Demas 1, Malika, Grobogan) in an irrigated soybean–chili relay at Samas, Indonesia, across two seasons in 2023 (CS1: January–May; CS2: July–October) using a randomized complete block design with three replications. Analysis of variance (ANOVA) and genotype-by-environment (GGE) biplots assessed genotype × environment interaction (GEI), and a Random Forest model with permutation importance identified agronomic predictors of seed weight per plant (SWP). Results showed that ANOVA detected significant GEI for SWP and several traits, and GGE grouped varieties as: (1) high-to-moderate yield with stability (Anjasmoro, Dena 1), (2) high yield with lower stability (Malika, Demas 1), and (3) low yield with relative stability (Grobogan). Random Forest ranked predictors as plant height >100-seed weight > pods per plant > seeds per plant > leaf area, indicating that canopy architecture and seed mass, supported by number components, underpin performance. Under the tested irrigated coastal-sand conditions (CS1–CS2 at one site-year), Anjasmoro was the most promising, whereas Dena 1 exhibited the greatest stability at moderate yield; broader recommendations require multi-location, multi-year validation.
{"title":"Soybean genotype performance and seasonal stability in relay cropping with chili on coastal sandy soils","authors":"Rohimah H.S. Lestari , Endang Sulistyaningsih , Eka Tarwaca Susila Putra , Benito Heru Purwanto","doi":"10.1016/j.egg.2025.100420","DOIUrl":"10.1016/j.egg.2025.100420","url":null,"abstract":"<div><div>Soybean production in Indonesia is constrained by land competition, yet coastal sandy soils planted with high-value chili offer a niche for soybean via relay cropping. We evaluated five varieties (Anjasmoro, Dena 1, Demas 1, Malika, Grobogan) in an irrigated soybean–chili relay at Samas, Indonesia, across two seasons in 2023 (CS1: January–May; CS2: July–October) using a randomized complete block design with three replications. Analysis of variance (ANOVA) and genotype-by-environment (GGE) biplots assessed genotype × environment interaction (GEI), and a Random Forest model with permutation importance identified agronomic predictors of seed weight per plant (SWP). Results showed that ANOVA detected significant GEI for SWP and several traits, and GGE grouped varieties as: (1) high-to-moderate yield with stability (Anjasmoro, Dena 1), (2) high yield with lower stability (Malika, Demas 1), and (3) low yield with relative stability (Grobogan). Random Forest ranked predictors as plant height >100-seed weight > pods per plant > seeds per plant > leaf area, indicating that canopy architecture and seed mass, supported by number components, underpin performance. Under the tested irrigated coastal-sand conditions (CS1–CS2 at one site-year), Anjasmoro was the most promising, whereas Dena 1 exhibited the greatest stability at moderate yield; broader recommendations require multi-location, multi-year validation.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100420"},"PeriodicalIF":0.0,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-27DOI: 10.1016/j.egg.2025.100419
Pham Trong Nhan , Le Hong En , Nguyen Van Ket , Le Ngoc Trieu
The genetic diversity and variation of two Calamus poilanei populations in the Southern Central Highlands, Vietnam, were comparatively assessed using three different DNA fingerprinting techniques: Start Codon Targeted Polymorphism (SCoT), Inter Simple Sequence Repeat (ISSR), and CAAT Box-Derived Polymorphism (CBDP).
Combined data revealed that the genetic diversity of the Cat Tien population was characterized by expected heterozygosity (He) = 0.2498, Shannon index (I) = 0.3772, and the proportion of polymorphic bands (PPB) = 78.47 %. The Dak R'Lap population showed slightly higher values: He = 0.2529, I = 0.3826, and PPB = 82.3 %. At the metapopulation level, He = 0.2611, I = 0.3998, and PPB = 92.34 %. Pairwise genetic similarity coefficients between individuals (SCs) ranged from 0.536 to 0.933 (average = 0.755) in the Cat Tien population, from 0.565 to 0.914 (average = 0.770) in the Dak R'Lap population, and from 0.512 to 0.933 (average = 0.755) for the metapopulation. Gene flow between populations (Nm) was high (12.88), leading to low genetic differentiation (GST = 0.0374) and genetic distance (D = 0.0264). The majority of total genetic variation occurred within populations (94 %), with only 6 % among populations.
Although the three techniques showed no consistent correlation in estimating He, I, or PPB, they showed agreement in estimating Nm, GST, and D. Among them, SCoT was the most effective in this study, considering its overall utility.
These findings contribute to conservation planning for Calamus poilanei and provide orientation for future studies on related species.
{"title":"Study on population genetic diversity and variation of Calamus poilanei Conrard in the Southern Central Highlands, Vietnam","authors":"Pham Trong Nhan , Le Hong En , Nguyen Van Ket , Le Ngoc Trieu","doi":"10.1016/j.egg.2025.100419","DOIUrl":"10.1016/j.egg.2025.100419","url":null,"abstract":"<div><div>The genetic diversity and variation of two <em>Calamus poilanei</em> populations in the Southern Central Highlands, Vietnam, were comparatively assessed using three different DNA fingerprinting techniques: Start Codon Targeted Polymorphism (SCoT), Inter Simple Sequence Repeat (ISSR), and CAAT Box-Derived Polymorphism (CBDP).</div><div>Combined data revealed that the genetic diversity of the Cat Tien population was characterized by expected heterozygosity (<em>H</em><sub>e</sub>) = 0.2498, Shannon index (<em>I</em>) = 0.3772, and the proportion of polymorphic bands (<em>PPB</em>) = 78.47 %. The Dak R'Lap population showed slightly higher values: <em>H</em><sub>e</sub> = 0.2529, <em>I</em> = 0.3826, and <em>PPB</em> = 82.3 %. At the metapopulation level, <em>H</em><sub>e</sub> = 0.2611, <em>I</em> = 0.3998, and <em>PPB</em> = 92.34 %. Pairwise genetic similarity coefficients between individuals (SCs) ranged from 0.536 to 0.933 (average = 0.755) in the Cat Tien population, from 0.565 to 0.914 (average = 0.770) in the Dak R'Lap population, and from 0.512 to 0.933 (average = 0.755) for the metapopulation. Gene flow between populations (<em>N</em><sub>m</sub>) was high (12.88), leading to low genetic differentiation (<em>G</em><sub>ST</sub> = 0.0374) and genetic distance (<em>D</em> = 0.0264). The majority of total genetic variation occurred within populations (94 %), with only 6 % among populations.</div><div>Although the three techniques showed no consistent correlation in estimating <em>H</em><sub>e</sub>, <em>I</em>, or <em>PPB</em>, they showed agreement in estimating <em>N</em><sub>m</sub>, <em>G</em><sub>ST</sub>, and <em>D</em>. Among them, SCoT was the most effective in this study, considering its overall utility.</div><div>These findings contribute to conservation planning for <em>Calamus poilanei</em> and provide orientation for future studies on related species.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100419"},"PeriodicalIF":0.0,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145519601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-27DOI: 10.1016/j.egg.2025.100418
Shabeena Banu M S , Sherlin Rosita A , Jebastin T , Jay Shree M , Shivani J , Thajuddin N , Nargis Begum T
The opportunistic pathogen Streptococcus oralis (COL85/1862) (S. oralis) is responsible for several illnesses, such as Infective Endocarditis and Bacteremia. The raising bacterial resistance demands innovative therapeutic strategies that selectively target essential bacterial proteins. The present study adopted a subtractive proteomics approach to identify substantial drug targets in S. oralis. The complete proteome of S. oralis was retrieved from the UniProtKB database, and a series of computational filtering steps was conducted to identify non-homologous proteins, essential proteins, and novel druggable proteins using bioinformatics tools such as BLASTp, Database of Essential Genes (DEG) and Cytoscape to determine druggable targets. Initially, to discover non-homologous proteins, the proteome was first compared to the human host using BLASTp. Out of the 1816 total proteins, 1543 were specific to bacteria. Subsequently, screening using the Database of Essential Genes (DEG) identified 399 key proteins necessary for bacterial viability. Subcellular localization analysis using the PSORTb v3.0 web server identified proteins exclusively associated with the cytoplasm and cytoplasmic membrane. Druggability assessment revealed 216 proteins with druggable domains. Among them, 10 hub proteins were identified through Cytoscape's Protein-Protein Interaction (PPI) network analysis, underscoring their importance in bacterial function and survival. VirulentPred 2.0 was used to assess the virulence of these proteins and identified two crucial proteins involved in S. oralis virulence. These final virulent proteins, which are primarily ribosomal, were structurally modelled and subjected to molecular docking with known antibiotics. This subtractive proteomics pipeline successfully identified potential therapeutic targets, aiding in the development of potential antibacterial agents against S. oralis.
机会致病菌口腔链球菌（COL85/1862） （S. oralis）可导致多种疾病，如感染性心内膜炎和菌血症。细菌耐药性的提高需要创新的治疗策略，选择性地靶向必需的细菌蛋白质。本研究采用减法蛋白质组学方法来鉴定口腔链球菌的实质性药物靶点。从UniProtKB数据库中检索口腔链球菌的完整蛋白质组，利用BLASTp、database of essential Genes （DEG）和Cytoscape等生物信息学工具进行一系列计算过滤步骤，鉴定非同源蛋白、必需蛋白和新型可药物蛋白，确定可药物靶点。最初，为了发现非同源蛋白，首先使用BLASTp将蛋白质组与人类宿主进行比较。在总共1816种蛋白质中，1543种是针对细菌的。随后，使用必要基因数据库（DEG）进行筛选，鉴定出399种细菌生存所必需的关键蛋白。使用PSORTb v3.0 web服务器进行亚细胞定位分析，鉴定出与细胞质和细胞质膜相关的蛋白质。药理评价发现216个蛋白具有药理结构域。其中，通过Cytoscape的蛋白-蛋白相互作用（PPI）网络分析鉴定出10个枢纽蛋白，强调了它们在细菌功能和生存中的重要性。VirulentPred 2.0用于评估这些蛋白的毒力，并鉴定了两个与口腔链球菌毒力有关的关键蛋白。这些主要是核糖体的最终毒性蛋白在结构上进行了建模，并与已知抗生素进行了分子对接。这种减法蛋白质组学方法成功地鉴定了潜在的治疗靶点，有助于开发针对口腔链球菌的潜在抗菌药物。
{"title":"Exploring druggable and virulent proteins in Streptococcus oralis (COL85/1862) through computational subtractive proteomics approach","authors":"Shabeena Banu M S , Sherlin Rosita A , Jebastin T , Jay Shree M , Shivani J , Thajuddin N , Nargis Begum T","doi":"10.1016/j.egg.2025.100418","DOIUrl":"10.1016/j.egg.2025.100418","url":null,"abstract":"<div><div>The opportunistic pathogen <em>Streptococcus oralis</em> (COL85/1862) <em>(S. oralis)</em> is responsible for several illnesses, such as Infective Endocarditis and Bacteremia. The raising bacterial resistance demands innovative therapeutic strategies that selectively target essential bacterial proteins. The present study adopted a subtractive proteomics approach to identify substantial drug targets in <em>S. oralis.</em> The complete proteome of <em>S. oralis</em> was retrieved from the UniProtKB database, and a series of computational filtering steps was conducted to identify non-homologous proteins, essential proteins, and novel druggable proteins using bioinformatics tools such as BLASTp, Database of Essential Genes (DEG) and Cytoscape to determine druggable targets. Initially, to discover non-homologous proteins, the proteome was first compared to the human host using BLASTp. Out of the 1816 total proteins, 1543 were specific to bacteria. Subsequently, screening using the Database of Essential Genes (DEG) identified 399 key proteins necessary for bacterial viability. Subcellular localization analysis using the PSORTb v3.0 web server identified proteins exclusively associated with the cytoplasm and cytoplasmic membrane. Druggability assessment revealed 216 proteins with druggable domains. Among them, 10 hub proteins were identified through Cytoscape's Protein-Protein Interaction (PPI) network analysis, underscoring their importance in bacterial function and survival. VirulentPred 2.0 was used to assess the virulence of these proteins and identified two crucial proteins involved in <em>S. oralis</em> virulence. These final virulent proteins, which are primarily ribosomal, were structurally modelled and subjected to molecular docking with known antibiotics. This subtractive proteomics pipeline successfully identified potential therapeutic targets, aiding in the development of potential antibacterial agents against <em>S. oralis.</em></div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100418"},"PeriodicalIF":0.0,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145465373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Psophocarpus tetragonolobus (Winged bean) is an underutilized legume with significant economic potential but is constrained by a prolonged maturation period. This study aimed to identify early maturing accessions using qualitative and quantitative traits, and molecular markers (ISSR and SCoT) in a randomized complete block design. Vegetative and yield characters including leaf shape, corolla colour, pod formation, plant height, leaf length and stem diameter, varied significantly among accessions, with TPt-6 exhibiting the highest plant height (71.96 cm) and TPt-11 showing the largest stem diameter (1.9 cm). Accessions TPt-19, TPt-6 and TPt-125 exhibited early flowering at 41, 42, and 45 days after planting, respectively, while TPt-6 and TPt-11 showed early pod formation at 54 and 58 days, respectively. Among the three ISSR and SCoT markers tested, UBC-811 (ISSR) and SCoT-3 (SCoT) exhibited the highest polymorphic information content (69.75 %) and gene diversity (0.75), indicating their effectiveness in detecting genetic variation. The accessions were grouped into two major clusters A and B, with TPt-19 and TPt-9 forming a subclade within Cluster B which suggests genetic distinctiveness. These findings highlight TPt-6, TPt-11, TPt-19 and TPt-125 as promising candidates for breeding programs focused on improving early maturity in winged bean.
{"title":"Assessment of early morphological traits and molecular characters of Psophocarpus tetragonolobus (L.) DC. (winged bean) using ISSR and SCoT markers","authors":"Odunayo Joseph Olawuyi , Hiqmoh Adekilekun Mutiu , Omolara Ifeoluwa Akinyoola , Opeyemi Muideen Mudasiru , Joshua Oluremi Odedeji , Abiodun Abeeb Azeez","doi":"10.1016/j.egg.2025.100416","DOIUrl":"10.1016/j.egg.2025.100416","url":null,"abstract":"<div><div><em>Psophocarpus tetragonolobus</em> (Winged bean) is an underutilized legume with significant economic potential but is constrained by a prolonged maturation period. This study aimed to identify early maturing accessions using qualitative and quantitative traits, and molecular markers (ISSR and SCoT) in a randomized complete block design. Vegetative and yield characters including leaf shape, corolla colour, pod formation, plant height, leaf length and stem diameter, varied significantly among accessions, with TPt-6 exhibiting the highest plant height (71.96 cm) and TPt-11 showing the largest stem diameter (1.9 cm). Accessions TPt-19, TPt-6 and TPt-125 exhibited early flowering at 41, 42, and 45 days after planting, respectively, while TPt-6 and TPt-11 showed early pod formation at 54 and 58 days, respectively. Among the three ISSR and SCoT markers tested, UBC-811 (ISSR) and SCoT-3 (SCoT) exhibited the highest polymorphic information content (69.75 %) and gene diversity (0.75), indicating their effectiveness in detecting genetic variation. The accessions were grouped into two major clusters A and B, with TPt-19 and TPt-9 forming a subclade within Cluster B which suggests genetic distinctiveness. These findings highlight TPt-6, TPt-11, TPt-19 and TPt-125 as promising candidates for breeding programs focused on improving early maturity in winged bean.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100416"},"PeriodicalIF":0.0,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145362281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yard-long bean (Vigna unguiculata subsp. sesquipedalis) is an important horticultural crop valued for its protein, fiber, vitamins, and minerals. Vegetable agroforestry (VAF), which integrates vegetable cultivation within tree-based systems, offers a sustainable farming strategy but requires genotypes tolerant to shading. This study evaluated physiological traits and stress tolerance indices of seven yard-long bean genotypes under contrasting shading conditions. We hypothesized that chlorophyll dynamics (total content and a/b ratio), carotenoid levels, and nitrate reductase activity would correlate with shade tolerance indices, enabling the identification of genotypes adapted to low-light environments. Physiological assessments showed that total chlorophyll content was generally higher under moderate shading (S1), while the chlorophyll a/b ratio decreased under intense shading (S2), reflecting an increase in chlorophyll-b to enhance light harvesting. Carotenoid responses were genotype-specific, with some genotypes showing higher accumulation under full sunlight, suggesting a role in photoprotection and antioxidant defense. Nitrate reductase activity, influenced by light intensity, indicated variation in nitrogen assimilation and stress resilience. Stress tolerance indices, including Geometric Mean Productivity (GMP), Relative Production (RP), Tolerance Value (TOL), and Stress Tolerance Index (STI), classified genotypic performance under shading. KP-6796-3-4-10 and KP-6796-3-4-7 exhibited the highest GMP and stable yields, while KP-6718-1-1-10 and KP-6796-3-4-7 demonstrated shade tolerance based on RP and STI. Integration of physiological traits with yield-based indices highlighted genotypes with favorable pigment composition and metabolic responses. These results suggest that specific yard-long bean genotypes possess adaptive traits suitable for shaded or intercropped environments, offering insights for agroforestry-oriented breeding programs.
{"title":"Chlorophyll dynamics and stress tolerance assessment of yard-long bean genotypes in response to shading conditions","authors":"Fajrin Pramana Putra, Florentina Kusmiyati, Syaiful Anwar, Muhamad Ghazi Agam Sas","doi":"10.1016/j.egg.2025.100417","DOIUrl":"10.1016/j.egg.2025.100417","url":null,"abstract":"<div><div>Yard-long bean (Vigna unguiculata subsp. sesquipedalis) is an important horticultural crop valued for its protein, fiber, vitamins, and minerals. Vegetable agroforestry (VAF), which integrates vegetable cultivation within tree-based systems, offers a sustainable farming strategy but requires genotypes tolerant to shading. This study evaluated physiological traits and stress tolerance indices of seven yard-long bean genotypes under contrasting shading conditions. We hypothesized that chlorophyll dynamics (total content and a/b ratio), carotenoid levels, and nitrate reductase activity would correlate with shade tolerance indices, enabling the identification of genotypes adapted to low-light environments. Physiological assessments showed that total chlorophyll content was generally higher under moderate shading (S1), while the chlorophyll <em>a</em>/b ratio decreased under intense shading (S2), reflecting an increase in chlorophyll-b to enhance light harvesting. Carotenoid responses were genotype-specific, with some genotypes showing higher accumulation under full sunlight, suggesting a role in photoprotection and antioxidant defense. Nitrate reductase activity, influenced by light intensity, indicated variation in nitrogen assimilation and stress resilience. Stress tolerance indices, including Geometric Mean Productivity (GMP), Relative Production (RP), Tolerance Value (TOL), and Stress Tolerance Index (STI), classified genotypic performance under shading. KP-6796-3-4-10 and KP-6796-3-4-7 exhibited the highest GMP and stable yields, while KP-6718-1-1-10 and KP-6796-3-4-7 demonstrated shade tolerance based on RP and STI. Integration of physiological traits with yield-based indices highlighted genotypes with favorable pigment composition and metabolic responses. These results suggest that specific yard-long bean genotypes possess adaptive traits suitable for shaded or intercropped environments, offering insights for agroforestry-oriented breeding programs.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100417"},"PeriodicalIF":0.0,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145362284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-10DOI: 10.1016/j.egg.2025.100413
Prisweta Bhattacharjee , Rajkumari Elizabeth , Sayani Roy , Anupam Das Talukdar , Manabendra Dutta Choudhury , Amitabha Bhattacharjee
This study investigates the prevalence, virulence gene profile, and antibiotic resistance of hypervirulent Klebsiella pneumoniae (hvKp) strains isolated from drainage water near healthcare facilities in Southern Assam. A total of 32 K. pneumoniae isolates were identified, with 19 carrying virulence genes out of which 13 isolates carrying multiple virulence genes, including those responsible for iron acquisition and siderophore biosynthesis. Antibiogram profiling revealed high resistance rates, particularly to norfloxacin (78.94 %), followed by ampicillin (73.68 %) and ciprofloxacin (68.42 %), while imipenem and meropenem retained higher effectiveness, despite some isolates showing resistance. These findings highlight the clinical-environmental reservoirs of multidrug-resistant, hypervirulent K. pneumoniae strains, posing significant challenges for infection control and treatment in healthcare settings.
{"title":"Molecular characterization and antibiogram profiling of hypervirulent Klebsiella pneumoniae isolated from clinical-environmental interface","authors":"Prisweta Bhattacharjee , Rajkumari Elizabeth , Sayani Roy , Anupam Das Talukdar , Manabendra Dutta Choudhury , Amitabha Bhattacharjee","doi":"10.1016/j.egg.2025.100413","DOIUrl":"10.1016/j.egg.2025.100413","url":null,"abstract":"<div><div>This study investigates the prevalence, virulence gene profile, and antibiotic resistance of hypervirulent <em>Klebsiella pneumoniae</em> (hvKp) strains isolated from drainage water near healthcare facilities in Southern Assam. A total of 32 <em>K. pneumoniae</em> isolates were identified, with 19 carrying virulence genes out of which 13 isolates carrying multiple virulence genes, including those responsible for iron acquisition and siderophore biosynthesis. Antibiogram profiling revealed high resistance rates, particularly to norfloxacin (78.94 %), followed by ampicillin (73.68 %) and ciprofloxacin (68.42 %), while imipenem and meropenem retained higher effectiveness, despite some isolates showing resistance. These findings highlight the clinical-environmental reservoirs of multidrug-resistant, hypervirulent <em>K. pneumoniae</em> strains, posing significant challenges for infection control and treatment in healthcare settings.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100413"},"PeriodicalIF":0.0,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145320616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-08DOI: 10.1016/j.egg.2025.100415
A.S. Shaibu, U. Abduljalil, A.B. Yakubu
Sesame (Sesamum indicum L.) is an important oil seed crop mainly grown for its edible seeds. However, several production constraints have limited the yield per unit area in Nigeria among which includes the identification of suitable and stable varieties. To identify high-yielding and stable sesame genotypes for the Nigerian savannas, this study evaluated 15 genotypes across four locations during the 2024 wet season. The objective was to assess stability using parametric, non-parametric, and multi-trait stability index (MTSI) models. Field trials were conducted in a randomized complete block design, and data on key agronomic traits were subjected to combined analysis of variance and AMMI models. Significant differences were observed among the genotypes (G), environments (E) and G × E interaction for all the traits studied, except for the effect of E and GEI on number of capsules per plant. NCRIBEN02M had the highest grain yield (447.76 kg/ha) followed by NCRIBEN04E (424.08 kg/ha). The AMMI ANOVA showed significant (p < 0.01) effects of environment, genotype and GEI on sesame yield. While parametric and AMMI analyses identified NCRIBEN02M as the most stable genotype, the MTSI, which considers multiple traits, ranked Kangarawa as the most ideal. The study recommends NCRIBEN02M for its high yield and broad stability, and Kangarawa for multi-trait stability.
{"title":"Stability analysis of sesame (Sesamum indicum L.) genotypes in the savannas of Nigeria using multi-traits stability index","authors":"A.S. Shaibu, U. Abduljalil, A.B. Yakubu","doi":"10.1016/j.egg.2025.100415","DOIUrl":"10.1016/j.egg.2025.100415","url":null,"abstract":"<div><div>Sesame (<em>Sesamum indicum</em> L.) is an important oil seed crop mainly grown for its edible seeds. However, several production constraints have limited the yield per unit area in Nigeria among which includes the identification of suitable and stable varieties. To identify high-yielding and stable sesame genotypes for the Nigerian savannas, this study evaluated 15 genotypes across four locations during the 2024 wet season. The objective was to assess stability using parametric, non-parametric, and multi-trait stability index (MTSI) models. Field trials were conducted in a randomized complete block design, and data on key agronomic traits were subjected to combined analysis of variance and AMMI models. Significant differences were observed among the genotypes (G), environments (E) and G × E interaction for all the traits studied, except for the effect of E and GEI on number of capsules per plant. NCRIBEN02M had the highest grain yield (447.76 kg/ha) followed by NCRIBEN04E (424.08 kg/ha). The AMMI ANOVA showed significant (p < 0.01) effects of environment, genotype and GEI on sesame yield. While parametric and AMMI analyses identified NCRIBEN02M as the most stable genotype, the MTSI, which considers multiple traits, ranked Kangarawa as the most ideal. The study recommends NCRIBEN02M for its high yield and broad stability, and Kangarawa for multi-trait stability.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"37 ","pages":"Article 100415"},"PeriodicalIF":0.0,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145266102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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