Ecological Genetics and Genomics最新文献_第3页

Genetic diversity analysis and population structure of Ethiopian lentil (Lens culinaris Medik.) using SSR markers 利用SSR标记分析埃塞俄比亚小扁豆（Lens culinaris Medik.）遗传多样性及群体结构

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-01 DOI: 10.1016/j.egg.2025.100430

Shiferaw Teshome , Alemneh Mideksa , Tsegaye Getahun , Tileye Feyissa , Demsachew Guadie

Lentil, one of the most important legume crops, is well known for its high nutritional and economic values. Ethiopia fails to meet its domestic lentil demand, although it is one of the centers of lentil diversity. Thus, understanding the existing genetic diversity of lentil accessions is essential to develop effective breeding programs. There is dearth of information on the genetic diversity of landrace and released varieties in Ethiopia using SSR markers. Therefore, the genetic diversity of 130 lentil accessions was assessed using 12 simple sequence repeat (SSR) markers. A total of 57 alleles with overall average of 4.75 alleles per locus were detected. The results revealed the existence of considerable genetic variation within and among lentil populations with an overall mean value of 0.49 gene diversity (h) and the highest (0.51) polymorphic information content (PIC). The resolving power of markers, PIC, indicated that all markers used in this study were highly informative, with average values of 0.40. SSR 317–2 and SSR 28 were the most informative loci with the highest (0.51) PIC value. Analysis of molecular variance revealed moderate genetic variation of within (95 %) and among (5 %) populations. The principal coordinate analysis showed the overall variation of 53.67 % and grouped the populations into three clusters. The UPGMA, neighbor-joining tree, and STRUCTURE analysis grouped the populations into four clusters. The population structure revelated that the lentil populations under the study were shared alleles from 4 subgroups (K = 4), showing higher genetic admixture. The overall genetic variations within landrace populations were larger than released variety and ICARDA populations. In this study, significant genetic variations across lentil populations which can serve as a starting point for upcoming breeding initiatives have been obtained.

小扁豆是最重要的豆科作物之一，具有很高的营养价值和经济价值。尽管埃塞俄比亚是扁豆多样性的中心之一，但它未能满足其国内对扁豆的需求。因此，了解现有的小扁豆遗传多样性对制定有效的育种计划至关重要。利用SSR标记对埃塞俄比亚地方品种和释放品种的遗传多样性进行了研究。为此，利用12个SSR标记对130份小扁豆材料的遗传多样性进行了评价。共检测到57个等位基因，平均每个位点4.75个等位基因。结果表明，小扁豆群体内和群体间存在较大的遗传变异，总体平均基因多样性(h)为0.49，多态性信息含量（PIC）最高（0.51）。标记物PIC的分辨能力表明，本研究中使用的所有标记物都具有很高的信息量，平均值为0.40。SSR 317-2和SSR 28信息量最大，PIC值最高（0.51）。分子变异分析显示群体内（95 %）和群体间（5 %）存在中等程度的遗传变异。主坐标分析显示总体变异率为53.67 %，并将人群分为3类。UPGMA、邻居连接树和结构分析将种群分为四类。群体结构显示，本研究的小扁豆群体共有4个亚群（K = 4）等位基因，具有较高的遗传杂合性。地方品种群体内的总体遗传变异大于释放品种和ICARDA群体。在这项研究中，扁豆群体之间的显著遗传变异可以作为即将到来的育种计划的起点。

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引用次数: 0

Advancing fisheries management in Saleh Bay, West Nusa Tenggara, Indonesia: Insights from DNA barcoding of orange-spotted grouper (Epinephelus coioides) 印尼西努沙登加拉萨利赫湾渔业管理的进步：来自橙斑石斑鱼（Epinephelus coioides） DNA条形码的见解

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-01 DOI: 10.1016/j.egg.2025.100432

Regi Darmawan , Budy Wiryawan , Ari Purbayanto , Irfan Yulianto , Asadatun Abdullah , Sonja Kleinertz

This study investigates the genetic diversity and population structure of the orange-spotted grouper (Epinephelus coioides) by analyzing 30 individuals collected from Saleh Bay (Indonesia), across multiple Indonesian regions (Pangandaran and Madura Island) and neighboring countries from GenBank, using mitochondrial DNA (COI) markers. The results showed that E. coioides exhibited 15 haplotypes across Indonesia and other countries, with a relatively high haplotypic diversity (Hd = 0.809). Based on the apparent genetic differentiation and gene flow among E. coioides populations in Indonesia and other countries indicates a low level. Also, In Indonesia, the populations of E. coioides in Saleh Bay (present study), Pangandaran, and Madura Island exhibit limited or low gene flow. Furthermore, the phylogenetic tree construction of population E. coioides in Indonesia revealed that all samples clustered into a single large clade and confirming their common species identity. Additionally, this study provides valuable of genetic diversity and genetic population structure insights that can serve as a scientific basis for informed and sustainable grouper fisheries management strategies in Saleh Bay. Due to the apparent geographical conditions and genetic isolation of the E. coioides population in Saleh Bay, the management of E. coioides in this region is conducted independently of that in other regions.

本研究利用线粒体DNA （COI）标记，分析了从印度尼西亚萨利赫湾（Saleh Bay）、印度尼西亚多个地区（Pangandaran和Madura岛）和GenBank邻国收集的30只橙斑石斑鱼（Epinephelus coioides）的遗传多样性和种群结构。结果表明，在印度尼西亚和其他国家共有15个大肠杆菌单倍型，具有较高的单倍型多样性（Hd = 0.809）。在印度尼西亚和其他国家的大叶蝉种群间，遗传分化和基因流动表明其水平较低。此外，在印度尼西亚的Saleh Bay（目前的研究）、Pangandaran和Madura岛的E. coioides种群表现出有限或低的基因流动。此外，通过构建印度尼西亚种群的系统发育树，发现所有样本都聚集在一个大进化枝上，证实了它们共同的物种身份。此外，本研究提供了有价值的遗传多样性和遗传种群结构的见解，可以为萨利赫湾石斑鱼渔业的知情和可持续管理策略提供科学依据。由于Saleh Bay的地理条件和种群的遗传隔离性，该地区的coioides管理独立于其他地区。

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引用次数: 0

The complete mitochondrial genome of Androctonus mauritanicus (Arachnida: Scorpiones) 毛里塔尼雄蛙线粒体全基因组（蛛形纲：天蝎）

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-01 DOI: 10.1016/j.egg.2025.100429

Douae EL Ghoubali , Stacy Pirro , Abdellah Idrissi Azami , Chakib Nejjari , Najib AL Idrissi , Abderrazak Rfaki , Rachid Eljaoudi , Lahcen Belyamani , Saaid Amzazi , Salsabil Hamdi , Hassan Ghazal

Androctonus mauritanicus is a significant species in the realm of venomous arthropods. Its native habitat in North Africa has led to its recognition as a large scorpion with highly potent venom, resulting in a critical number of fatalities among humans annually. The specimen used in this study was collected in Marrakech, Morocco, in 2019. To understand its genetic diversity, we sequenced, assembled, and annotated the mitochondrial genome of A. mauritanicus and compared it with those of other scorpions. The assembled mitochondrial genome resulted in 14886 base pairs of circular DNA with 32.37 % GC content. Genome annotation predicted 13 protein-coding genes, 21 transfer RNAs (with a notable absence of tRNA-Asp), and 2 ribosomal RNA genes. The nucleotide composition exhibits an AT bias of 67.7 %, with heterogeneity across codon positions. Phylogenetic analysis consistently shows A. mauritanicus is closely related to Buthus occitanus and Androctonus australis, with an evolutionary distance of 0.178 to A. australis. Selection pressure analysis using codon-based Z-tests indicates significant purifying selection across most mitochondrial protein-coding genes, with diminishing significance in more distantly related species, while positive selection was not statistically significant. This study improves our knowledge of scorpion biology, ecology and evolution and would further our ability to explore practical applications for medicine and species conservation.

毛利塔尼雄蛙是有毒节肢动物领域的一个重要物种。它在北非的原生栖息地使它被认为是一种具有强大毒液的大型蝎子，每年导致人类死亡的人数达到临界水平。本研究中使用的标本于2019年在摩洛哥马拉喀什收集。为了了解其遗传多样性，我们对毛利塔尼亚蝎子的线粒体基因组进行了测序、组装和注释，并与其他蝎子的线粒体基因组进行了比较。组装的线粒体基因组得到14886个碱基对的环状DNA， GC含量为32.37 %。基因组注释预测了13个蛋白质编码基因，21个转移RNA（明显缺少tRNA-Asp）和2个核糖体RNA基因。核苷酸组成显示出67.7 %的AT偏倚，具有密码子位置的异质性。系统发育分析结果一致表明，毛利塔尼古猿与褐尾Buthus occitanus和南方雄蚊亲缘关系密切，与南方古猿的进化距离为0.178。基于密码子的z检验的选择压力分析表明，大多数线粒体蛋白编码基因存在显著的纯化选择，在亲缘关系越远的物种中，这种选择的显著性越低，而正选择在统计学上不显著。这项研究提高了我们对蝎子生物学、生态学和进化的认识，并将进一步提高我们探索蝎子在医学和物种保护方面的实际应用能力。

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引用次数: 0

Comparative and pan-genome analysis of the complete genomes of the periodontal pathogen Tannerella forsythia reveals unique tetracycline resistance protein Q and GT22 carbohydrate-active enzyme family in strain 92A2 通过对牙周病原菌连翘单宁菌（Tannerella forsythia）全基因组的比较和泛基因组分析，发现菌株92A2具有独特的四环素抗性蛋白Q和GT22糖活性酶家族

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-11-17 DOI: 10.1016/j.egg.2025.100428

Roja Suresh , Susanthika Jayachandiran , Pratebha Balu , Dhamodharan Ramasamy

Tannerella forsythia is a key periodontal pathogen associated with chronic periodontitis, yet comprehensive genomic comparisons based on complete genomes remain limited. In this study, we conducted a comparative and pan-genome analysis of all available complete genomes of T. forsythia using various bioinformatics tools to identify core, accessory and unique genes and their functional annotations. Phylogenetic analyses based on all 59 and 27 high-quality genomes revealed intra-cluster divergence supported by ANI and dDDH comparisons. Comparative genomics revealed the existence of a conserved core genome with strain-specific variations linked to virulence and antimicrobial resistance, coupled with genome plasticity. Specifically, the tetracycline resistance gene tet(Q) was identified solely in T. forsythia 92A2 (found in 3 copies) and not in KS16 or 3313, suggesting possible strain-specific resistance. KEGG pathway analyses indicated that 74 core pathways were conserved across all strains, 13 were shared between 92A2 and 3313, 2 were shared by KS16 and 92A2, and KS16 and 3313 exclusively shared none. CAZyme analysis revealed conserved profiles with strain-specific differences and a unique GT22 family in strain 92A2. The pan-genome held 3575 gene clusters with 61.6 % core genes and 22.6 % strain-specific genes. These results provide the first complete genome-based pan-genomic profile of T. forsythia, indicating its genomic diversities, prospects of antibiotic resistance, and its conserved metabolic traits.

连翘单宁菌是一种与慢性牙周炎相关的关键牙周病原体，但基于全基因组的全面基因组比较仍然有限。本研究利用多种生物信息学工具对连翘（T. forsythia）全基因组进行比较和泛基因组分析，鉴定核心基因、辅助基因和独特基因及其功能注释。基于所有59个和27个高质量基因组的系统发育分析显示，ANI和dDDH比较支持簇内差异。比较基因组学揭示了一个保守的核心基因组的存在，该基因组具有与毒力和抗菌素耐药性相关的菌株特异性变异，以及基因组的可塑性。其中，四环素耐药基因tet(Q)仅在连翘92A2（3个拷贝）中发现，而在KS16和3313中未发现，提示可能存在菌株特异性耐药。KEGG通路分析表明，所有菌株共有74条核心通路，其中92A2与3313共有13条，KS16与92A2共有2条，KS16与3313完全不共享。CAZyme分析显示菌株92A2具有菌株特异性差异和独特的GT22家族。该泛基因组包含3575个基因簇，其中核心基因占61.6 %，菌株特异性基因占22.6% %。这些结果提供了第一个完整的基于基因组的连翘泛基因组图谱，表明了连翘的基因组多样性、抗生素耐药性的前景及其保守的代谢特性。

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引用次数: 0

Machine learning classification of mutagen treatment types in crop breeding: A comparative analysis 作物育种中诱变剂处理类型的机器学习分类：比较分析

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-11-14 DOI: 10.1016/j.egg.2025.100427

Lawal AbdulRafiu Abiodun , Godwin Baret Mangshin , Mehdi Rahimi

Mutation breeding is a vital tool for crop improvement, yet mutagen selection still relies largely on trial-and-error. This study developed a machine learning (ML) framework to predict mutagen treatment types using 2815 curated entries from the FAO/IAEA Mutant Variety Database. The dataset included crop descriptors, mutagen details, and trait outcomes. Preprocessing involved removal of incomplete entries, standardization of categories, and class balancing with SMOTE and weighted models. Three classifiers—Random Forest (RF), Support Vector Machine (SVM), and Logistic Regression (LR)—were trained using stratified 80/20 splits and 10-fold cross-validation. Model performance was assessed with accuracy, precision, recall, F1-score, and ROC-AUC, with statistical comparisons via Friedman and Wilcoxon tests. RF and SVM achieved the highest accuracies (96.3 %), while LR performed slightly lower (95.7 %). SVM demonstrated superior recall (0.695) and F1-score (0.624), improving detection of minority classes such as EMS and somaclonal variation (p < .05). Gamma rays dominated overall, but EMS produced broader phenotypic and agronomic improvements. These findings demonstrate ML—particularly SVM—as a decision-support tool to guide mutagen selection, reduce experimental inefficiency, and accelerate breeding for food and climate resilience.

突变育种是作物改良的重要手段，但诱变剂的选择仍然主要依赖于反复试验。本研究开发了一个机器学习（ML）框架，使用来自FAO/IAEA突变品种数据库的2815个策划条目来预测诱变剂治疗类型。该数据集包括作物描述符、诱变剂细节和性状结果。预处理包括删除不完整的条目、标准化类别以及使用SMOTE和加权模型进行类平衡。三个分类器-随机森林（RF），支持向量机（SVM）和逻辑回归(LR) -使用分层80/20分裂和10倍交叉验证进行训练。通过准确性、精密度、召回率、f1评分和ROC-AUC评估模型性能，并通过Friedman和Wilcoxon检验进行统计比较。RF和SVM的准确率最高（96.3% %），而LR的准确率略低（95.7% %）。SVM在召回率（0.695）和f1得分（0.624）上均有优势，提高了EMS和体细胞无性系变异等少数类别的检测（p <； .05）。伽玛射线总体上占主导地位，但EMS产生了更广泛的表型和农艺改善。这些发现表明，机器学习（尤其是支持向量机）是指导诱变剂选择的决策支持工具，可以减少实验效率低下，加快粮食和气候适应能力的育种。

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引用次数: 0

Bacterial abundance and diversity in rhizosphere and bulk soils of organic and conventional rice cultivation fields 有机稻田和常规稻田根际和块状土壤细菌丰度和多样性

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-11-10 DOI: 10.1016/j.egg.2025.100426

Wubayehu Gebremedhin , Tantriani , Weiguo Cheng , Keitaro Tawaraya

The rhizosphere microbiome plays a critical role in plant growth, particularly under organic cultivation. However, the combined effects of rice agroecosystem (upland vs. lowland) and cultivation systems (organic vs. conventional) on rhizosphere bacterial communities remain poorly understood. In this study, we investigated bacterial abundance and diversity in rhizosphere and bulk soils under six treatments combining water regime and fertilizer input: organic lowland, organic upland, organic bulk soil, conventional lowland, conventional upland, and conventional bulk soil. Rice (Oryza sativa L.) was grown under controlled upland and lowland conditions using soils collected from organic and conventional fields. Amplicon sequencing of 16S rRNA genes revealed that organic upland significantly increased bacterial abundance, richness, and Shannon diversity at both phylum and genus levels compared to conventional upland. Similarly, organic lowland and organic bulk soil supported greater bacterial richness and diversity than their conventional counterparts (conventional lowland and conventional bulk soil, respectively). A total of 57 microbial phyla and 819 genera were identified, with Pseudomonadota and Actinomycetota dominating across samples. Notably, organic upland exhibited the highest genus-level bacterial richness and the largest number of unique operational taxonomic units, suggesting enhanced microbial niche differentiation. Principal component analysis further confirmed distinct community structuring between organic and conventional systems. These results demonstrate that organic cultivation fosters a more diverse and abundant rhizosphere bacterial community, highlighting its potential to increase microbial-driven soil health and ecosystem functioning in rice agroecosystems.

根际微生物群在植物生长中起着至关重要的作用，特别是在有机栽培下。然而，水稻农业生态系统（旱地vs低地）和耕作系统（有机vs传统）对根际细菌群落的综合影响仍然知之甚少。研究了有机低地、有机高地、有机大块土、常规低地、常规高地和常规大块土6种水肥结合处理下根际土壤和块土细菌的丰度和多样性。水稻（Oryza sativa L.）利用从有机田和常规田收集的土壤，在控制旱地和低地条件下种植。16S rRNA基因扩增子测序结果显示，与常规旱地相比，有机旱地在门和属水平上显著增加了细菌丰度、丰富度和Shannon多样性。同样，有机低地和有机块状土壤比常规土壤（分别为常规低地和常规块状土壤）支持更大的细菌丰富度和多样性。共鉴定出微生物57门819属，以假单胞菌门和放线菌门为主。有机高地具有最高的属级细菌丰富度和最多的独特操作分类单位，表明微生物生态位分化增强。主成分分析进一步证实了有机系统与常规系统之间存在明显的群落结构。这些结果表明，有机栽培培养了更多样化和丰富的根际细菌群落，突出了其在提高微生物驱动的土壤健康和水稻农业生态系统功能方面的潜力。

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引用次数: 0

Deciphering the genetic basis of milk composition in cattle through pathway analysis and identification of key genes 通过途径分析和关键基因的鉴定，解读牛乳成分的遗传基础

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-11-04 DOI: 10.1016/j.egg.2025.100424

Heydar Ghiasi , Majid Khaldari , Reza Taherkhani , Navid Ghavi Hossein-Zadeh

A total of 1724 genes reported to influence milk composition traits (MCT) in cattle were compiled from the Animal QTL Database (up to October 10, 2022) and used for pathway analysis and the identification of hub and common genes. MCT included the following traits: milk fat yield (MFY), milk protein yield (MPY), milk fat percentage (MFP), and milk protein percentage (MPP). These genes were primarily derived from studies in Holstein cattle but also included other dairy breeds. For each trait, a gene set was established, and the overlap among gene sets was examined. Using the R package SuperExactTest, we identified 130 genes shared across all four traits. Pathway analysis of these 130 genes using g:Profiler revealed 39 significant pathways. The most significant pathways (P < 0.009) included the PI3K-Akt signaling pathway, Growth Hormone (GH) signaling, SHC-related events triggered by IGF1R, focal adhesion, basement membrane collagen trimer, collagen network, collagen type IV trimer, and network-forming collagen trimer. A gene network was subsequently constructed, and hub genes were identified using Cytoscape and cytoHubba. Ten hub genes (IGF1R, IGF2, LEP, IGF1, PDGFRB, GH1, ERBB2, GHR, PTK2, and CDKN1A) were highlighted as central regulators of milk composition traits. These findings provide insights into the shared genetic architecture of MCT across traits and suggest candidate genes for simultaneous genomic selection in dairy cattle.

从动物QTL数据库（截至2022年10月10日）中共收集了1724个影响牛乳成分性状（MCT）的基因，并用于途径分析和枢纽基因和共同基因的鉴定。MCT包括乳脂产量（MFY）、乳蛋白产量（MPY）、乳脂率（MFP）和乳蛋白率（MPP）。这些基因主要来源于对荷斯坦牛的研究，但也包括其他奶牛品种。对于每个性状，建立一个基因集，并检查基因集之间的重叠。使用R包SuperExactTest，我们确定了这四个性状共有的130个基因。利用g:Profiler对这130个基因进行通路分析，发现了39条重要通路。最显著的通路（P <； 0.009）包括PI3K-Akt信号通路、生长激素（GH）信号通路、IGF1R触发的shc相关事件、局灶黏着、基底膜胶原三聚体、胶原网络、胶原IV型三聚体和网状胶原三聚体。随后构建了基因网络，并利用Cytoscape和cytoHubba对枢纽基因进行了鉴定。10个中心基因（IGF1R、IGF2、LEP、IGF1、PDGFRB、GH1、ERBB2、GHR、PTK2和CDKN1A）是乳成分性状的中心调控因子。这些发现提供了MCT跨性状共享遗传结构的见解，并为奶牛同时进行基因组选择提供了候选基因。

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引用次数: 0

Morpho-agronomic diversity and population-environment interactions in Crocus sativus L. revealed by multivariate analysis 多变量分析揭示藏红花形态农艺多样性及种群与环境的相互作用

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-11-02 DOI: 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.

藏红花（Crocus sativus L.）是一种高价值的作物，以其独特的香气，着色特性和药用用途而闻名。本研究历时两年（2013-2014），评估了地中海气候条件下土耳其和伊朗藏红花种群的农业形态和产量相关性状。分析了14个数量性状，包括花器官尺寸、生物量组成和花数，探讨了表型变异和基因型 × 环境（G × E）的相互作用。观察到显著的年效应和种群效应。伊朗基因型在温暖、干燥的条件下表现出更大的稳定性和性能，而土耳其种群在凉爽、潮湿的气候下更高产。主成分分析表明，花柱长度、柱头长度、鲜柱头重和花数是性状变异的主要影响因子，对总变异的贡献率为56.4% %。花丰度和柱头生物量之间的权衡反映了不同的资源分配策略。气候变量，特别是开花期间的降雨和温度，对性状表达有重大影响。这些结果支持在变化的气候条件下优化藏红花种植的种群特异性选择策略。

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引用次数: 0

Evaluating the ligninolytic potential of soil bacteria isolated from Western Ghats, India 印度西高止山脉土壤细菌降解木质素的潜力评价

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-10-31 DOI: 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.

木质素是植物生物量的一种复杂而顽固的成分，仍然是农业废物价值化和生物处理的主要瓶颈，突出了微生物降解作为可持续解决方案的重要性。在这项研究中，从印度卡纳塔克邦生态丰富的西高止山脉地区收集的24种不同土壤样品中分离出112株木质素降解细菌。它们在含有木质素的基质（包括水稻秸秆、杨木和卡夫木质素（KL））上有或没有营养补充的生长，显示出木质素分解潜力的巨大差异。分离物对天青B、亚甲基蓝、甲苯胺蓝O、刚果红和瑞马唑亮蓝R也表现出模仿木质素的染料脱色活性，脱色效率为0 %至100% %。其中，24株菌株的KL降解率为50 ~ 60 %。GC-MS和LC-MS分析证实木质素解聚，检测到低分子量芳香族中间体和有机酸，如咖啡酸、新树醇、松柏醇、肉桂酸、丁香酚、草酸、苯甲酸和丁酸。结果表明，最高效的菌株为灰绿链霉菌CRDT-EB-21.6、绿赭杆菌CRDT-EB-22.2、红树链霉菌CRDT-EB-18.4、链霉菌sp. CRDT-EB-19.7和链霉菌sp. CRDT-EB-21.12。griseorubens crpt - eb -21.6的全基因组测序显示，存在与木素降解和芳香物质同化途径相关的关键基因，包括β-酮己二酸、酚分解代谢和龙胆酸途径，以及支持细胞外过氧化物酶产生的谷胱甘肽过氧化物酶基因。这些数据共同强调，这些从西高止山脉分离的木质素分解细菌是有效的木质素降解剂，在生物炼制、生物修复和可持续生物质增值方面具有相当大的潜力。

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引用次数: 0

Genomic insights into plant-microbe interactions 植物与微生物相互作用的基因组学见解

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-10-30 DOI: 10.1016/j.egg.2025.100421

Pushpa Gehlot, Jyoti Yadav, Poonam Meena, Priya Soni, Tripta Jain

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.

植物与微生物的相互作用是植物健康、生态系统功能和农业可持续性的基础，但它们的复杂性需要超越单层分析的方法。在过去的十年中，基因组学、转录组学、蛋白质组学、代谢组学和元组学等组学技术已经彻底改变了我们表征微生物群落及其功能角色的能力。虽然之前的综述主要集中在单个组学层面，但这篇综述独特地强调了多组学数据集与系统生物学、人工智能和基因编辑创新的整合，为理解植物-微生物动力学提供了一个整体框架。通过综合对共生、病原体相互作用、信号通路和环境微生物组的见解，我们强调跨学科整合如何完善机制模型，并加速从实验室发现到现场应用的转化。在此过程中，我们强调了未充分开发的机会，如表观基因组学、空间组学和原位移动测序的作用，同时关键地解决了数据整合、可重复性和标准化方面的挑战。因此，本综述不仅对现有知识进行了综合，而且还提出了前瞻性观点，将人工智能和系统生物学支持的多组学整合定位为开发抗灾作物、推进可持续农业和促进环境管理的变革范例。

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引用次数: 0