Ecological Genetics and Genomics最新文献_第6页

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 Epub Date: 2025-11-19 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 : 2025-12-01 Epub 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

Stability analysis of sesame (Sesamum indicum L.) genotypes in the savannas of Nigeria using multi-traits stability index 利用多性状稳定性指数分析尼日利亚热带稀树草原芝麻基因型的稳定性

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-01 Epub Date: 2025-10-08 DOI: 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.

芝麻（Sesamum indicum L.）是一种重要的油料作物，主要因其种子可食用而种植。然而，一些生产限制限制了尼日利亚的单位面积产量，其中包括确定合适和稳定的品种。为了确定尼日利亚稀树草原高产稳定的芝麻基因型，本研究评估了2024年雨季四个地点的15个基因型。目的是使用参数、非参数和多性状稳定性指数（MTSI）模型评估稳定性。田间试验采用随机完全区组设计，关键农艺性状数据采用方差分析和AMMI模型联合分析。除E和GEI对单株蒴果数的影响外，其余性状的基因型(G)、环境(E)和G × E互作均存在显著差异。NCRIBEN02M籽粒产量最高（447.76 kg/ha），其次是NCRIBEN04E （424.08 kg/ha）。AMMI方差分析显示，环境、基因型和GEI对芝麻产量影响显著（p < 0.01）。虽然参数分析和AMMI分析确定NCRIBEN02M是最稳定的基因型，但考虑多种性状的MTSI将袋鼠列为最理想的基因型。该研究推荐NCRIBEN02M高产且广泛稳定，而Kangarawa具有多性状稳定性。

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引用次数: 0

Chlorophyll dynamics and stress tolerance assessment of yard-long bean genotypes in response to shading conditions 遮荫条件下长豆基因型叶绿素动态及抗逆性评价

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-01 Epub Date: 2025-10-21 DOI: 10.1016/j.egg.2025.100417

Fajrin Pramana Putra, Florentina Kusmiyati, Syaiful Anwar, Muhamad Ghazi Agam Sas

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.

码长豆（Vigna unguiculata subsp.）倍足是一种重要的园艺作物，它富含蛋白质、纤维、维生素和矿物质。蔬菜农林业（VAF）将蔬菜种植整合到基于树木的系统中，提供了一种可持续的农业战略，但需要耐受遮阳的基因型。研究了不同遮荫条件下7种基因型大豆的生理性状和抗逆性指标。我们假设叶绿素动态（总含量和a/b比）、类胡萝卜素水平和硝酸盐还原酶活性与耐荫性指标相关，从而鉴定出适应弱光环境的基因型。生理评价结果表明，中等遮荫条件下叶绿素总含量总体较高（S1），而强遮荫条件下叶绿素a/b比值降低（S2），反映了叶绿素b的增加以增强光收获。类胡萝卜素的响应具有基因型特异性，某些基因型在充分光照下积累量更高，提示其具有光保护和抗氧化防御作用。硝态氮还原酶活性受光照强度的影响，反映了氮素同化和胁迫恢复能力的变化。通过几何平均生产力（GMP）、相对产量（RP）、耐受性值（TOL）和耐压指数（STI）等指标对遮荫条件下的抗逆性进行了分类。KP-6796-3-4-10和KP-6796-3-4-7表现出最高的GMP和稳定的产量，而KP-6718-1-1-10和KP-6796-3-4-7表现出基于RP和STI的耐荫性。将生理性状与产量指标相结合，突出具有良好色素组成和代谢反应的基因型。这些结果表明，特定的码长豆基因型具有适合遮荫或间作环境的适应性性状，为农林业育种计划提供了见解。

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引用次数: 0

Evaluation of yield traits and essential oil yield of Istanbul oregano (Origanum vulgare subsp. hirtum) genotypes across two Mediterranean environments 伊斯坦布尔牛至产量性状及挥发油产量评价。hirtum)基因型跨越两个地中海环境

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-01 Epub Date: 2025-09-13 DOI: 10.1016/j.egg.2025.100407

Olcay Arabacı , Emine Bayram , Çiğdem Sönmez , Gülsüm Boztaş , Nazlıcan Ataman , Elif Büyükkayhan

Origanum vulgare subsp. hirtum (Istanbul oregano) is a commercially valuable aromatic and medicinal plant widely used in the food, pharmaceutical, and cosmetic industries due to its high essential oil content and bioactive properties. This study evaluated the agronomic performance of 22 Istanbul oregano genotypes, including commercial varieties and selected clones, across two Mediterranean environments (Aydın and İzmir) over two years (2021–2022). Significant genotype × environment interactions were detected for plant height, fresh herb yield (FHY), drug herb yield (DHY), drug leaf yield (DLY), and essential oil yield (EOY) (p < 0.01). Average FHY ranged from 2.39 t ha⁻¹ in 2021 to 21.97 and 8.32 t ha⁻¹ in the first and second cuts of 2022, respectively. DHY increased from 0.75 to 1.01 t ha⁻¹ in 2021 to 6.50–5.81 t ha⁻¹ in 2022, while DLY peaked at 15.87 t ha⁻¹ during the first cut of 2022. Inter-annual climatic variation strongly influenced EOY. In the first cut of 2022, means reached 503.5 L ha⁻¹ in Aydın and 259.7 L ha⁻¹ in İzmir, 15- to 8-fold higher than the overall mean of 2021 (32.3 L ha⁻¹). However, summer drought and heat stress sharply reduced second cut yields, particularly in Aydın, where EOY declined by about 75 %. Genotypes such as C-417 and A-420 exhibited high plasticity and stability, while the commercial variety Tınmaz performed well only under favorable conditions. Genotypes combining stability and high yield across environments represent promising candidates for breeding and sustainable oregano production under Mediterranean climates.

土一枝亚种。伊斯坦布尔牛至是一种具有商业价值的芳香和药用植物，由于其高精油含量和生物活性特性，被广泛用于食品、制药和化妆品行业。本研究评估了22种伊斯坦布尔牛至基因型（包括商业品种和精选无性系）在两种地中海环境（Aydın和İzmir）中两年（2021-2022年）的农艺表现。株高、鲜草产量（FHY）、中药材产量（DHY）、药叶产量（DLY）和精油产量（EOY）的基因型与环境的交互作用显著（p < 0.01）。平均FHY范围从2021年的2.39 t / hm2到2022年第一次和第二次削减的21.97和8.32 t / hm2。DHY从2021年的0.75 - 1.01 t / ha - 1增加到2022年的6.50-5.81 t / ha - 1，而在2022年的第一次削减期间，DLY达到了15.87 t / ha - 1的峰值。年际气候变化强烈影响EOY。在2022年的第一次削减中，Aydın的平均值达到503.5 L ha - 1， İzmir的平均值达到259.7 L ha - 1，比2021年的总体平均值（32.3 L ha - 1）高出15至8倍。然而，夏季干旱和高温胁迫大大降低了二次减产产量，特别是Aydın， EOY下降了约75%。C-417和A-420等基因型表现出较高的可塑性和稳定性，而商品品种Tınmaz只有在有利条件下才能表现良好。在地中海气候条件下，结合稳定性和高产的基因型是培育和可持续牛至生产的有希望的候选者。

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引用次数: 0

Analysis of microbiomes in irrigation water, soil and lettuce from community farms in the Phoenix metro area 凤凰城城区社区农场灌溉用水、土壤和生菜微生物组分析

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-01 Epub Date: 2025-10-01 DOI: 10.1016/j.egg.2025.100409

Saul Lopez-Salas , Theresa Morales , Theodore M. Ransome , Marianne Smith , Sudipta Biswas

This research compares the bacterial profile in soil, irrigation water, and lettuce from farms located in food deserts (FD; low income and limited access to grocery stores), and non-food deserts (n-FD; high income and easier food access) in the Phoenix metropolitan area. It was hypothesized that farms from FD areas would have high coliform bacteria in soil, irrigation water, and lettuce compared to n-FD farms and appropriate controls. Serially diluted soil samples were cultured on agar plates for bacterial growth. Meanwhile, water samples were tested for coliform bacteria, nitrate, phosphate, temperature, pH levels, and were plated on petri film to identify any coliform presence. DNA extracted from lettuce, sequenced on the Illumina Nextseq2000 Sequencing System was used to create the 16S rRNA sequencing data. Soil results indicated that FD had more total coliform bacteria and high E. coli compared to n-FD and controls. Only some of the water samples from FD showed a statistically significant presence of coliform bacteria in irrigation water. The lettuce microbial profile revealed that FD had a 90% abundance of cyanobacteria and 4–8% abundance in proteobacteria like Pseudomonas and Enterobacteriales like E. coli. n-FD farms showed a predominance of facultative anaerobes from family Marinilabiliaceae and 2% abundance of Proteobacteria like Pseudomonas, Acinetobacter, and Staphylococcus. Phylogenetic tree mapping, revealed the presence of certain pathogenic bacteria like Pseudomonas in all the samples. Further research is needed to identify the source of bacterial contamination in the soil and to develop strategies to control their spread in fresh produce.

这项研究比较了凤凰城大都市区位于食物沙漠（FD；低收入和进入杂货店的机会有限）和非食物沙漠（n-FD；高收入和更容易获得食物）的农场的土壤、灌溉水和生菜中的细菌特征。据推测，与非FD农场和适当的对照相比，FD地区的农场在土壤、灌溉水和生菜中有较高的大肠菌群。连续稀释的土壤样品在琼脂板上培养细菌生长。同时，对水样进行了大肠菌群细菌、硝酸盐、磷酸盐、温度、pH值的检测，并将水样镀在培养皿上以确定大肠菌群的存在。从生菜中提取DNA，在Illumina Nextseq2000测序系统上测序，用于创建16S rRNA测序数据。土壤结果表明，与n-FD和对照相比，FD有更多的总大肠菌群和高大肠杆菌。只有FD的部分水样显示灌溉水中大肠菌群的存在具有统计学意义。生菜微生物谱显示，FD的蓝藻菌丰度为90%，假单胞菌等变形菌和大肠杆菌等肠杆菌丰度为4-8%。n-FD养殖场显示，Marinilabiliaceae家族的兼性厌氧菌占主导地位，假单胞菌、不动杆菌和葡萄球菌等变形菌的丰度为2%。系统发育树图谱显示，所有样品中均存在假单胞菌等致病菌。需要进一步的研究来确定土壤中细菌污染的来源，并制定策略来控制它们在新鲜农产品中的传播。

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引用次数: 0

Study on population genetic diversity and variation of Calamus poilanei Conrard in the Southern Central Highlands, Vietnam 越南中部高地南部蒲菖蒲种群遗传多样性及变异研究

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-01 Epub Date: 2025-10-27 DOI: 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 (H_e) = 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: H_e = 0.2529, I = 0.3826, and PPB = 82.3 %. At the metapopulation level, H_e = 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 (N_m) was high (12.88), leading to low genetic differentiation (G_ST = 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 H_e, I, or PPB, they showed agreement in estimating N_m, G_ST, 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.

采用起始密码子靶向多态性（SCoT）、间简单序列重复（ISSR）和CAAT盒源多态性（CBDP） 3种不同的DNA指纹图谱技术，对越南中南部高原2个菖蒲居群的遗传多样性和变异进行了比较分析。综合数据表明，猫天群体遗传多样性的预期杂合度（He） = 0.2498，Shannon指数(I) = 0.3772，多态性频带比例（PPB） = 78.47 %。Dak R’lap种群值稍高，He = 0.2529,I = 0.3826,PPB = 82.3 %。在元种群水平上，He = 0.2611,I = 0.3998,PPB = 92.34 %。个体（SCs）间的成对遗传相似系数在猫田群体中为0.536 ~ 0.933（平均 = 0.755），在达克·R·拉普群体中为0.565 ~ 0.914（平均 = 0.770），在元群体中为0.512 ~ 0.933（平均 = 0.755）。群体间基因流（Nm）高（12.88），导致遗传分化程度低（GST = 0.0374），遗传距离低（D = 0.0264）。大部分遗传变异发生在群体内（94 %），群体间仅6 %。虽然这三种技术在估计He、I或PPB方面没有一致的相关性，但它们在估计Nm、GST和d方面表现一致。其中，考虑到其整体效用，SCoT在本研究中是最有效的。这些发现有助于制定菖蒲的保护规划，并为今后对其近缘种的研究提供方向。

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引用次数: 0

Morphogenesis modulation of Rhizopus oryzae by peptone enhances lipase production during submerged fermentation 蛋白胨对米根霉形态发生的调节促进了深层发酵过程中脂肪酶的产生

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-01 Epub Date: 2025-09-05 DOI: 10.1016/j.egg.2025.100406

Ayda Torchi

Lipases are industrially important enzymes with broad applications in food, pharmaceuticals, and biofuels. However, their large-scale production remains challenging. This study aimed to enhance lipase productivity by modulating Rhizopus oryzae morphogenesis through the supplementation of different peptone sources under submerged fermentation. Distinct cellular macromorphologies was found to strongly influence growth performance and lipase productivity. Lipase production was enhanced six –fold compared to previous studies, with a maximum of 492 IU/mL recorded after 76h. Subsequent molecular analysis underscored the crucial role of key regulatory proteins in understanding the production systems of R.oryzae and how its metabolism adapts to various nitrogen sources. These findings offer a promising approach to employ innovative morphological engineering techniques to precisely adjust the morphological development of industrially relevant fungi.

脂肪酶是工业上重要的酶，在食品、制药和生物燃料中有着广泛的应用。然而，它们的大规模生产仍然具有挑战性。本研究旨在通过在深层发酵条件下添加不同蛋白胨源，调节米根霉的形态发生，从而提高其脂肪酶产量。发现不同的细胞大形态强烈影响生长性能和脂肪酶产量。与之前的研究相比，脂肪酶的产量提高了6倍，76h后最高达到492 IU/mL。随后的分子分析强调了关键调节蛋白在理解r.m oryzae生产系统及其代谢如何适应各种氮源方面的关键作用。这些发现为采用创新的形态工程技术来精确调整工业相关真菌的形态发展提供了一种有希望的方法。

引用次数: 0

Exploring druggable and virulent proteins in Streptococcus oralis (COL85/1862) through computational subtractive proteomics approach 通过计算减法蛋白质组学方法探索口腔链球菌（COL85/1862）的药物和毒力蛋白

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-12-01 Epub Date: 2025-10-27 DOI: 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。

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引用次数: 0

Comparative metagenomic profiling of gut microbiota in wild and reared Rhynchophorus phoenicis (Coleoptera: Dryophthoridae) across developmental stages in central-west côte d'Ivoire côte科特迪瓦中西部野生和饲养的腓胫蝗（鞘翅目：干蝗科）不同发育阶段肠道微生物群的宏基因组比较分析

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-09-01 Epub Date: 2025-07-07 DOI: 10.1016/j.egg.2025.100385

Adjoua Christiane Eunice Boko , Dago Liliane Yao , Sika Hortense Blei , Okran Beyosse Christophe Kacou , Djédoux Maxime Angaman

The African palm weevil (Rhynchophorus phoenicis) is a nutrient-rich edible insect widely consumed in West and Central Africa. Despite its dietary significance, limited information is available on the gut microbial communities associated with this insect, particularly concerning the influence of farming practices and developmental stages. This study investigated the taxonomic and functional profiles of gut microbiota in R. phoenicis collected from both wild and reared environments across larval and adult stages. Shotgun metagenomic sequencing was performed on four groups, namely reared adults (AE), reared larvae (LE), wild adults (AS) and wild larvae (LS), using the PacBio Revio platform. Taxonomic profiling ranged from phylum to species levels, and functional annotations were based on KEGG pathway predictions. Results revealed that AE samples exhibited the highest microbial richness and functional diversity (Shannon index up to 3.2; Simpson index up to 0.95). Reared individuals (AE and LE) harbored more balanced and metabolically versatile microbial communities, enriched in pathways related to carbohydrate metabolism, vitamin biosynthesis, and xenobiotic degradation. In contrast, wild individuals, particularly LS, displayed lower diversity and narrower functional profiles. Beta diversity analysis (Bray-Curtis) showed distinct clustering according to both rearing condition and developmental stage (PERMANOVA, p < 0.01). The results underscore the pivotal role of the rearing environment in shaping the gut microbiota composition and functional potential of R. phoenicis, offering valuable perspectives for optimizing insect farming practices aimed at improving food safety, nutritional quality, and microbiome stability.

非洲棕榈象甲（Rhynchophorus phoenicis）是一种营养丰富的食用昆虫，在西非和中非广泛食用。尽管其饮食意义重大，但关于与这种昆虫相关的肠道微生物群落的信息有限，特别是关于耕作方式和发育阶段的影响。本研究研究了在野生和饲养环境中收集的腓尼基鼠幼虫期和成虫期肠道微生物群的分类和功能特征。采用PacBio Revio平台对饲养成虫（AE）、饲养幼虫（LE）、野生成虫（AS）和野生幼虫（LS） 4组进行鸟枪宏基因组测序。分类分析范围从门到种，功能注释是基于KEGG途径预测。结果表明，AE样品微生物丰富度和功能多样性最高(Shannon指数为3.2；Simpson指数达0.95)。饲养个体（AE和LE）拥有更平衡和代谢多样的微生物群落，丰富了与碳水化合物代谢，维生素生物合成和异种生物降解相关的途径。与此相反，野生个体（尤其是LS）的多样性较低，功能谱较窄。β -多样性分析（Bray-Curtis）显示，不同饲养条件和发育阶段的雏鸡具有明显的聚类性(PERMANOVA, p <；0.01)。这些结果强调了饲养环境在塑造凤凰鸡肠道微生物群组成和功能潜力方面的关键作用，为优化昆虫养殖方式以提高食品安全、营养质量和微生物群稳定性提供了有价值的视角。

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引用次数: 0