Research Articles (Biochemistry, Genetics and Microbiology (BGM))

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Revisiting the African mtDNA landscape through complete mitochondrial genomes
Lankheet, Imke; Chowdhury, Afifa; Tellgren-Roth, Christian; Jolly, Cecile; Soares, Andre E.R.; De Navascues, Miguel; Pacchiarotti, Sara; Maselli, Lorenzo; Kouarata, Guy; Donzo, Jean-Pierre; Coetzee, Vinet; De Castro, Minique; Ebbesen, Peter; Priehodova, Edita; Podgorna, Eliska; Cerny, Viktor; Green, Susanne T.; Harena, Pakou; Bakrobena, Lebarama; Fomine, Forka Leypey Mathew; Tolesa, Zelalem GebreMariam; Mengesha, Wendawek Abebe; De Jongh, Michael; Soodyall, Himla; Bostoen, Koen; Barbieri, Chiara; Larena, Maximilian; Malmstrom, Helena; Schlebusch, Carina M. (Nature Research, 2026-06-03)
Africa harbors the richest diversity of mitochondrial DNA lineages, reflecting its central role in human evolutionary history. Early studies of mtDNA variation provided the first genetic evidence for the African origin of modern humans. With complete mitochondrial genome sequencing, we can now reconstruct maternal lineages with high resolution, yet large parts of the continent remain underrepresented. Using a newly developed long-range sequencing assay, we generated 1176 complete mitochondrial genomes from 13 countries across sub-Saharan Africa, focusing on previously understudied regions. We combined these with over 3600 publicly available African mitogenomes to produce a comprehensive dataset and updated overview of maternal genetic diversity across the continent. We contextualized this diversity with autosomal structure and information on major human expansions, integrating archeological and linguistic evidence. Our analyses suggest an initial demographic expansion of Niger-Congo speakers around 17 thousand years ago (kya), and an initial expansion associated with Bantu-speaking groups around 6 kya. We identify haplogroup L3e as a key marker of this early Bantu expansion, tracking its spread across sub-Saharan Africa. Distinct demographic signatures also emerge for different geographic sub-branches of Bantu speakers. These findings highlight the power of mitochondrial DNA to trace maternal ancestry and demographic history in Africa, while also acknowledging its limitations for phylogeographic reconstruction.
Evolution of protein domains and protein domain combinations provides insights into the origin and diversification of land plants
Xue, Jia-Yu; Yang, Cheng-Ao; Hu, Shuaiya; Fan, Hai-Yun; Zhang, Yan-Mei; Shao, Zhu-Qing; Li, Linzhou; Wang, Sibo; Wei, Tong; Dong, Shanshan; Liu, Yang; Li, Zhen; Van de Peer, Yves (Elsevier, 2026-04-08)
Protein domains are fundamental units determining protein functions. This study identified all protein domains and domain combinations from 446 genomes across all major plant lineages. We discovered more domains and domain combinations in land plants than in algae. Many novel “core” protein domains were acquired in the early evolution of streptophytes, substantially enriching the genomic toolkit that enabled plants to shift from unicellular to multicellular organization and to adapt to terrestrial life. After conquering the land, the number of ancestral core domains kept decreasing in land plants; in contrast, an increasing number of non-core domains were acquired, which, together with enhanced activity of domain shuffling, generated various novel domain combinations and expanded protein diversity. We speculate that losing existing genetic elements (core domains) is not always detrimental, as it may have reduced evolutionary constraint upon species, paving the way for biological innovation (speciation) and adaptation to changing environments. HIGHLIGHTS • Comparative analysis of 446 plant genomes reveals domain evolution patterns • Early intensive domain gains enriched genetic toolkits for plant terrestrial adaptation • Continuous loss of core domains likely released existing evolutionary constraint • Non-core domain gains and domain shuffling expanded land-plant protein diversity
PLANeT : understanding and leveraging the genome of land plants for a sustainable future
Wang, Li; Amar, Mohamed; Arbizu, Carlos I.; Bowman, John L.; Cannon, Charles H.; Cantrill, David J.; Cao, Xiaofeng; Chen, Shilin; Chen, Xiaoya; Chen, Xuemei; Chong, Kang; Deng, Xingwang; Weinan, E.; Guo, Hongwei; He, Chuan; Hollingsworth, Peter; Hu, Qing; Kong, Hongzhi; Leitch, Ilia J.; Li, Dezhu; Li, Jiayang; Liu, Hongtao; Lucas, William; Mizrachi, Eshchar; Rakotoarinivo, Mijoro; Ren, Hai; Rieseberg, Loren; Ruan, Jue; Scherson, Rosa; Schneider, Harald; Soltis, Douglas E.; Sun, Hang; Silva-Filho, Marcio C.; Smith, Stephen; Twyford, Alex; Usadel, Bjorn; Van de Peer, Yves; Van den Berg, Cassio; Varshney, Rajeev K.; Viccini, Lyderson Facio; Wang, Qingfeng; Wang, Xiao-Quan; Wang, Yadong; Wendel, Jonathan; Wing, Rod; Wong, Gane Ka-Shu; Xing, Yaowu; Xu, Xun; Yan, Nieng; Yang, Huanming; Zhang, Shouzhou; Zhu, Yuxian; Soltis, Pamela S.; Weigel, Detlef; Huang, Sanwen (Elsevier, 2026-04)
Land plants underpin civilization and planetary health, yet their genomic diversity remains largely uncharted. Current resources are unstandardized and scarce, lacking reference genomes for 95% of genera, 70% of families, and 51% of orders, impeding evolutionary and functional insight. We thus propose the PLANeT initiative, an international effort to generate high-quality, standardized genomes across the plant tree of life. Integrating artificial intelligence (AI) with genomics, we will decode conserved principles to advance fundamental plant biology, biodiversity conservation, crop improvement, and natural product discovery. Engaging around 100 labs to train 1,000 scientists, we will tackle pivotal questions for a sustainable future.
Eucalyptus grandis A uxin R esponse F actor 10 (EgrARF10) is associated with the modulation of secondary xylem cell wall chemistry
Makhura, Ipeleng; Ployet, Raphael; Myburg, Alexander A.; Cassan-Wang, Hua; Hussey, Steven Grant (Springer, 2026-07-28)
Auxin Response Factors (ARFs) are of vital importance in plant growth and vascular development. Class A ARFs are the core auxin-driven drivers of embryogenesis, vascular pattern development, (pro)cambial stem cell initiation and xylem cell fate specification, while class B ARFs may attenuate or fine-tune auxin-mediated development. The potential roles of class C ARFs in vascular development and xylogenesis, however, remain largely unexplored. In this study, we identified Eucalyptus grandis ARF10 (EgrARF10) as a potential regulator of secondary cell wall (SCW) development. We show that EgrARF10 is nucleus-localised and strongly associated with SCW biosynthetic genes and transcription factors across co-expression and multi-omic networks. Mining of published spatial and single cell transcriptomic data revealed preferential expression of EgrARF10 in vessel and fusiform organizer cells of secondary xylem tissue, while EgrARF10 orthologs in other species exhibit diverse cell type-specific expression ranging from root cap vascular and metaxylem to cork cambium. Heterologous overexpression of EgrARF10 in hybrid poplar did not alter overall growth or morphology but resulted in a significant reduction in stem lignification, accompanied by relative increases in D-glucose, D-xylose and D-mannose, indicating altered SCW composition. While the molecular mechanism by which EgrARF10 acts remains unknown, these findings provide the first evidence for the role of a class C ARF in xylem SCW biology.
Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes
Shi, Tao; Van de Peer, Yves (American Association for the Advancement of Science, 2026-01)
Whole-genome duplication (WGD) has been proposed as a catalyst for evolutionary innovation in seed plants and angiosperms, yet their occurrence remains contentious. By integrating gene dosage balance principles with phylogenomic reconciliation and probabilistic modeling, we revisit the debated ancestral seed and angiosperm WGDs. Leveraging dosage-sensitive orthologous gene groups (OGs) as evolutionary markers across representative plants for gene tree/species tree reconciliation, we demonstrate that gene retention patterns in Amborella and Aristolochia—early-diverging plants lacking post–angiosperm origin WGDs—reveal a single gene duplication peak predating the seed plant diversification, with no signal of ancestral angiosperm WGD. Correlation analyses of observed and expected OG copy numbers, given proposed WGD(s), further refute an angiosperm WGD. Probabilistic retention modeling analysis corroborates these findings and shows that retention rates of dosage-sensitive genes from the putative angiosperm WGD are extremely low. Besides, our study establishes that genes inferred to have higher dosage sensitivity based on their sequential retention following WGD events may have increased utility in resolving ancestral polyploidy.
Long-reads metagenomics reveals the effects of dulse supplementation on the poultry caecal bacteriome and its associated genetic repertoire
Cambara, Julio Cesar Ortega; Cuber, Piotr; Khattak, Farina; Lebre, Pedro Humberto; Galgano, Salvatore; Houdijk, Jos; Smallman, Duncan; Estridge, Patricia; Allen, Michael J.; Short, Fiona; Sutcliffe, Martin; Mkrtchyan, Hermine V. (Frontiers Media, 2026-07)
INTRODUCTION : Dulse (Palmaria palmata) is a macroalgal feed ingredient rich in polysaccharides and bioactive compounds that offers a sustainable strategy to enhance animal health and productivity through modulation of gut microbiota. However, the impact of dulse supplementation on the taxonomic composition and genetic repertoire of the broiler chicken caecal microbiota remains poorly characterised. METHODS : We applied long-read shotgun metagenomic sequencing on 18 caecal samples collected from 27-day-old male Ross 308 broilers following a 7-day feeding trial with three dietary treatments — a reference diet, a soyabean meal-supplemented diet, and a diet supplemented with 30% dulse — to investigate the effects of dulse inclusion on microbial community composition, genetic diversity, and antimicrobial resistance (AMR) and virulence determinants. RESULTS : Across all dietary treatments, the Clostridia class predominated (71%), whereas primary fermenters (L. phocaeense), lactic acid bacteria (L. salivarius), and hydrogenotrophic cross-feeders (B. hydrogenotrophica) were enriched in the reference diet, dulse-supplemented and soyabean meal-supplemented groups, respectively (KW p < 0.05), contributing to potential improvements in caecal function, immune resilience, and nutrient utilisation while reducing pathogen load. The overall resistome profiles were comparable across dietary treatments and were dominated by genes conferring resistance to tetracyclines, lincosamides, and aminoglycosides. In contrast, the virulome displayed diet-associated shifts: Enterobacteriaceae were enriched in the dulse and reference diets relative to the soyabean meal diet, with an expanded functional repertoire of virulence-associated genes, particularly those involved in adhesion, iron acquisition, and secretion systems. Multidrug resistance genes, virulence determinants, and Col/IncF-type plasmid replicons were associated with E. coli reads, highlighting its potential resistance and virulence arsenal within the caecal microbiota. DISCUSSION : Our findings suggest that the benefits of dulse extend beyond its nutritional value, residing in its ability to foster ecosystem resilience; by promoting a diverse, niche-stabilised microbiota, dulse minimises the risk of opportunistic pathogen proliferation, supporting its use as a sustainable, functional feed ingredient.
Identification of Botryosphaeriaceae species in the South African National Collection of Fungi, including a novel species of Oblongocollomyces
Jami, Fahimeh; Truter, Mariëtte; Pavlic, Draginja; Chen, ShuaiFei; Roux, Jolanda (South African National Biodiversity Institute, 2026-07-06)
The Botryosphaeriaceae is a diverse group of fungi that includes several important plant pathogens. This study aimed to identify the 201 Botryosphaeriaceae isolates deposited at the South African National Collection of Fungi (NCF). The isolates were revived and phylogenetic analyses, based on multiple loci (ITS, tef1-α, rpb2, tub2), revealed several distinct clades, leading to the identification of 15 known species from Botryosphaeria, Lasiodiplodia, Neofusicoccum and a new species of Oblongocollomyces. This study expands the known diversity and host ranges of the Botryosphaeriaceae in South Africa and China, significantly contributing to our understanding of this family. The results highlight the importance of national collections as valuable resources for fungal biodiversity research. Further research is needed to explore the pathogenicity and distribution of these species in local agricultural ecosystems.
The National Onion Bacterial Strain Collection (NOBSC), a repository of over 2,200 publicly available bacterial strains isolated from onion
Kvitko, Brian; MacKay, Heather; Patel, Krunal; LaForest, Joseph; Shin, Gi Yoon; Smith, Amy; Wilson, Rob; Aegerter, Brenna; Coutinho, Teresa A.; Zhao, Mei; MacLellan, Michelle Pena; Dutta, Bhabesh; Cramer, Christopher S.; Mazzone, Jennie; Neupane, Ram; Gugino, Beth; Hoepting, Christy; Khanal, Manzeal; Bhatta, Bed Prakash; Malla, Subas; Nischwitz, Claudia; Sidhu, Jaspreet; Burke, Antoinette Machado; Davey, Jane; Uchanski, Mark; Wood, Benjamin; Rosnow, Josh; Woodhall, James; Asselin, Jo Ann; Stodghill, Paul; Derie, Michael L.; Du Toit, Lindsey J. (American Phytopathological Society, 2026)
The National Onion Bacterial Strain Collection (NOBSC) is a publicly accessible resource comprising more than 2,200 bacterial strains isolated primarily from diseased onion plants across major U.S. onion-producing regions. Developed as part of the United States Department of Agriculture National Institute of Food and Agriculture Specialty Crops Research Initiative project “Stop the Rot” (award no. 2019-51181-30013), the NOBSC represents a substantial curation of onion-associated bacteria available to the research community. The collection houses strains from genera that include species with important onion pathogens—Burkholderia, Enterobacter, Pantoea, Pseudomonas, Rahnella, and Xanthomonas—as well as isolates of more than 130 other genera recovered from symptomatic onion tissues (foliage and bulbs). Accompanying metadata include geographic origin, host tissue type, phenotypic assessments (including onion pathogenicity assays), and 16S rRNA-based genus assignments. The NOBSC provides an excellent resource for plant pathology studies, comparative genomics, and the development of molecular diagnostic tools, as well as standardized strain material for phenotypic screening of onion germplasm for resistance to bacterial pathogens. All strains are available for request directly from nobsc.alliumnet.com at cost-recovery rates, contingent on the requester having appropriate permitting. The collection is maintained at the University of Georgia.
Differential gene expression analysis of Dohne merino sheep naturally infected with Haemonchus contortus
Ramantswana, Tondani M.; Malatji, Dikeledi P.; Pierneef, Rian Ewald; Soma, Pranisha; Van der Nest, Magrieta Aletta; Muchadeyi, Farai C. (Nature Research, 2025-11-25)
Gastrointestinal nematode (GIN) infections, particularly caused by Haemonchus contortus, are a major concern in sheep farming, resulting in significant economic losses Genetic resistance, used alongside chemical control, nutrition, and pasture management, provides a sustainable strategy to mitigate these infections in industrial livestock systems The South African Dohne Merino sheep, known for their resilience and suitability for both wool and meat production, offer a potential genetic resource for breeding GIN resistance, providing an alternative to chemical control. This study utilised RNA-Seq and differential gene expression (DEG) analysis to investigate the molecular mechanisms underlying H. contortus infection in Dohne Merino sheep. Six adult ewes from Wauldby farm (Eastern Cape Province), naturally exposed to H. contortus, were selected. The animals were categorised into resistant (n = 3) and susceptible (n = 3) groups based on Estimated Breeding Values (EBVs) from faecal egg count (FEC) phenotypes. DEG analysis revealed 34 significantly differentially expressed genes (DEGs) related to immune responses and external stimuli, with involvement in key pathways such as Rap1 and PI3K-Akt signaling, linked to H. contortus resistance. Additionally, segment-specific analysis of the gastrointestinal tract identified DEGs in different regions: 146 in the abomasum, 302 in the ileum, 584 in the jejunum, and 332 in the duodenum. The findings highlight genes and pathways contributing to GIN resistance and tissue-specific response mechanisms. These insights can support the selection and breeding of sheep with enhanced resistance to H. contortus, offering a genetic approach to combating GIN infections.
Biodegradation and detoxification of malachite green dye by crude manganese peroxidase produced by Pseudomonas aeruginosa MF14446.1 and Enterobacter roggenkampii CP033800.1
Ngcobo, Bongekile Precious; Osunsanmi, Foluso Oluwagbemiga; Ikhane, Albert Olufemi; Mosa, Rebamang Anthony; Opoku, Andrew Rowland (Nature Research, 2025-12-29)
Effluent discharge from dye-using industries like the textile, leather, food processing, cosmetics, paper, and related industries remains an emerging concern for the environment and public health. This study evaluates the efficiency of manganese peroxidase (MnP) produced by Pseudomonas aeruginosa (MF14446.1) and Enterobacter roggenkampii (CP033800.1) to detoxify and degrade Malachite green (MG) dye. Bacteria isolates were characterized using 16 S rDNA. MnP activities of the crude enzymes obtained from the freeze-dried supernatants of the bacteria cultures were confirmed by the ability to oxidize NAD(P)H in the absence of H2O2. The enzymes’ optimal temperature, pH, incubation period, H2O2, and enzyme concentration required to decolourise the dye were investigated. The Michaelis-Menten model equation was used to obtain the enzyme kinetics (Vmax, Km, and the turnover number, kcat value (as Vmax/enzyme protein concentration). The efficiency of the degradation was evaluated by the toxicity of the degraded (treated) and untreated dyes on the growth of two Gram-positive (Bacillus cereus ATCC 14579 and Staphylococcus aureus LCT-SA112) and two Gram-negative (Proteus mirabilis H14320 and Escherichia coli ATCC 9637) bacteria. The crude enzymes of both E. roggenkampii and P. aeruginosa were found to be most efficient at the enzyme concentration of 20–50 mg/ml, with a pH range of 5–7, requiring dye concentration of 100–200 mg/l. Optima temperatures ranged between 30 and 40 °C, and about 56–70% of the dye were decolourised within 100 min in the proximity of 0.25–1.5 mM H2O2. P. aeruginosa’s crude extracts showed higher MnP activity (7.4 × 10− 3 u/l) compared to the extract from Enterobacter roggenkampii: The kinetic parameters for P. aeruginosa’s crude extracts observed were Km (45.5 mM/min), Vmax (66.7 mM/L) and kcat (5 × 10− 3Mm/min). The treated dye supported the growth of gram-positive and gram-negative test organisms, which the untreated dye could not, deeming the enzymes to be both decolourizers and detoxifiers.
Repeatability of phenotypic consequences due to whole-genome duplication in Spirodela polyrhiza
Mortier, Frederik; Bafort, Quinten; Bonte, Dries; Van de Peer, Yves (Wiley, 2026-08)
Whole-genome duplication (WGD) is widespread in plants, yet the extent to which it yields predictable phenotypic outcomes remains unclear. Here, we show that the phenotypic consequences of genome doubling in a duckweed model system, Spirodela polyrhiza, are highly repeatable and largely deterministic. We previously generated three independent colchicine-induced autotetraploids from each of nine globally distributed diploid genotypes and now quantified growth and morphology across a salt gradient. In benign conditions, diploids grew faster, whereas tetraploids had larger, thicker fronds. As salinity increased, the diploid growth advantage diminished, and tetraploids frequently matched or exceeded diploid growth rates. By partitioning the components of variance in growth in our experimental design, we found that ploidy per se explained a comparable amount of phenotypic variation in growth and substantially more variation in salt tolerance than the genotypic background, with evidence of rare within-genotype stochastic differences between tetraploids. These results indicate that the shifts in morphology and stress tolerance from genome doubling are predictable and can match the phenotypic effect from genetic sequence diversity.
Persistence of high-risk antimicrobial resistance genes in extracellular DNA along an urban wastewater-river continuum
Makumbi, John Paul; Leareng, Samuel K.; Bezuidt, Oliver Keoagile Ignatius; Coelho, Luis Pedro; Makhalanyane, Thulani Peter (Cell Press, 2026-04-28)
Inadequate wastewater treatment can drive the spread of antimicrobial resistance (AMR), threatening ecosystems and human health. Extracellular DNA (exDNA) stabilizes antimicrobial resistance genes (ARGs) in the environment and facilitates horizontal gene transfer, yet its taxonomic structure and influence on AMR ecology remain poorly understood, especially in African aquatic systems. We profile exDNA-associated resistomes across nine South African wastewater treatment plants and receiving rivers, comparing single-stage activated sludge process (ASP-only) and combined ASP-biofilter systems. exDNA harbors high-risk mobile ARGs conferring resistance to last-resort antibiotics, with enrichment in effluents and downstream rivers. Surprisingly, upstream river samples also carry abundant ARGs, indicating cumulative inputs from multiple environmental reservoirs. ARGs are mainly associated with Pseudomonadota and Bacteroidota, suggesting that exDNA constitutes an ecologically distinct AMR reservoir dominated by key taxa. These findings underscore the need to integrate exDNA into AMR surveillance and highlight its broader role in microbial adaptation within freshwater environments. HIGHLIGHTS • Extracellular DNA harbors high-risk antimicrobial resistance genes (ARGs) • Multi-stage wastewater treatment is more effective in the reduction of exDNA-ARGs • exDNA is an ecologically distinct AMR reservoir, dominated by a few key taxa • River water is an important reservoir of exDNA-associated ARGs
Cunninghamia lanceolata genome illuminates the evolutionary dynamics of gymnosperms
Lin, Si-Zu; Chen, Yu; Wu, Chao; Sun, Wei-Hong; Li, Zhen; Chen, Heng-Chi; Wang, Jie-Yu; Ji, Chang-Mian; Li, Shu-Bin; Wang, Zhi-Wen; Tsai, Wen-Chieh; Ma, Xiang-Qing; Lan, Si-Ren; Zhang, Fei-Ping; Xie, Ya-Cong; Yao, Lei; Zhang, Yan; Lu, Meng-Meng; Zhang, Jia-Jun; Zhang, Di-Yang; Ye, Yi-Quan; Yu, Xia; Xu, Shan-Shan; Ma, Zhi-Hui; Ding, Guo-Chang; Cao, Guang-Qiu; He, Zong-Ming; Wu, Peng-Fei; Lin, Kai-Min; Liu, Ai-Qin; Lin, Yan-Qing; Ruan, Shao-Ning; Liu, Bao; Cao, Shi-Jiang; Zhou, Li-Li; Li, Ming; Shuai, Peng; Hou, Xiao-Long; Wu, Yi-Han; Li, Nuo; Xiong, Sheng; Hao, Yang; Zhou, Zhuang; Liu, Xue-Die; Zuo, Dan-Dan; Li, Jia; Wang, Pei; Zhang, Jian; Liu, Ding-Kun; Chen, Gui-Zhen; Huang, Jie; Huang, Ming-Zhong; Li, Yuan-Yuan; Zheng, Qin-Yao; Zhao, Xue-Wei; Zhao, Xiang; Zhong, Wen-Ying; Zhang, Xue-Wen; Xia, Zheng-Bao; Yu, Ying; Liu, Zhi-Wei; Zheng, Hong-Kun; Ming, Ray; Van de Peer, Yves; Liu, Zhong-Jian (Cell Press, 2026-07-28)
Cupressaceae , a gymnosperm family, draws attention due to its controversial phylogenetic position. Here, we present a comprehensive genome analysis of Chinese fir (Cunninghamia lanceolata), a Cupressaceae species, to enhance our understanding of gymnosperm evolution. The 11.24 Gb assembled genome, shaped by inefficient long terminal repeat removal, offers insights into its phylogenetic position. Phylogenetic analysis refines gymnosperm relationships between Cycads-Ginkgo and their relation to Gnetales-Pinaceae. Whole-genome duplication (WGD) analysis reveals no evidence for an ancient polyploidization event in the lineage of C. lanceolata, and confirms a seed-plant-shared WGD event. We also explore genomic evidence to explain the population history and adaptability of C. lanceolata, including potential glacial refugia, dispersal centers, and unique sterility. Furthermore, the refined (A)B(C) model for reproductive organ development in C. lanceolata has broader applications across gymnosperms. This study provides a valuable genome sequence and contributes to the understanding of gymnosperm evolution. HIGHLIGHTS • A chromosome-level genome of Cunninghamia lanceolata is presented • Cupressaceae forms a sister group to Gntales-Welwitschia and pine clade among conifer • No ancient polyploidization exists in C. lanceolata, seed-plant-shared WGD is confirmed • Astringent seeds formation and reproductive organs’ evolution are explored
The rise of polyploids during environmental upheaval
Chen, Hengchi; Almeida-Silva, Fabricio; Logghe, Garben; Maere, Steven; Bonte, Dries; Van de Peer, Yves (Cell Press, 2026-06-11)
Polyploidy, or whole-genome duplication (WGD), serves as both a significant evolutionary force and a potential evolutionary dead end, particularly among angiosperms. Despite the prevalence of polyploid organisms, instances of ancient polyploidy are surprisingly rare, presenting a paradox that remains poorly understood. In this study, we constructed a comprehensive genomic dataset of 470 angiosperm species and dated 132 ancient WGD events that are non-randomly distributed, revealing a clustering around pivotal periods of environmental upheaval and extinction. Notably, our findings highlight a strong correlation between waves of paleopolyploidization and significant events such as the Middle Miocene Disruption, the Eocene-Oligocene Transition (EOT), the Paleocene-Eocene Thermal Maximum (PETM), the Cretaceous-Paleogene (K-Pg) extinction, and different oceanic anoxic events (OAEs). We propose that polyploid organisms have an increased chance of survival during times of great environmental turmoil, a conclusion with important implications in the context of contemporary climate change and rapid global warming. HIGHLIGHTS • All angiosperm lineages bear traces of ancient polyploidy • The overall WGD establishment rate is negatively correlated with species richness over time • There is lower polyploid establishment under stable, species-rich conditions • Polyploids mainly establish during times of great environmental upheaval
Preserving the biologically coherent generic concept of Phytophthora, “plant destroyer”
Brasier, Clive M.; Grünwald, Niklaus J.; Bourret, Tyler B.; Govers, Francine; Scanu, Bruno; Cooke, David E.L.; Bose, Tanay; Hawksworth, David L.; Abad, Gloria; Albarracin, M. Victoria; Alsultan, Wael; Altamirano-Junqueira, Astrid E.; Arifin, Arild R.; Arnet, Matthew J.; Aumentado, Herbert Dustin R.; Bakonyi, József; Belisle, Wei H.; Benigno, Alessandra; Bienapfl, John C.; Bilodeau, Guillaume J.; Blair, Jaime E.; Botella, Leticia; Brandano, Andrea; Cacciola, Santa Olga; Carbone, Ignazio; Castroagudin, Vanina L.; Chaendaekattu, Narayanan; Consford, Jonathan D.; Corcobado, Tamara; Covey, Paul A.; Daniels, Hazel A.; Deidda, Antonio; Dorrance, Anne E.; Dort, Erika N.; Drenth, André; Drizou, Fryni; Evangelisti, Edouard; Fajardo, Sebastian N.; Fang, Yufeng; Ference, Christopher M.; Frankel, Susan J.; Goss, Erica M.; Guest, David I.; Hardy, Giles E.S.J.; Harris, Anna R.H.; Hawku, Mehari Desta; Heungens, Kurt; Hong, Chuanxue; Horner, Ian J.; Jung, Marília Horta; Iyanda, Olumayowa J.; Jamieson, Brittney-Aidan; Jeffers, Steven N.; Judelson, Howard S.; Junaid, Muhammad; Kalogeropoulou, Eleni; Kamoun, Sophien; Kang, Seogchan; Kasuga, Takao; Kudlácek, Tomáš; LeBoldus, Jared; Lee, Christopher A.; Li, DeWei; Llanos, Alejandro K.; Lopez-Nicora, Horacio D.; Machado, Helena; Di San Lio, Gaetano Magnano; Maia, Cristiana; Mandal, Kajal; Manosalva, Patricia; Martin, Frank N.; Matson, Michael E.H.; McDougal, Rebecca L.; McDowell, John M.; Michelmore, Richard W.; Milenkovi´c, Ivan; Moricca, Salvatore; Mostowfizadeh-Ghalamfarsa, Reza; Nagy, Zoltán Á.; Nikolaeva, Ekaterina V.; Ortega-López, Paula; Paap, Trudy; Parada-Rojas, Camilo H.; Peduto Hand, Francesca; Pérez-Sierra, Ana; Pettersson, Martin; Prasad, Pramod; Puig, Alina S.; Raco, Milica; Rajput, Nasir A.; Ristaino, Jean B.; Rooney-Latham, Suzanne; Seidl, Michael F.; Shamoun, Simon F.; Solla, Alejandro; Spies, Christoffel F. J.; Sudermann, Martha A.; Swiecki, Tedmund J.; Tian, Miaoying; Tripathy, Sucheta; Uematsu, Seiji; Van Poucke, Kris; Vichou, Aikaterini E.; Walter, Monika; Webber, Joan F.; Williams, Nari M.; Wingfield, Michael J.; Yadav, Dhananjay; Yang, Xiao; Jung, Thomas (American Phytopathological Society, 2025-06)
Phytophthora is a long-established, well-known, and globally important genus of plant pathogens. Phylogenetic evidence has shown that the biologically distinct, obligate biotrophic downy mildews evolved from Phytophthora at least twice. Because, cladistically, this renders Phytophthora “paraphyletic,” it has been proposed that Phytophthora evolutionary clades be split into multiple genera (Crous et al. 2021; Runge et al. 2011; Thines 2023, 2024). In this letter, we review arguments for the retention of the generic name Phytophthora with a broad circumscription made by Brasier et al. (2022) and by many delegates at an open workshop organized by The American Phytopathological Society. We present our well-considered responses to the genus splitting proposals, both in general terms and in terms of the specific proposals for new genera, alongside new information regarding the biological properties and mode of origin of the Phytophthora clades. We consider that the proposals are mostly non-rigorous and not supported by the scientific evidence. Further, given (i) the apparent lack of any distinguishing biological characteristics (synapomorphies) between the Phytophthora clades; (ii) the fundamental monophyly of Phytophthora in the original Haeckelian sense (Haeckel 1877); (iii) the fact that paraphyly is not a justification for taxonomic splitting; and (iv) the considerable likely damage to effective scientific communication and disease management from an unnecessary breakup of the genus, we report that workshop delegates voted unanimously in favor of preserving the current generic concept and for seeking endorsement of this view by a working group of the International Commission on the Taxonomy of Fungi.
The human Chk1 inhibitor CHIR-124 shows multistage activity against the human malaria parasite Plasmodium falciparum via polypharmacological inhibition of PfArk1 and hemozoin formation
Wicht, Kathryn J.; Woodland, John G.; Garnie, Larnelle F.; Langeveld, Henrico; Taylor, Dale; Godoy, Luiz C.; Pasaje, Charisse Flerida A.; De Souza, Mariana Laureano; Siqueira-Neto, Jair L.; Ghidelli-Disse, Sonja; Lafuente-Monasterio, Maria Jose; Gamo, Francisco-Javier; Coertzen, Dina; Reader, Janette; Van der Watt, Mariette Elizabeth; Bridgford, Jessica L.; Girling, Gareth; Coyle, Rachael; Scheurer, Christian; Wittlin, Sergio; Alder, Arne; Gilberger, Tim-Wolf; Lee, Marcus C.S.; Voss, Till S.; Winzeler, Elizabeth A.; Fidock, David A.; Niles, Jacquin C.; Birkholtz, Lyn-Marie; Coulson, Lauren B.; Chibale, Kelly (American Chemical Society, 2026-07)
The high burden of malaria and growing resistance to frontline antimalarials demand new drug target combinations with reduced propensities for conferring parasite resistance. An attractive approach for circumventing antimalarial drug resistance is target repurposing, in which known drugs that act through protein targets of human origin that are also active against the human malaria parasite Plasmodium falciparum are exploited to identify novel antimalarial drug targets. Here, we show that the human checkpoint kinase 1 (Chk1) inhibitor CHIR-124 is active in vitro against both drug-sensitive and drug-resistant asexual blood stage parasites and competitively binds to several Plasmodium kinases. The compound also shows moderate activity against both the liver and gametocyte forms of the parasite. Further target investigation of CHIR-124 via conditional knockdown experiments confirmed that P. falciparum Aurora-related kinase 1 (PfArk1) is implicated in its parasiticidal activity. Notably, CHIR-124 also inhibits β-hematin (synthetic hemozoin) formation and causes a dose-dependent increase in free heme that correlates with inhibition of parasite growth. These findings suggest that polypharmacology is involved in the activity of CHIR-124 against P. falciparum via the dual inhibition of Plasmodium PfArk1 and hemozoin formation, both essential for parasite proliferation. This is further supported by in vitro drug combination experiments, morphological studies, and resistance generation attempts. This study validates the feasibility of dual Plasmodium kinase/hemozoin formation inhibitors active against resistant strains with decreased resistance risks in the fight against malaria.
Comparative analysis of mitochondrial genomes in the Ceratocystidaceae reveals highly conserved gene organization despite substantial genome size variation
Viljoen, Anien; Duong, Tuan A.; Kanzi , Aquillah M.; Wingfield, Brenda D. (BMC, 2026-03-19)
BACKGROUND : Comparative studies of mitochondrial genomes can assist in determining evolutionary and phylogenetic relationships. In the Ceratocystidaceae fungal family, mitochondrial genomes from only two genera are publicly available. In this study, mitochondrial genomes from 10 genera in Ceratocystidaceae were characterised and comparatively analysed. RESULTS : Mitochondrial (mt) genomes were fully assembled and characterized for 18 species and 10 genera of the Ceratocystidaceae. These mt genomes displayed a remarkable level of diversity owing to the variation in the intergenic regions and intron, both in size and number. Despite large variation in size, these mt genomes displayed high levels of synteny and sequence conservation in the oxidative phosphorylation (OXPHOS) genes and the ribosomal RNA and tRNA genes. The genes are found in identical order and orientation in all mt genomes characterized and the coding sequence of all the OXPHOS genes are highly conserved. Phylogenetic analysis of mitochondrial and nuclear DNA sequences reveals significant differences in evolutionary relationships among species and genera of Ceratocystidaceae. CONCLUSION : The remarkable variation in mt genome sizes in species of the Ceratocystidaceae is due to the variation observed in the intergenic regions and intron size and number in the conserved protein-coding genes. The gene order and content are identical across all species investigated.
Whole-genome sequences of 240 indigenous African cattle from Egypt, Uganda, and South Africa
Dlamini, Njabulo; Gao, Junxin; Ginja, Catarina; Kantanen, Juha; Ghanem, Nasser; Kugonza, Donald R.; Makgahlela, Mahlako; Elnahas, Ahmed; Zwane, Avhashoni Agnes; Zawedde, Barbara Mugwanya; Nakkazi, Christine; Behabura, Generous; Nxumalo, Khaniysani; Malima, Maano; Radwan, Mohamed Ali; Elsawy, Mohamed Hamada; Agaba, Morris; Fahim, Nadia Hamdi; Khfagy, Rana Atef; Agamy, Rania; Okwasiimire, Rodney; Waibi, Sarah; Lashmar, Simon; Crooijmans, Richard P.M.A. (Nature Research, 2026-06-18)
Indigenous cattle are central to livestock production in Africa, valued for their adaptability to harsh tropical environments despite lower productivity than commercial breeds. Genome analyses offer critical insights into the genetic potential for enhancing both resilience and productive traits, supporting the advancement of worldwide cattle farming systems. Here, we generated whole-genome sequence data for 240 indigenous cattle representing breeds from distinct agro-climatic regions in Egypt, Uganda, and South Africa. The dataset comprises over ten terabytes of paired-end reads generated using the Illumina NovaSeq. 6000 platform, with an average genome coverage of approximately 10×. Post-filtering reads were mapped to the ARS-UCD1.2 reference genome with a mean mapping rate of 99.2% (range: 64.5–99.9%). Variant calling identified ~43 million SNPs and 6 million indels (≤50 bp) unevenly distributed across the genome. Functional annotation indicated that many variants were located within or near known genes. This comprehensive genomic resource provides a foundation for future studies of genetic diversity, breed identity, population structure, local adaptation, breed-specific traits, or strategies for global cattle conservation.
Metagenomic analysis of fecal and environmental microbiota in rural mixed livestock farming systems in South Africa
Mthembu, Thobeka Promise; Hlongwane, Nompilo Lucia; Salawu-Rotimi, Adeola; Hadebe, Khanyisile; Pierneef, Rian Ewald (Frontiers Media, 2026-07-09)
In South African rural areas, farmers often practice mixed extensive livestock farming, facilitating microbial exchange among and between animal species and their environment. The composition and transmission potential of microbiomes between animals and their environments in these smallholder livestock systems remain largely unexplored, creating a gap in understanding how mixed-livestock farming affects gut and environmental microbiomes. Shotgun metagenomics was used to uncover the fecal and environmental microbiota in smallholder mixed livestock systems, aiming to understand microbiome transfer within these systems. A total of 111 samples were collected in KwaZulu-Natal and Eastern Cape provinces of South Africa, including 76 fecal samples from cattle, goats, sheep, pigs, and chickens; 18 soil samples; and 17 water samples. Taxonomic analysis of the sequencing data identified Proteobacteria as the dominant phylum across most hosts, except that pigs were dominated by Firmicutes. Moraxellaceae and Pseudomonadaceae were the differentiating families between monogastrics and ruminants. Although microbial diversity differences were significantly attributed to the host, genera such as Acinetobacter, Chryseobacterium, Flavobacterium, Pedobacter, and Pseudomonas were consistently found across all animal and environmental hosts. Cattle shared more genera with the environment than other animal species. Opportunistic pathogens, including Enterococcus spp., Escherichia coli, and Clostridium spp., were found across all the livestock species, and were highest in chickens. Additionally, some pathogens were detected in water but none in soil, suggesting water as a potential medium for pathogen transmission. The microbial exchange between livestock and their surroundings highlights the permeability of host-environment boundaries in smallholder systems.
Autoimmune hepatitis : a review of molecular mechanisms and research gaps in African populations
Wheeler, Caitlin; Scholefield, Janine; Hurrell, Tracey; Naidoo, Jerolen (MDPI, 2026-02-28)
Autoimmune hepatitis (AIH) is an inflammatory liver disease characterised by immune-mediated hepatic injury, often leading to liver failure. The underlying molecular mechanisms of AIH remain poorly elucidated, hindering diagnostic and therapeutic advances. This review overviews the current understanding of AIH pathogenesis, which arises from a complex interplay of genetic predisposition, environmental triggers, and immune mechanisms (loss of tolerance, regulatory T cell dysfunction). Furthermore, current technologies and models which are being used to deconvolve the molecular profiles and pathophysiology of AIH are also discussed. Although AIH has a low reported global burden, AIH research is critically skewed towards European ancestry populations. This leaves a significant knowledge gap in diverse ancestry groups, such as those of African ancestry, where emerging research suggests that these patients may experience a more aggressive disease. Collectively, this highlights the need for research in underrepresented global populations to develop tailored diagnostics and effective targeted treatments.

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