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

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Brucella pituitosa strain BU72, a new hydrocarbonoclastic bacterium through exopolysaccharide-based surfactant production
Mahjoubi, Mouna; Cherif, Hanene; Aliyu, Habibu; Chouchane, Habib; Cappello, Simone; Neifar, Mohamed; Mapelli, Francesca; Souissi, Yasmine; Borin, Sara; Cowan, Don A.; Cherif, Ameur (Springer, 2025-02)
Hydrocarbon and heavy metal pollution are amongst the most severe and prevalent environmental problems due to their toxicity and persistence. Bioremediation using microorganisms is considered one of the most effective ways to treat polluted sites. In the present study, we unveil the bioremediation potential of Brucella pituitosa strain BU72. Besides its ability to grow on multiple hydrocarbons as the sole carbon source and highly tolerant to several heavy metals, BU72 produces different exopolysaccharide-based surfactants (EBS) when grown with glucose or with crude oil as sole carbon source. These EBS demonstrated particular and specific functional groups as determined by Fourier transform infrared (FTIR) spectral analysis that showed a strong absorption peak at 3250 cm−1 generated by the -OH group for both EBS. The FTIR spectra of the produced EBS revealed major differences in functional groups and protein content. To better understand the EBS production coupled with the degradation of hydrocarbons and heavy metal resistance, the genome of strain BU72 was sequenced. Annotation of the genome revealed multiple genes putatively involved in EBS production pathways coupled with resistance to heavy metals genes such as arsenic tolerance and cobalt-zinc-cadmium resistance. The genome sequence analysis showed the potential of BU72 to synthesise secondary metabolites and the presence of genes involved in plant growth promotion. Here, we describe the physiological, metabolic, and genomic characteristics of Brucella pituitosa strain BU72, indicating its potential as a bioremediation agent.
Blood pressure and APOL1 risk variants in a South African chronic haemodialysis population of African ancestry
Van Hougenhouck-Tulleken, Wesley G.; Rheeder, Paul; Janse van Rensburg, Elizabeth (Oxford University Press, 2026-09)
BACKGROUND : APOL1 risk variants are strongly associated with kidney disease in individuals of recent African ancestry, but their haemodynamic effects remain incompletely characterised, particularly in African dialysis populations. We evaluated the association between APOL1 variants and blood pressure phenotypes in a South African haemodialysis cohort. METHODS : In this cross-sectional study, 115 adults receiving maintenance haemodialysis in Pretoria were included. All participants were self-identified Black Africans. APOL1 genotyping (G1: rs73885319, rs60910145; G2: rs71785313) was performed, and genetic models were analysed as additive, dominant, and recessive. Pre-dialysis blood pressure was the mean of five consecutive measurements. Outcomes included systolic blood pressure (SBP), diastolic blood pressure (DBP), mean arterial pressure (MAP), and pulse pressure (PP). Associations were assessed using linear mixed-effects models with dialysis site as a random effect, with sequential adjustment for age, sex, and antihypertensive class burden. RESULTS : APOL1 risk allele distribution was 53.0% zero, 36.5% one, and 10.4% two alleles. There were no consistent associations between APOL1 genotype and SBP, DBP, or MAP in univariate analyses. In multivariable models, SBP was significantly lower in APOL1 risk allele carriers under additive and dominant models. By contrast, PP was consistently lower in APOL1 risk allele carriers and remained significant after full adjustment (additive model, one vs. zero: β -7.772, 95% confidence interval (CI) -13.009 to -2.535, P = 0.004; dominant model: β -7.69 95% CI -12.622 to -2.757, P = 0.003). No consistent associations were observed for DBP or MAP. CONCLUSIONS : In this cohort of Black African haemodialysis patients, APOL1 risk variants were associated with lower PP and, after adjustment, lower SBP, without differences in DBP or MAP. These findings suggest a distinct haemodynamic phenotype characterised by reduced arterial pulsatility and highlight the need for further mechanistic and prospective studies, particularly in the context of emerging APOL1-targeted therapies.
Quambalaria spp. : emerging tree pathogens of concern
Jamieson, Brittney-Aiden; Paap, Trudy; Pegg, Geoff S.; Carnegie, Angus J.; Wingfield, Michael J.; Roux, Jolanda; Hardy, Giles ESt J.; Drenth, Andre; Hammerbacher, Almuth; Bose, Tanay (Springer, 2026-05-23)
PURPOSE OF REVIEW : Quambalaria spp. are fungal pathogens originating from Australian eucalypt species that are becoming increasingly important globally. For example, Quambalaria eucalypti, which was once considered a minor pathogen, now poses a significant threat to plantation productivity and forest health across continents. Their spread has been made possible through the expansion of eucalypt plantation forestry outside Australia, the movement of plant material and the increase in travel and trade, which facilitates the intercontinental movement of pathogens. This review summarises current knowledge regarding the taxonomy, distribution, life cycle and ecological and commercial impacts of Quambalaria spp. and some considerations for their control. RECENT FINDINGS : Recent studies have discovered new species of Quambalaria and there is emerging evidence of host shifts to other genera in the Myrtaceae. Outbreaks in Brazil, China, Indonesia and South Africa illustrate the rapid spread of Quambalaria spp. to new plantation environments. These pathogens threaten eucalypt plantations worldwide because clonal propagation reduces tree diversity and the trade of plant material facilitates their spread. Evidence of sexual reproduction has been identified in one species, Quambalaria pitereka, alluding to a high evolutionary potential. Although new molecular diagnostics and resistance screening tools are emerging, their use in the control of these pathogens remains limited. SUMMARY : Quambalaria spp. are important tree pathogens that are increasing their impact beyond their ancestral home in Australia. Their impact on plantation forestry and native forests underscores the broader vulnerabilities of forest ecosystems. Mitigating their impact will require integrated approaches that combine resistance breeding, enhanced surveillance, stringent quarantine measures, integrated disease management and changes to silviculture. Further research into host range, infection biology and pathogen evolution and the development of effective disease control is essential to safeguard global forests and ensure sustainable plantation forestry.
Gold nanoparticles coated with the antimicrobial peptide Os-C(W5) : anticandidal and biological activity
Palm, Pierre Jean-Moné; Chirombo, Rumbidzai Ruth; Chiramba, Court Kudakwashe; Serem, June Cheptoo; Taute, Helena; Van der Walt, Mandelie; Gaspar, Anabella Regina Marques; Bester, Megan Jean (Wiley, 2026-09)
Candida albicans is a critical-priority fungal pathogen due to its global burden of infection, biofilm-forming ability, and increasing drug resistance. Previously, the tick-derived antimicrobial peptide (AMP), Os-C, demonstrated antifungal, antioxidant, and nitric oxide (NO) scavenging activity. Subsequent tryptophan end-tagging produced Os-C(W5) which improved antifungal activity and reduced salt sensitivity; however, the proteolytic susceptibility of Os-C(W5) remained a limitation. Researchers have shown that N-terminal tryptophan tagging of a gold binding peptide generated gold nanoparticle (GNPs) of a clinically relevant size. We successfully applied this method with minor modifications to generate GNPs coated with Os-C(W5). GNP@Os-C(W5) exhibited an average diameter of 14.2 ± 0.32 nm, with preserved peptide disorder in peptide secondary structure after conjugation. Compared with free Os-C(W5), GNP@Os-C(W5) activity against planktonic C. albicans was reduced, but antibiofilm activity was maintained, associated with a reduction in biofilm biomass. Ultrastructural changes to planktonic C. albicans included roughened and irregular surfaces, membrane indentations, and extracellular debris indicating cell lysis. Samples treated with Os-C(W5) and GNP@Os-C(W5) showed visibly less dense biofilm architecture and fewer apparent hyphal structures relative to the untreated control. Both Os-C(W5) and GNP@Os-C(W5) were non-cytotoxic to HaCat cells. Most importantly, resistance to the protease trypsin was increased. However, antioxidant properties of Os-C(W5) were lost with GNP conjugation, whereas both Os-C(W5) and GNP@Os-C(W5) compared with Os-C lacked NO scavenging activity. Overall, this method of GNP conjugation provides a viable strategy to achieve enhanced AMP stability, retained antifungal activity, although the ability of GNP@Os-C(W5) to reduce oxidative stress was compromised.
Structure-guided optimization of novel inhibitors of Plasmodium lysyl-tRNA synthetase with multistage activity against malaria parasites
Forte, Barbara; Bellany, Fiona; Campbell, Peter S.; Chemi, Giulia; Dawson, Alice; Anderson, Mark; Aniweh, Yaw; Burkhard, Anna Y.; Aguiar, Anna Caroline Campos; Churchyard, Alisje; Cooper, Caitlin A.; Dos Santos Ferreira, Amalia; Famodimu, Mufuliat Toyin; Fang, Francis G.; Hu, Xiao; Huijs, Tonnie; Baud, Delphine; Jansen, Chimed; Jimenez Diaz, Maria Belen; Bonnert, Roger; Boyd, Susan; Crespo-Fernandez, Benigno; Mitasev, Branko; Montagna, Simone; Mok, Sachel; Murugesan, Dinakaran; Narwal, Sunil K.; Norcross, Neil R.; Okombo, John; Park, Heekuk; Peet, Caroline; Pereira, Dhelio B.; Post, John M.; Reader, Janette; Riley, Jennifer; Robinson, David A.; Shinkyo, Raku; Simeons, Frederick R.C.; Simpson, Laura; Smith, Alasdair; Smith, Dennis; Striepen, Josefine; Teles, Carolina B.G.; Van der Laak, Rianne; Uhlemann, Anne-Catrin; Vantaux, Amelie; Wilson, Caroline; Witkowski, Benoit; Wood, Gavin; Yeo, Tomas; Zuccotto, Fabio; Angulo-Barturen, Inigo; Baum, Jake; Bolscher, Judith M.; Guido, Rafael Victorio Carvalho; Birkholtz, Lyn-Marie; Delves, Michael J.; Dembele, Laurent; Fidock, David A.; Gamo, Francisco Javier; Kyle, Dennis E.; Maher, Steven P.; Popovici, Jean; Walpole, Chris; Gusovsky, Fabian; Willis, Paul A.; Read, Kevin D.; Gilbert, Ian H.; Baragana, Beatriz (American Chemical Society, 2026-06)
A fused dihydropyrrolidino-pyrimidine hit with low lipophilicity and excellent ligand efficiency was identified in a biochemical screen of the Global Health Chemical Diversity Library (GHCDL) against Plasmodium lysyl-tRNA synthetase (KRS). Structure-guided lead optimization delivered analogues with potent parasite growth inhibition, excellent biochemical and cellular selectivity (>1000-fold), and oral efficacy in the malaria NOD-scid-IL2Rγnull (SCID) mouse model. Structural information and computational methods were deployed to identify a potent and selective basic KRS inhibitor (30) with an extended half-life to reduce the dose regimen to a single-dose cure. Compound 30 displayed a long half-life across preclinical species, favorable safety, and activity across Plasmodium species as well as against drug-resistant and sensitive P. falciparum strains and field isolates. Unfortunately, 30 lacked oral bioavailability, which could not be mitigated with a prodrug approach. Nevertheless, learnings from this series will assist future KRS programs in delivering a clinical candidate with this novel mode of action.
Lineage-specific diversity of pheromone response pathway genes is independent of mating strategy in Ceratocystidaceae
Lane, Frances Alice; Wingfield, Brenda D.; Wingfield, Michael J.; Wilken, P. Markus (BioMed Central, 2026-02-23)
The pheromone-receptor system plays a crucial role in mate recognition and fertilisation of ascomycete fungi and is strongly regulated by proteins coded for in the mating-type locus. This locus also determines the mating strategy, sexual identity and mate compatibility of fungal species. Genome assemblies are available for many species in the Ceratocystidaceae, a family of fungi with diverse mating strategies. This provided an opportunity to investigate the relationship between sexual strategy and the pheromone-receptor system in these species. The pheromone and pheromone-receptor genes were identified and characterised from the genome sequences of 52 isolates representing 35 species from 14 genera in the Ceratocystidaceae. Additionally, these data were used to elucidate patterns linked to differences between the pheromones and pheromone receptors, and mating strategies. To do this, the target genes were identified using homologous- and syntenic-based approaches. Putative protein sequences and genomic locations were then compared across the entire family, including species of Huntiella that had previously been characterised. With a few exceptions, putatively functional pheromones and receptors were identified in all the Ceratocystidaceae genomes. The results showed no discernible link between the presence, genomic location or structure of these proteins and mating strategy. Interspecific conservation in sequence and genomic locations revealed greater correlation to taxonomic relatedness, although intraspecific variation was also observed. Interestingly, despite reports of sexual reproduction in Ambrosiella species, all genomes of these species lacked the α-pheromone gene and encoded a non-functional α-pheromone receptor. This is the most extensive study of pheromones and their receptors in a Sordariomycetes family and complements efforts aimed at understanding the complex history of sexual reproduction in the Ceratocystidaceae.
First report of Melanterius inconspicuus (Coleoptera: Curculionidae: Cleogonini) from KwaZulu-Natal, South Africa, with observations of its development in black wattle
Nel, Wilma Janine; Barnes, Irene; Jali, Sandisiwe; Impson, Fiona; Oberprieler, Rolf G.; Hurley, Brett Phillip (Taylor and Francis, 2026)
Melanterius is a large genus of small weevils that primarily feed on the seeds of Acacia species occurring in their native range in Australia. In the latter part of the 20th century, five seed-feeding Melanterius species were released against several weedy Acacia species in South Africa as biological control agents. In early 2024, Melanterius weevils were detected damaging the vegetative plant tissues of trees in a commercial black wattle (Acacia mearnsii) compartment in the KwaZulu-Natal, South Africa. Morphological identification and DNA sequencing revealed that the weevils represent the species Melanterius inconspicuus, which is not one of the five species introduced in South Africa. This finding represents the first record of this Melanterius species outside of its native range in Australia and infesting black wattle, as well as the first record of a Melanterius species infesting vegetative tissues.
An overview of the genetic diversity and epidemiological potential of Yersinia pestis populations in natural plague foci of Kazakhstan
Abdirassilova, Aigul; Yessimseit, Duman; Kassenova, Altynai; Rysbekova, Altyn; Abdeliyev, Beck; Zhumadilova, Zauresh; Abdel, Ziyat; Mussagaliyeva, Raikhan; Meka-Mechenko, Tatyana; Sairambekova, Galiya; Begimbayeva, Elmira; Nurpeisova, Ainur; Sagidulin, Temirkhan; Maksatova, Ayaulym; Agzam, Sanzhar; Nissanova, Raikhan; Motin, Vladimir; Reva, Oleg N. (MDPI, 2026-05-20)
This review provides a comprehensive overview of the genetic diversity and epidemiological potential of Yersinia pestis in Kazakhstan’s natural plague foci, emphasizing the link between genotypic variation and outbreak capacity. Integrating historical epidemiological records with contemporary microbiological and genomic data (including PCR, VNTR/MLVA, SNP analysis, and whole-genome sequencing), we evaluate core and accessory genome variations. The data reveal substantial regional heterogeneity. High-risk desert foci (Caspian and Aral regions) are dominated by the Medievalis biovar, including atypical genovariants lacking canonical markers. Conversely, high-mountain foci (Sarydzhaz, Talas) harbor the Antiqua and Talas biovars, primarily linked to enzootic circulation. Notably, the Ili River focus exhibits extreme genomic variability, featuring strains with plesiomorphic traits. Furthermore, the widespread distribution of mobile elements like the cryptic plasmid pCKF suggests significant horizontal transfer contributing to pathogen adaptation. Ultimately, Central Asian plague dynamics are driven by complex evolutionary and ecological interactions. Given climate change and expanding human–wildlife interfaces, continuous genomic and ecological surveillance is essential for the early detection of high-risk Y. pestis genovariants and improving public health preparedness.
Trace gas oxidation supports sub-surface microbial communities across Namib Desert fog and aridity gradients
Tribbia, Dana Z.; Lebre, Pedro Humberto; Vazquez-Campos, Xabier; Ray, Angelique E.; Laird, Thomas; Machado de Lima, Nathali; Maggs-Kolling, Gillian; Cowan, Don A.; Ferrari, Belinda C. (American Society for Microbiology, 2026-08)
Widely accepted climate predictions indicate that drylands will expand to cover more than half of the Earth’s terrestrial surface by the end of the 21st century. In these environments, harsh conditions, including nutrient and water limitations, restrict plant and animal life, thereby increasing the importance of soil microbial communities in nutrient cycling and ecosystem functioning. The Namib Desert is a distinctive dryland ecosystem characterized by a steep natural aridity gradient, transitioning from a coastal hyperarid zone influenced by frequent fog deposition to an inland arid region receiving seasonal rainfall. This study investigates the impact of water availability and moisture regime on microbial trace gas oxidation and community composition across this aridity gradient. Quantitative analyses revealed that total microbial abundance and activity indicators, including ATP concentrations and respiration rates, were significantly (P < 0.005) reduced in hyperarid soils compared to their arid counterparts. In contrast, hyperarid fog-dominated soils exhibited significantly (P < 0.0005) elevated rates of atmospheric hydrogen oxidation, even in the absence of water inputs. We propose that sustained high-affinity hydrogen oxidation, coupled with rapid microbial resuscitation following wetting events, supports shallow sub-surface microbial communities in the Namib Desert, particularly in the coastal hyperarid zone. Together, these findings challenge current understanding of the lower limits of microbial activity and reveal alternative metabolic pathways that enable microbial persistence in hyperarid hot desert soils. IMPORTANCE : Drylands are expanding globally, yet the mechanisms that allow microbial life to persist under extreme and sustained water limitation remain poorly understood. This study demonstrates that atmospheric trace gas oxidation, particularly high-affinity hydrogen oxidation, supports active and resilient microbial communities in hyperarid soils of the Namib Desert, even in the absence of liquid water inputs. By revealing how microbes may couple trace gas metabolism to energy and water generation, our findings provide new insight into the lower limits of microbial activity in dry, hot desert soils and highlight the need to investigate how microbes persist and sustain soil ecosystem functioning.
First report of pepper ringspot virus infecting sunflower (Helianthus annuus) in South Africa
Burger, Vida; Esterhuizen, Lindy; Read, David Alan (Springer, 2026-02)
No abstract available.
Genera of phytopathogenic fungi known from culture : 1-379
Crous, Pedro W.; Groenewald, J.Z.; Bensch, K.; Gene, J.; Guarro, J. (Westerdijk Fungal Biodiversity Institute, 2025-12-03)
Approximately 200000 species of fungi have been described to date, representing nearly 8000 currently recognised genera. Many of these genera are regarded as plant pathogenic, as they include at least one species proven to cause pre- or postharvest plant disease. Following the abandonment of dual nomenclature and the advent of DNA sequencing and phylogenetic approaches, numerous para- and polyphyletic clades were resolved into distinct genera. These genera are now defined based on morphology, ecology, and DNA phylogeny. The present paper represents the first in a series that aims to provide descriptions, classification, illustrations, significant species, disease symptoms, and DNA data for the common genera of phytopathogenic fungi known from culture, including the first treatment of 379 genera. In addition, several new combinations, lecto-, epi-, or neotypes are also proposed.
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.

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