Donna Huber, Author at Center for Tropical and Emerging Global Diseases

PGDD 2.0: Plant Genome Duplication Database with updated content and tools

Donna Huber on November 26, 2025

Polyploidy and small-scale duplication have repeatedly reshaped plant genomes, making synteny and colinearity indispensable for evolutionary inference. We present PGDD 2.0 (accessible at chibba.agtec.uga.edu and pgdd2.org), a major update to the Plant Genome Duplication Database (PGDD) that now aggregates >120 complete telomere-to-telomere (T2T) assemblies, including many chromosome-scale genomes spanning all major Viridiplantae lineages. Each genome sequence is processed with a standardized pipeline to call intra- and intergenomic colinear (syntenic) blocks, estimate Ks, and block score metrics and age distributions. PGDD 2.0 introduces (i) interactive synteny networks for pattern discovery across taxa, (ii) a “riparian” or synteny alignment view for visualizing mesosynteny and rearrangements, and (iii) an embedded SynVisio module for rendering user-supplied or PGDD-downloaded MCScanX results directly in the browser. Together, these advances support tasks from resolving ancient whole-genome duplication signatures to tracing the postduplication fates of specific gene families with T2T-level precision and beyond. PGDD 2.0 delivers an up-to-date, uniform, and user-centered platform for plant comparative genomics, accelerating discovery regarding polyploidy, gene duplication, and genome evolution.

Ankush Sharma, John E Bowers, Tae-Ho Lee, Mingrui Xu, Ramandeep Kaur, Jessica C Kissinger, Xin Qiao, Peng W Chee, Andrew H Paterson. Nucleic Acids Res. 2025 Nov 26:gkaf1287. doi: 10.1093/nar/gkaf1287.

Four nudivirus core genes present in the genome of Venturia canescens are required for virus-like particle formation and prevention of encapsulation of parasitoid wasp eggs

Donna Huber on November 20, 2025

Fig 1 VcVLP morphogenesis in calyx cells from different aged pupae or newly emerged adults that were injected with ds-egfp when P1 pupae.

Venturia canescens is a parasitoid wasp that harbors a domesticated endogenous virus (DEV) and parasitizes host insects like Ephestia kuehniella. The V. canescens DEV evolved from an alphanudivirus and produces virus-like particles (VLPs) in females that protect wasp eggs from a host immune defense called encapsulation. In contrast, very few DEV genes required for VLP formation and function have been identified. In this study, we characterized five V. canescens DEV genes of unknown function that all nudiviruses encode. Three of these genes are single copy (OrNVorf18-like, OrNVorf61-like, and OrNVorf76-like), while OrNVorf41-like has expanded into a six-member family and OrNVorf47-like has expanded into a three-member family. Sequence analysis indicated all of these genes retain essential motifs present in nudivirus homologs, while transmission electron microscopy (TEM) studies characterized the timing of VLP formation during the wasp pupal stage. RNA interference (RNAi) assays identified OrNVorf18-like, OrNVorf61-like, OrNVorf41-like-1, and OrNVorf41-like-2 as genes that are required for normal VLP formation. Knockdown of OrNVorf47-like family members did not affect VLP formation but did disable binding of VLPs to V. canescens eggs and protection against encapsulation. Disabled formation of VLPs in response to RNAi knockdown of OrNVorf18-like, OrNVorf61-like, OrNVorf41-like-1, and OrNVorf41-like-2 also resulted in wasp eggs being encapsulated. In contrast, knockdown of OrNVorf76-like had no effect on VLP assembly, egg binding, or encapsulation. Altogether, reported results significantly advance our understanding of V. canescens VLP (VcVLP) formation and function.

Importance: Understanding how V. canescens coopted an alphanudivirus to produce VcVLPs is of interest to the study of virus evolution. Our results show that three nudivirus core genes have essential functions in VcVLP formation, while one is essential for the novel function of binding to wasp eggs and protection from encapsulation, which is the most important immune defense of insects against parasitoids.

Meng Mao, Corinne M Stouthamer, Ange Lorenzi, Michael R Strand, Gaelen R Burke. J Virol. 2025 Nov 20:e0130525. doi: 10.1128/jvi.01305-25.

Temporal Variation in Target Site Mutations Is Associated with Diamide Cross-Resistance in Diamondback Moth Populations (Lepidoptera: Plutellidae) from Florida and Georgia, USA

Donna Huber on November 19, 2025

Collection sites, dates, and coordinates for all diamondback moth populations in this study.

The Diamondback moth (DBM), Plutella xylostella (L.), the most significant worldwide pest of Brassica crops, is notorious for resistance to a diverse number of insecticides. Field populations bioassayed in Georgia and Florida, USA, in 2018 were resistant to chlorantraniliprole but susceptible to cyantraniliprole. Subsequently, populations assayed in 2021, 2022, and 2023 were cross-resistant to both diamides. We used NextSeq analysis of the ryanodine receptor PxRyR, the target of diamides, to quantify target site mutations associated with resistance. Three populations sampled in 2018 had a high prevalence (75.0-98.3% of total reads) of the G4946E mutation, associated with resistance to chlorantraniliprole, and additionally, in one population, a very low (2.7%) prevalence of another mutation, I4790K, was associated with diamide cross-resistance. Populations sampled in 2021 had a decreased prevalence of G4946E (0.7 and 8.4%) and increased prevalence of I4790K (9.3 and 18.0%). The G4946E allele was almost absent (0.2% to 3.9%) in populations sampled in 2022 and 2023, while I4790K was present at frequencies from 34.1% to 84.0%. These data suggest a remarkable shift in PxRyR target site mutations, replacing G4946E with I4790K, which occurred between 2018 and 2022, and were associated with the recent occurrence of cross-resistance in DBM populations in the Southeastern USA.

Thomas P Dunn, Md Abdullah Al Baki, Paulo S G Cremonez, David G Riley, Alton N Sparks Jr, Hugh Smith, Donald E Champagne. Insects. 2025 Nov 19;16(11):1179. doi: 10.3390/insects16111179.

Calcium transfer from the ER to other organelles for optimal signaling in Toxoplasma gondii

Donna Huber on November 12, 2025

Hypothetical model showing Ca2+ entry through two different types of Ca2+ channels, uptake by T. gondii sarco/endoplasmic reticulum Ca2+- ATPase (TgSERCA) into the endoplasmic reticulum (ER) and distribution to the other organelles via transfer from the ER to the mitochondria, Plant-Like Vacuolar Compartment (PLVAC), and apicoplast.

Ca2+ signaling in cells begins with the opening of Ca2+ channels in either the plasma membrane (PM) or endoplasmic reticulum (ER), leading to a sharp increase in the physiologically low (<100 nM) cytosolic Ca2+ level. The temporal and spatial regulation of Ca²+ is crucial for the precise activation of key biological processes. In the apicomplexan parasite Toxoplasma gondii, which infects approximately one-third of the global population, Ca²+ signaling governs essential aspects of the parasite’s infection cycle. T. gondii relies on Ca²+ signals to regulate pathogenic traits, with several Ca²+-signaling components playing critical roles. Ca2+ entry from the extracellular environment has been demonstrated in T. gondii for both, extracellular parasites, exposed to high Ca2+, and intracellular parasites, which acquire Ca²+ from host cells during host Ca²+ signaling events. Active egress, an essential step of the parasite’s infection cycle, is preceded by a large increase in cytosolic Ca2+, most likely initiated by release from intracellular stores. However, extracellular Ca2+ is also necessary to reach a cytosolic Ca2+ threshold required for timely egress. In this study, we investigated the mechanism of intracellular Ca²+ store replenishment and identified a central role for the SERCA-Ca2+-ATPase in maintaining Ca²+ homeostasis within the ER and in other organelles. We demonstrate mitochondrial Ca2+ uptake, which occurs by transfer of Ca2+ from the ER, likely through membrane contact sites. Our findings suggest that the T. gondii ER plays a key role in sequestering and redistributing Ca²+ to intracellular organelles following Ca²+ influx at the PM.

Zhu-Hong Li, Beejan Asady, Le Chang, Myriam Andrea Hortua Triana, Catherine Li, Isabelle Coppens, Silvia N J Moreno. Elife. 2025 Nov 12:13:RP101894. doi: 10.7554/eLife.101894.

Selenocyanate-Containing Molecules as Trypanosoma cruzi Inhibitors: Impact of Regioisomerism, Conformational Restriction, and Second-Ring Substitution

Donna Huber on November 11, 2025

As a continuation of the project aimed at searching for new chemotherapeuticagents against Chagas disease or American trypanosomiasis, new selenocyanate derivatives are designed, synthesized, and biologically evaluated against the clinically more relevant dividing amastigote form of Trypanosoma cruzi, the etiologic agent of this illness. Furthermore, as all the title compounds are fluorine-containing molecules, it seemed to be reasonable to explore the role of fluorine atoms in the aromatic system and to determine the optimal position at the terminal phenoxy group, and therefore, various regioisomers are prepared. The conformationally restricted selenocyates structurally related to WC-9Se exhibited improved antiparasitic activity compared to the lead drugs, Out to be extremely potent inhibitors of T. cruzi growth. In particular, (±)-5-(3-fluorophenoxy)-2-(selenocyanatomethyl)-2,3-dihydrobenzofuran exhibited an EC₅₀ value of 0.032 µM, which resulted in the most potent selenocyanate developed in the laboratory. The presence of the fluorine atom together with the rigidity of the molecules are beneficial for the anti-T. cruzi effect. The resulting antiparasitic activity provides further insight into the role of the selenocyanate group in its effective and putative anti-T. cruzi action.

Hugo S Steingrüber, Mayara S Bertolini, Margarita M Vallejos, Sergio H Szajnman, Roberto Docampo, Juan B Rodriguez. ChemMedChem. 2025 Nov 11:e202500658. doi: 10.1002/cmdc.202500658.

Genomic Characterization of Cryptosporidium spp. via iNextEra Library Preparation and Hybridization Bait Capture

Donna Huber on October 28, 2025

Next-generation DNA sequencing (NGS) is used to study the genome sequences of Cryptosporidium spp., but NGS is challenging when pure Cryptosporidium oocysts are limited in number or not available. Varying levels of parasites present in fecal samples, combined with the abundance of host cells, bacterial and other microbial cells, and undigested food particles, often result in fecal DNA samples with ~0.1% Cryptosporidium DNA, making genome-scale sequencing of Cryptosporidium from such samples cost-prohibitive. DNA extractions from fecal samples are, however, widely available and commonly used for polymerase chain reaction (PCR)-based diagnostics which can detect fg levels of Cryptosporidium DNA in complex DNA mixtures. Here, we describe an Illumina NGS sample preparation protocol (iNextEra) that can generate libraries from a wide range of DNA input (<1 ng to >60 ng). We then use those libraries within a modified myBaits capture hybridization protocol using CryptoCap_100K baits to enrich Cryptosporidium genomic DNA from a complex DNA background to increase the percentage of generated sequence reads that map to target Cryptosporidium reference genome sequences. Thus, iNextEra libraries and capture hybridization facilitate genome-level sequencing of this critical pathogen from widely available samples with less cost, thereby opening new opportunities to understand the complex biology of this important pathogen.

Mohammad Imtiaj Uddin Bhuiyan, Fiifi Agyabeng-Dadzie, Amanda H Sullivan, Megan S Beaudry, Kelly N Petersen, Piotr T Tuczapski, Michael E Grigg, Jessica C Kissinger, Travis C Glenn. Methods Mol Biol. 2026:2978:41-64. doi: 10.1007/978-1-0716-4824-7_4.

More extraordinary model systems for regeneration

Donna Huber on October 28, 2025

Fig. 3 The rat tapeworm Hymenolepis diminuta.

The ability of organisms to replace and regenerate anatomical structures following their loss or damage has piqued the curiosity of biologists for centuries. In addition to Development’s ‘Model systems for regeneration’ collection, which introduced some of the most well-studied model organisms in the field, we published a Perspective in 2024 highlighting some of the lesser-known species with extraordinary regenerative abilities from plants to vertebrates ( Accorsi et al., 2024). Here, we revisit this topic again, hearing the perspectives of five experts, each of whom studies an amazing species with remarkable regenerative potential.

José E García-Arrarás, Chunyi Li, Tania Rozario, Mansi Srivastava, Andrew Willoughby. Development. 2025 Oct 15;152(20):dev205215. doi: 10.1242/dev.205215.

Characterization of β-Carboline Derivatives Reveals a High Barrier to Resistance and Potent Activity against Ring-Stage and DHA-Induced Dormant Plasmodium falciparum

Donna Huber on October 17, 2025

Malaria, caused by Plasmodium falciparum, remains a major global health challenge, with an estimated 263 million new infections and 597,000 deaths annually. Increasing resistance to current antimalarial drugs underscores the urgent need for new therapeutics that target novel pathways in the parasite. We previously reported a novel class of β-carboline antimalarials, exemplified by PRC1584, which demonstrated a favorable oral pharmacokinetic profile, in vivo efficacy in Plasmodium berghei-infected mice, and no cross-resistance with other antimalarials in various P. falciparum strains. In this study, we demonstrate that PRC1584 exhibits a high resistance barrier and retains potent activity against fresh Ugandan P. falciparum isolates. PRC1584, along with its more potent analog PRC1697, demonstrated strong in vitro potency against both actively proliferating ring stages and dihydroartemisinin-induced dormant stages. Additionally, our study demonstrated that PfKelch13-C580Y mutation was associated with an increased susceptibility to PRC1584, whereas PfKelch13-R549T and Pfcoronin-R100 K-E107V mutations were not associated with this effect. These findings underscore the therapeutic potential of this new “irresistible” compound class, support a possible novel mechanism of action, and suggest the future development of novel ACTs active against resistant parasites by targeting DHA dormancy, an essential survival mechanism of P. falciparum.

Reagan S Haney, Joshua H Butler, Lyric A Wardlaw, Emilio F Merino, Victoria Mendiola, Caitlin A Cooper, Jopaul Mathew, Patrick K Tumwebaze, Philip J Rosenthal, Roland A Cooper, Dennis E Kyle, Zaira Rizopoulos, Delphine Baud, Stephen Brand, Maxim Totrov, Paul R Carlier, Maria Belen Cassera. ACS Infect Dis. 2025 Oct 17. doi: 10.1021/acsinfecdis.5c00714.

Amplicon sequencing detects, identifies, and quantifies minority variants in mixed-species infections of Cryptosporidium parasites

Donna Huber on October 8, 2025

Fig 1 Cryptosporidium species identification using 18S amplicon sequencing.

Cryptosporidium is a globally endemic parasite genus with over 40 recognized species. While C. hominis and C. parvum are responsible for most human infections, human cases involving other species have also been reported. Furthermore, there is increasing evidence of simultaneous infections with multiple species. Therefore, we devised a new means to identify various species of Cryptosporidium in mixed infections by sequencing a 431 bp amplicon of the 18S rRNA gene encompassing two variable regions. Using the DADA2 pipeline, amplicons were first identified to a genus using the SILVA 132 reference database; then Cryptosporidium amplicons to a species using a custom database. This approach demonstrated sensitivity, successfully detecting and accurately identifying as little as 0.001 ng of C. parvum DNA in a complex stool background. Notably, we differentiated mixed infections and demonstrated the ability to identify potentially novel species of Cryptosporidium both in situ and in vitro. Using this method, we identified Cryptosporidium parvum in Egyptian rabbits with three samples showing minor mixed infections. By contrast, no mixed infections were detected in Egyptian children, who were primarily infected with C. hominis. Thus, this pipeline provides a sensitive tool for Cryptosporidium species-level identification, allowing for the detection and accurate identification of minor variants and mixed infections.

IMPORTANCE Cryptosporidium is a eukaryotic parasite and a leading global cause of waterborne diarrhea, with over 40 recognized species infecting livestock, wildlife, and people. While we have effective tools for detecting Cryptosporidium in clinical and agricultural water samples, there is still a need for a method that can efficiently identify known species as well as infections with multiple Cryptosporidium species, which are increasingly being reported. In this study, we utilized sequencing of a specific region to develop a sensitive and accurate identification workflow for Cryptosporidium species based on high-throughput sequencing. This method can distinguish between all 40 recognized species and accurately detect mixed infections. Our approach provides a sensitive and reliable means to identify Cryptosporidium species in complex clinical and agricultural samples. This has important implications for clinical diagnostics, biosurveillance, and understanding disease transmission, ultimately benefiting clinicians and produce growers.

Randi Turner, Doaa Naguib, Elora Pierce, Alison Li, Matthew Valente, Travis C Glenn, Benjamin M Rosenthal, Jessica C Kissinger, Asis Khan. mBio. 2025 Oct 8;16(10):e0110925. doi: 10.1128/mbio.01109-25.

Large DNA Viruses That Parasitoid Wasps Transmit to Hosts

Donna Huber on October 7, 2025

Many types of viruses have been identified in parasitoid wasps and other Hymenoptera. Parasitoid wasps also transmit several viruses to hosts through the piercing ovipositors that females use to lay eggs. Most viruses that are known to be transmitted by parasitoids have large double-stranded DNA genomes. We summarize the range of interactions that have evolved between parasitoid wasps and the viruses they transmit. Some viruses are mechanically transmitted to hosts, which can reduce the fitness of wasp offspring. Others have evolved into beneficial symbionts or reproductive parasites that replicate in wasps and hosts. Some large dsDNA viruses have also been co-opted into domesticated endogenized viruses that are vertically transmitted to offspring but still produce virions or virus-like particles that wasps use to parasitize hosts. We conclude by discussing future directions and why parasitoid wasps likely transmit many more viruses than are currently known.

Michael R Strand, Kelsey A Coffman, Gaelen R Burke. Annu Rev Entomol. 2025 Oct 7. doi: 10.1146/annurev-ento-121423-013425.

Author: Donna Huber