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1. First Chromosome-Level Genome Assembly of a Ribbon Worm from the Hoplonemertea Clade, Emplectonema gracile. and Its Structural Annotation

   https://doi.org/10.1093/gbe/evae127  

   Valero-Gracia, Alberto; Roberts, Nickellaus G; Yap-Chiongco, Meghan; Capucho, Ana Teresa; Kocot, Kevin M; Matschiner, Michael; Struck, Torsten H (July 2024, Genome Biology and Evolution)

   Wheat, Christopher (Ed.)

   Genome-wide information has so far been unavailable for ribbon worms of the clade Hoplonemertea, the most species-rich class within the phylum Nemertea. While species within Pilidiophora, the sister clade of Hoplonemertea, possess a pilidium larval stage and lack stylets on their proboscis, Hoplonemertea species have a planuliform larva and are armed with stylets employed for the injection of toxins into their prey. To further compare these developmental, physiological, and behavioral differences from a genomic perspective, the availability of a reference genome for a Hoplonemertea species is crucial. Such data will be highly useful for future investigations toward a better understanding of molecular ecology, venom evolution, and regeneration not only in Nemertea but also in other marine invertebrate phyla. To this end, we herein present the annotated chromosome-level genome assembly for Emplectonema gracile (Nemertea; Hoplonemertea; Monostilifera; Emplectonematidae), an easily collected nemertean well suited for laboratory experimentation. The genome has an assembly size of 157.9 Mb. Hi-C scaffolding yielded chromosome-level scaffolds, with a scaffold N50 of 10.0 Mb and a score of 95.1% for complete BUSCO genes found as a single copy. Annotation predicted 20,684 protein-coding genes. The high-quality reference genome reaches an Earth BioGenome standard level of 7.C.Q50. 

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2. Coral Venom and Toxins as Protection Against Crown‐of‐Thorns Sea Star Attack

   https://doi.org/10.1111/mec.70202  

   Gorman, Lucy M; Huffmyer, Ariana S; Byrne, Maria; Mills, Suzanne C; Putnam, Hollie M (November 2025, Molecular Ecology)

   ABSTRACT Crown‐of‐thorns sea star (CoTS) outbreaks are a main cause of hard coral cover decline across the Indo‐Pacific, posing a major threat to the resilience of coral reefs. However, the drivers underlying CoTS feeding on preferred (e.g.,Acroporaspecies) versus non‐preferred (e.g.,Poritesspecies) are poorly understood. We hypothesised that coral venom may influence CoTS prey preferences. To investigate this hypothesis, we compared the coral venom toxin families across the genomes of preferred (A. digitifera,A. hyacinthus,A. milleporaandA. tenuis) and non‐preferred (P. australiensis,P. compressa,P. luteaandP. rus) prey species of CoTS. We also included one species from each genus inhabiting the Caribbean, where CoTS are absent (A. cervicornisandP. astreoides), to broaden our identification of venom constituents shared within each genus and investigate geographic differences. We collected known cnidarian toxins, and along with the cnidarian Tox‐Prot database, used these to identify putative toxins and investigate their phylogeny. The most abundant toxins across all coral species included neurotoxins (kunitz‐type and SCRiPS) and pore‐forming toxins (actinoporins and MAC‐PFs). We found genera‐specific differences with jellyfish toxins (CFXs) only present inPoritesspecies. Similarly, onlyAcroporaspecies harboured pore‐forming toxins with the aerolysin domain. Two toxin homologues only present in Indo‐Pacific corals (CFX and MAC‐PF homologues) showed evidence of positive selection, suggesting their evolution is shaped by environmental pressures, including exposure to CoTS. These findings provide a foundation for future studies of scleractinian venoms, which have direct applications to assessing reef coral's susceptibility to future CoTS outbreaks and active reef management. 

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3. Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage

   https://doi.org/10.1371/journal.pcbi.1009871  

   Moutoussamy, Emmanuel E.; Waheed, Qaiser; Binford, Greta J.; Khan, Hanif M.; Moran, Shane M.; Eitel, Anna R.; Cordes, Matthew H.; Reuter, Nathalie (February 2022, PLOS Computational Biology)

   Wei, Guanghong (Ed.)

   Spider venom GDPD-like phospholipases D ( SicTox ) have been identified to be one of the major toxins in recluse spider venom. They are divided into two major clades: the α clade and the β clade. Most α clade toxins present high activity against lipids with choline head groups such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups ( Sicarius terrosus , St_βIB1). A structural comparison of available structures of phospholipases D (PLDs) reveals a conserved aromatic cage in the α clade. To test the potential influence of the aromatic cage on membrane-lipid specificity we performed molecular dynamics (MD) simulations of the binding of several PLDs onto lipid bilayers containing choline headgroups; two SicTox from the α clade, Loxosceles intermedia αIA1 (Li_αIA) and Loxosceles laeta αIII1 (Ll_αIII1), and one from the β clade, St_βIB1. The simulation results reveal that the aromatic cage captures a choline-headgroup and suggest that the cage plays a major role in lipid specificity. We also simulated an engineered St_βIB1, where we introduced the aromatic cage, and this led to binding with choline-containing lipids. Moreover, a multiple sequence alignment revealed the conservation of the aromatic cage among the α clade PLDs. Here, we confirmed that the i-face of α and β clade PLDs is involved in their binding to choline and ethanolamine-containing bilayers, respectively. Furthermore, our results suggest a major role in choline lipid recognition of the aromatic cage of the α clade PLDs. The MD simulation results are supported by in vitro liposome binding assay experiments. 

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4. Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: role of a conserved aromatic cage.

   https://doi.org/10.1371/journal.pcbi.1009871  

   Moutoussamy, EE; Waheed, Q; Binford, GJ; Cordes, MHJ; Khan, HM; Reuter, N (February 2022, PLOS computational biology)

   Spider venom GDPD-like phospholipases D (SicTox) have been identified to be one of the major toxins in recluse spider venom. They are divided into two major clades: the α clade and the β clade. Most α clade toxins present high activity against lipids with choline head groups such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups (Sicarius terrosus, St_βIB1). A structural comparison of available structures of phospholipases D (PLDs) reveals a conserved aromatic cage in the α clade. To test the potential influence of the aromatic cage on membrane-lipid specificity we performed molecular dynamics (MD) simulations of the binding of several PLDs onto lipid bilayers containing choline headgroups; two SicTox from the α clade, Loxosceles intermedia αIA1 (Li_αIA) and Loxosceles laeta αIII1 (Ll_αIII1), and one from the β clade, St_βIB1. The simulation results reveal that the aromatic cage captures a choline-headgroup and suggest that the cage plays a major role in lipid specificity. We also simulated an engineered St_βIB1, where we introduced the aromatic cage, and this led to binding with choline-containing lipids. Moreover, a multiple sequence alignment revealed the conservation of the aromatic cage among the α clade PLDs. Here, we confirmed that the i-face of α and β clade PLDs is involved in their binding to choline and ethanolamine-containing bilayers, respectively. Furthermore, our results suggest a major role in choline lipid recognition of the aromatic cage of the α clade PLDs. The MD simulation results are supported by in vitro liposome binding assay experiments. 

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5. Duvernoy’s Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes

   https://doi.org/10.3390/toxins13050336  

   Hofmann, Erich P.; Rautsaw, Rhett M.; Mason, Andrew J.; Strickland, Jason L.; Parkinson, Christopher L. (May 2021, Toxins)

   null (Ed.)

   The venoms of small rear-fanged snakes (RFS) remain largely unexplored, despite increased recognition of their importance in understanding venom evolution more broadly. Sequencing the transcriptome of venom-producing glands has greatly increased the ability of researchers to examine and characterize the toxin repertoire of small taxa with low venom yields. Here, we use RNA-seq to characterize the Duvernoy’s gland transcriptome of the Plains Black-headed Snake, Tantilla nigriceps, a small, semi-fossorial colubrid that feeds on a variety of potentially dangerous arthropods including centipedes and spiders. We generated transcriptomes of six individuals from three localities in order to both characterize the toxin expression of this species for the first time, and to look for initial evidence of venom variation in the species. Three toxin families—three-finger neurotoxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)—dominated the transcriptome of T. nigriceps; 3FTx themselves were the dominant toxin family in most individuals, accounting for as much as 86.4% of an individual’s toxin expression. Variation in toxin expression between individuals was also noted, with two specimens exhibiting higher relative expression of c-type lectins than any other sample (8.7–11.9% compared to <1%), and another expressed CRISPs higher than any other toxin. This study provides the first Duvernoy’s gland transcriptomes of any species of Tantilla, and one of the few transcriptomic studies of RFS not predicated on a single individual. This initial characterization demonstrates the need for further study of toxin expression variation in this species, as well as the need for further exploration of small RFS venoms. 

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