Ecological Genetics and Genomics最新文献_第4页

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-01-01

引用次数: 0

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-01-01

引用次数: 0

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2026-01-01

引用次数: 0

Species-specific gut microbiomes in Anomala beetle larvae suggest predicted carbohydrate and xenobiotic processing capacities 异常甲虫幼虫的物种特异性肠道微生物组提示预测碳水化合物和异种生物处理能力

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-30 DOI: 10.1016/j.egg.2025.100439

R. Karthik , Henry Joseph Oduor Ogola , Ramganesh Selvarajan , Abhishek Walia , Suresh Kumar Mahala , R.S. Chandel

Soil-dwelling scarab beetle larvae rely on gut microbiomes for nutrient extraction from complex plant polymers and potentially for tolerating xenobiotic compounds, yet comparative functional insights across closely related species remain limited. Here, we characterized gut bacterial communities of four economically important cogeneric Anomala species (A. dorsalis, A. dimidiata, A. varicolor, and A. polita) using 16S rDNA amplicon sequencing and PICRUSt2 functional profiling. After quality filtering, 16,822–21,440 reads per species were analyzed, revealing distinct species-specific microbiome signatures. A. dorsalis exhibited the highest bacterial diversity (133 ASVs, Shannon = 3.83), followed by A. dimidiata and A. varicolor, while A. polita showed the lowest diversity (77 ASVs, Shannon = 3.04). All species were dominated by Bacillota_A (Firmicutes) (35.1–46.7 %), but taxonomic composition varied significantly. A. dorsalis, A. dimidiata, and A. varicolor were enriched in fermentative families (Lachnospiraceae, Anaerotignaceae: 10–14 %), whereas A. polita was characterized by Pseudomonadaceae (14.8 %) and minimal Lachnospiraceae (<0.9 %). Core microbiome analysis identified 23 shared genera accounting for 57.4 % relative abundance, alongside species-specific genera. Functional predictions revealed extensive carbohydrate-active enzyme (CAZyme) repertoires in all species, with A. dorsalis and A. dimidiata showing higher predicted abundances of cellulases (GH5/GH9; ∼1.8–2-fold) and xylanases (GH10/GH11; ∼1.5–1.9-fold) relative to A. polita. Predicted xenobiotic degradation pathways varied, with enrichment in glutathione S-transferases and peroxidases A. dimidiata (∼1.6–2.0-fold), and carboxylesterase genes (∼1.7-fold) in A. polita. These findings indicate that Anomala larvae employ distinct, ecology-linked microbial strategies balancing carbohydrate metabolism and detoxification, generating testable hypotheses for functional validation and microbiome-informed pest management.

居住在土壤中的圣甲虫幼虫依靠肠道微生物群从复杂的植物聚合物中提取营养物质，并可能耐受外源化合物，但在密切相关的物种之间的比较功能研究仍然有限。在这里，我们利用16S rDNA扩增子测序和PICRUSt2功能分析，对四种经济上重要的共属异常物种（A. dorsalis， A. dimidiata， A. varicolor和A. polita）的肠道细菌群落进行了表征。经过质量过滤，每个物种分析了16,822-21,440个reads，揭示了不同物种特异性的微生物组特征。dorsalis的细菌多样性最高（133种，Shannon = 3.83），其次是A. dimidiata和A. varicolor，而A. polita的细菌多样性最低（77种，Shannon = 3.04）。所有种均以Bacillota_A（厚壁门）为优势种（35.1 ~ 46.7 %），但分类组成差异较大。A. dorsalis， A. dimidiata和A. varicolor在发酵科（Lachnospiraceae, Anaerotignaceae: 10-14 %）中丰富，而A. polita以Pseudomonadaceae（14.8 %）和最少的Lachnospiraceae （<0.9 %）为特征。核心微生物组分析鉴定出23个共有属，相对丰度为57.4% %，以及物种特异性属。功能预测显示，所有物种都具有广泛的碳水化合物活性酶（CAZyme）谱，与A. dorsalis和A. dimidiata相比，其纤维素酶（GH5/GH9；约1.8 - 2倍）和木聚糖酶（GH10/GH11；约1.5 - 1.9倍）的预测丰度更高。预测的外源降解途径各不相同，在A. polita中富集谷胱甘肽s -转移酶和过氧化物酶A. dimidiata（约1.6 - 2.0倍）和羧酸酯酶基因（约1.7倍）。这些发现表明，异常幼虫采用独特的、与生态相关的微生物策略来平衡碳水化合物代谢和解毒，为功能验证和微生物组信息虫害管理提供了可测试的假设。

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引用次数: 0

Exploration of genetic diversity and population structure in North Indian Aegle marmelos accessions using ISSR markers 利用ISSR标记对北印度安吉尔甜瓜遗传多样性和群体结构的研究

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-29 DOI: 10.1016/j.egg.2025.100438

Prince Minhas , Rajvinder Minhas , Atul Chamyal , Rakesh Kumar , Kanika Aggarwal , Rahul Kumar , Maneet Rana , Vikas Sharma

Aegle marmelos (L.) Correa, commonly known as Bael in North India, is an important underutilized fruit tree with immense medicinal, nutritional, and cultural significance across the Indian subcontinent. Despite its widespread distribution and traditional value, comprehensive genetic diversity studies are still limited, particularly across diverse agroclimatic regions. In the present study, 58 accessions of A. marmelos collected from Punjab, Haryana and Himachal Pradesh were analyzed using 12 polymorphic Inter-Simple Sequence Repeat (ISSR) markers to assess genetic diversity and population structure. A total of 56 polymorphic bands were generated by these 12 primers, with an average of 4.66 bands per primer. The size of amplified fragments ranged from 400 bp to 2000 bp. Polymorphism Information Content (PIC) and Marker Index (MI) values indicated high levels of genetic variability among the accessions. UPGMA-based cluster analysis grouped all accessions into three major clusters with subgroups. STRUCTURE analysis also revealed the presence of three distinct genetic populations with evidence of admixture. The results suggest a moderate to high degree of genetic diversity and heterozygosity, underscoring the potential of analyzed accessions for the selection of elite accessions for breeding and conservation purpose. The study demonstrates the efficiency of ISSR markers in distinguishing A. marmelos accessions and highlights the need for systematic conservation strategies and genetic enhancement programs in this plant. Specifically, samples with codes Pd, K7, N, H,H7, U4 and U11 can be selected on priority basis for various purposes. These findings can contribute to the improvement and sustainable utilization of this traditionally and pharmacologically important species.

安吉尔甜瓜（L.）Correa，在印度北部通常被称为Bael，是一种重要的未被充分利用的果树，在整个印度次大陆具有巨大的药用、营养和文化意义。尽管遗传多样性具有广泛的分布和传统价值，但对遗传多样性的综合研究仍然有限，特别是在不同的农业气候区域。利用12个多态性间简单序列重复（ISSR）标记对来自印度旁遮普、哈里亚纳邦和喜马偕尔邦的58份蜜瓜种质资源进行遗传多样性和群体结构分析。12条引物共产生56条多态性条带，平均每个引物产生4.66条多态性条带。扩增片段大小在400 ~ 2000 bp之间。多态性信息含量（PIC）和标记指数（MI）表明各材料间存在较高的遗传变异。基于upgma的聚类分析将所有接入分组为三个主要的类和子组。结构分析还揭示了三个不同的遗传群体的存在，并有混合的证据。结果表明，所分析的材料具有中等至高度的遗传多样性和杂合性，这表明所分析的材料具有选择优良材料进行育种和保护的潜力。本研究证明了ISSR标记在柑橘种质资源鉴别中的有效性，并强调了对柑橘种质资源进行系统保护和遗传增强的必要性。具体来说，根据不同的用途，可以优先选择代码为Pd、K7、N、H、H7、U4、U11的样品。这些发现有助于对这一传统和药理上重要的物种进行改良和可持续利用。

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引用次数: 0

Characterization of heterozygosity-enriched regions and population structure in Indian cattle breeds 印度牛品种杂合性富集区及种群结构特征

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-27 DOI: 10.1016/j.egg.2025.100437

Aditi Yadav , Pallavi Rathi , S.P. Dixit , Indrajit Ganguly , Sanjeev Singh

Heterozygosity-rich regions (HRR) refer to genomic regions exhibiting increased heterozygosity, linked to influencing traits like immune response, survival, fertility, and other fitness-related characteristics. Analyzing HRR helps to identify areas of the genome with high genetic variation, thus providing deep insights into a population's genetic diversity and revealing specific genome segments where increased diversity is beneficial. In this study, heterozygosity rich regions were identified in 158 animals of eleven Indian cattle breeds (Bos indicus) using 777K BovineHD BeadChip. In total, 8127 heterozygous regions were identified. Among the breeds studied, the short-statured Ladakhi breed exhibited the highest number of heterozygous regions (1412), while the Sahiwal, a prominent dairy breed of the Indian subcontinent, exhibited the lowest (467). The Mean genome length of RoHet was maximum in the Ladakhi breed (44.09 Mb) and minimum in the Hariana breed (12.16 Mb). The highest number of RoHet was observed on chromosome 7 in the short statured Vechur breed spanning 9.2 % of the chromosome's length. In most breeds, the maximum average length of Runs of heterozygosity (ROHet) was found on the sixth chromosome, while the fifth chromosome harboured the highest number of ROHet. Functional classification of the 193 annotated genes identified in the heterozygous regions were involved in cellular processes, biological regulation, and metabolic process. Principal component analysis of ROHet regions to study the population structure revealed distinct clustering of short statured cattle breeds (Ladakhi and Vechur) from rest of the Indian breeds while the dairy and dual-purpose breeds clustered together.

杂合度丰富区域（HRR）是指杂合度增加的基因组区域，与影响免疫反应、生存、生育和其他健康相关特征等性状有关。分析HRR有助于确定基因组中具有高遗传变异的区域，从而深入了解种群的遗传多样性，并揭示增加多样性有益的特定基因组片段。本研究利用777K BovineHD BeadChip对11个印度牛品种（Bos indicus）的158头牛进行了杂合性富集区鉴定。共鉴定出8127个杂合区。拉达克品种RoHet的平均基因组长度最大（44.09 Mb），哈里亚纳品种最小（12.16 Mb）。在矮小的维库尔品种中，7号染色体上RoHet的数量最多，占染色体长度的9.2% %。在大多数品种中，最大平均长度的杂合性（ROHet）发现在第6染色体，而第5染色体拥有最多的ROHet数。在杂合区鉴定的193个注释基因的功能分类涉及细胞过程、生物调控和代谢过程。通过对ROHet地区种群结构的主成分分析发现，矮小牛品种（Ladakhi和Vechur）与其他印度品种明显聚集在一起，而乳制品和两用品种则聚集在一起。

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引用次数: 0

Dimensional and morphological variability of traditional rice cultivars in South India: Implications for food processing and market application 南印度传统水稻品种的尺寸和形态变异：对食品加工和市场应用的影响

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-24 DOI: 10.1016/j.egg.2025.100436

Jayanthi B, Harshini KK, Bhavadharani T, Sudharsana S

This study evaluates the varietal impact on the engineering and dimensional properties of traditional South Indian rice cultivars. Twenty-two rice varieties were cultivated and evaluated under similar conditions using a random block design experiment. Width, length, and thickness of the rice varieties ranging from 1.90 to 3.14 mm, 5.13–7.85 mm, and 0.94–2.96 mm, respectively. Mean diameter, sphericity (0.33–0.67), aspect ratio (0.24–0.56), and surface area (12.66–36.75 mm²) were calculated. Heatmaps highlighted variability and correlations between dimensional variables, with Pearson correlation indicating positive relationships. Hierarchical clustering classified rice varieties into four groups, and factor analysis revealed two major components, explaining 78.55 % and 19.26 % of the variance, respectively. This research offers valuable insights into the dimensional properties of traditional rice varieties, aiding the design of food processing equipment and enhancing their potential applications in future markets.

本研究评价了品种对南印度传统水稻品种工程性状和尺寸性状的影响。采用随机区组设计试验，在相似条件下栽培22个水稻品种。水稻品种的宽度、长度和厚度分别为1.90 ~ 3.14 mm、5.13 ~ 7.85 mm和0.94 ~ 2.96 mm。计算平均直径、球度（0.33 ~ 0.67）、纵横比（0.24 ~ 0.56）和表面积（12.66 ~ 36.75 mm2）。热图突出了维度变量之间的可变性和相关性，皮尔逊相关性表明了正相关关系。分层聚类将水稻品种分为4类，因子分析揭示了两个主要成分，分别解释了78.55 %和19.26 %的方差。这项研究为了解传统水稻品种的尺寸特性提供了有价值的见解，有助于食品加工设备的设计，并增强其在未来市场上的潜在应用。

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引用次数: 0

Generation mean analysis, genetic variability, advance, and heterosis for seed size traits in cowpea (Vigna unguiculata L. Walp.) 豇豆（Vigna unguiculata L. Walp.）种子大小性状的世代平均分析、遗传变异、进展及杂种优势

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-24 DOI: 10.1016/j.egg.2025.100435

Frederick Justice Awuku , Francis Kusi , John Saviour Eleblu , Isaac Asante , Kwadwo Ofori , Yosef Alemu Bekele , Patrick Attamah , Emmanuel Yaw Owusu , Gloria Mensah , Salim Lamini , Victoria Dedoe Larweh

A comprehensive understanding of gene action, heterosis, and genetic advance is essential for the effective improvement of cowpea traits. This study investigated the inheritance of seed size and related traits using four cowpea crosses: Wang Kae × SpM028, KT × SpM028, Bigbean × BR, and Agyenkwa × Padituya. Six generations (P₁, P₂, F₁, BC_1:1, BC_1:2, F₂) from each cross were evaluated in a randomised complete block design with three replications. Significant differences were observed across generations, indicating trait variability from one generation to another. The F₁ generation exhibited intermediate performance between parental means, highlighting additive allelic effects. Positive mid-parent heterosis was observed for all traits, indicating potential improvement through selection; however, some traits displayed negative heterobeltiosis. Generation mean analysis revealed significant means [m] and additive [a] effects, with additive × dominance [ad] epistatic interactions playing a key role. Traits such as seed volume showed solely additive × dominance effects, while hundred seed weight exhibited varying epistatic effects across the four crosses. Duplicate epistatic gene actions were prevalent, although complementary actions appeared in some traits. Positive dominance effects were identified for most traits, except for hundred seed weight in Wang Kae × SpM028, which showed negative dominance. Partial dominance was noted for large seed size and seed volume. High heritability and genetic advance suggested strong potential for trait improvement through selection. The genetic architecture of large-seed cowpea varieties from this study offers valuable opportunities for breeding programs aimed at enhancing seed size and related traits in cowpea.

全面了解基因作用、杂种优势和遗传进展对豇豆性状的有效改良至关重要。以王科 × SpM028、KT × SpM028、Bigbean × BR和Agyenkwa × Padituya 4个豇豆杂交组合为材料，研究了籽粒大小及相关性状的遗传特性。每个杂交的6代（P1、P2、F1、BC1:1、BC1:2、F2）采用3个重复的随机完全区组设计进行评估。代际间观察到显著差异，表明性状在代际之间存在差异。F1代表现为亲本之间的中间性状，突出了加性等位基因效应。所有性状中亲本杂种优势均为正，表明有通过选择改善的潜力；但部分性状表现为负杂种优势。代均值分析显示显著的均值[m]和加性[a]效应，其中加性 × 显性[和]上位相互作用起关键作用。种子体积等性状表现为单纯加性 × 显性效应，百粒重表现为不同的上位性效应。重复上位基因作用普遍存在，但在某些性状中存在互补作用。除百粒重王科 × SpM028为负显性外，其余性状均存在正显性效应。种子大小和种子体积大，为部分显性。高遗传率和遗传先进性表明，通过选择进行性状改良的潜力很大。本研究获得的大种子豇豆品种的遗传结构为提高豇豆种子大小和相关性状的育种计划提供了宝贵的机会。

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引用次数: 0

Biological macromolecules in bioremediation: Exploring OMICs approaches for environmental cleanup 生物修复中的生物大分子：探索环境净化的组学方法

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-11 DOI: 10.1016/j.egg.2025.100434

Priti Duhan , Kumkum Verma , Charu Lata , Bhupesh Gupta , Poonam Bansal

Bioremediation is used for eliminating hazardous compounds from environment by using various microorganisms which attaining fame. Recently, the degradation of the environment has emerged as a significant threat to human life. The mechanism behind bioremediation and eco-friendly approach to mitigating environmental pollution depends on biological macromolecules including nucleic acids, proteins, carbohydrates and lipids. The integration of OMICs technologies like genomics, transcriptomics, proteomics and metabolomics has transformed the understanding of these macromolecules and their roles in pollutant degradation, microbial adaptation and ecosystem restoration. Further, bioinformatics approaches are emerging technologies for bioremediation process by taking data from diverse biological databases like database of structure and composition, enzymes, microorganism's degradation pathways, RNA and protein expression, organic compounds and comparative genome analysis to understand the degradation pathway supported by a specific microbe for exact waste product. Diverse bioinformatics tools are employed to analyze these sources for study bioremediation to develop more operative environmental cleaning techniques. This review explores the synergistic application of OMICs technologies to study biological macromolecules in bioremediation, highlighting their potential to optimize pollutant removal and enhance environmental cleanup efforts. By integrating molecular biology with environmental science, OMICs-driven approaches offer precise, effective and sustainable solutions for addressing complex contamination challenges and advancing global restoration efforts.

生物修复是利用各种微生物来消除环境中有害化合物的一种方法，已获得广泛的应用。最近，环境退化已成为对人类生活的重大威胁。生物修复和生态友好的方法减轻环境污染的机制取决于包括核酸、蛋白质、碳水化合物和脂类在内的生物大分子。基因组学、转录组学、蛋白质组学和代谢组学等组学技术的整合，改变了人们对这些大分子及其在污染物降解、微生物适应和生态系统恢复中的作用的理解。此外，生物信息学方法是一种新兴的生物修复技术，它从不同的生物数据库中获取数据，如结构和组成、酶、微生物降解途径、RNA和蛋白质表达、有机化合物和比较基因组分析等，以了解特定微生物对确切废物的降解途径。不同的生物信息学工具被用来分析这些来源，研究生物修复，以开发更有效的环境清洁技术。本文综述了组学技术在生物修复中的协同应用，强调了它们在优化污染物去除和加强环境清理方面的潜力。通过将分子生物学与环境科学相结合，omics驱动的方法为应对复杂的污染挑战和推进全球恢复工作提供了精确、有效和可持续的解决方案。

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引用次数: 0

Gut microbiota of superworm (Zophobas atratus) in plastic biodegradation: Implications for microplastic mitigation and circular bio-economy 超级蠕虫（zoophobas atratus）在塑料生物降解中的肠道微生物群：对微塑料缓解和循环生物经济的影响

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-01 DOI: 10.1016/j.egg.2025.100425

Adi Sutanto , Iswahyudi Iswahyudi , Marchel Putra Garfansa , Siti Alfiatul Amani , Imbang Dwi Rahayu , Asmah Hidayati , Annisa Dwi Puspitarini , Sri Utami Lestari , Moh Subhan

Plastic pollution, particularly in the form of microplastics, has emerged as one of the most pressing global environmental challenges due to the persistence and accumulation of synthetic polymers in terrestrial and aquatic ecosystems. Recent studies highlight the remarkable ability of superworms (Zophobas atratus) to consume and degrade various plastics, a process largely facilitated by their gut microbiota. This review synthesizes current knowledge on the diversity and enzymatic functions of gut microorganisms, such as Pseudomonas, Enterobacter, Citrobacter, and Enterococcus, which play pivotal roles in the oxidative and hydrolytic breakdown of polystyrene, polyethylene, polypropylene, and other polymers. Enzymes including oxygenases, dehydrogenases, and alkane hydroxylases enable the conversion of complex polymers into smaller monomers and organic acids, thereby reducing the formation of secondary microplastics. Beyond environmental benefits, by-products such as frass and larval biomass present opportunities for integration into a circular bio-economy as fertilizer or feed ingredients. Nevertheless, challenges remain regarding enzyme stability, the sustainability of microbial consortia, and potential risks associated with plastic additives. This review provides novel insights by emphasizing gut microbiota-mediated mechanisms in superworms, distinguishing it from prior reviews that predominantly focused on larval feeding behavior. The implications extend to biotechnological innovations in bio-augmentation, synthetic microbial consortia, and bioreactor engineering, offering promising strategies for sustainable plastic waste management.

由于合成聚合物在陆地和水生生态系统中持续存在和积累，塑料污染，特别是微塑料污染，已成为最紧迫的全球环境挑战之一。最近的研究强调了超级蠕虫（zoophobas atratus）消耗和降解各种塑料的非凡能力，这一过程在很大程度上是由它们的肠道微生物群促进的。本文综述了目前关于肠道微生物的多样性和酶功能的知识，如假单胞菌、肠杆菌、柠檬酸杆菌和肠球菌，它们在聚苯乙烯、聚乙烯、聚丙烯和其他聚合物的氧化和水解分解中起关键作用。包括加氧酶、脱氢酶和烷烃羟化酶在内的酶能够将复杂的聚合物转化为更小的单体和有机酸，从而减少二次微塑料的形成。除了环境效益外，草叶和幼虫生物量等副产品作为肥料或饲料成分也为融入循环生物经济提供了机会。然而，在酶的稳定性、微生物群落的可持续性以及与塑料添加剂相关的潜在风险方面，挑战仍然存在。这篇综述通过强调肠道菌群介导的超级蠕虫机制提供了新的见解，区别于先前主要关注幼虫摄食行为的综述。其影响延伸到生物增强、合成微生物联合体和生物反应器工程方面的生物技术创新，为可持续塑料废物管理提供了有前途的战略。

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引用次数: 0