Pedro Gabriel Nachtigall

• Bellini, Natália Karla; Nachtigall, Pedro Gabriel; Lima, Pedro Leonardo Carvalho de; Silva, Herbert Guimarães de Sousa; Pires, David da Silva & Souza, Vinicius Carius de [Show all 12 contributors for this article] (2026). First genome-wide centromere map of Trypanosoma cruzi suggests linear and 3D compartment boundaries and spatial clustering. BMC Genomics. 27. doi: 10.1186/s12864-026-13072-4. Full text in Research Archive Show summary

  Background Trypanosoma cruzi, the etiological agent of Chagas disease, possesses a highly repetitive genome that has historically hindered high-quality assembly and structural characterization. Despite significant advances in assembling T. cruzi genomes, major gaps remain. Among these, the complete repertoire of centromeric sequences has remained elusive, representing a critical missing piece in our understanding of chromosome structure and inheritance. Results Here, we generated high-coverage Hi-C (genome-wide chromosome conformation capture) data for the widely used T. cruzi Dm28c strain improving its genome assembly by scaffolding contigs and producing a more contiguous and accurate genome. To investigate centromere organization, we performed ChIP-seq using the mNeonGreen-myc-tagged kinetochore proteins KKT2 and KKT3, resulting in the identification of 33 KKT-enriched peaks across 27 scaffolds. These peaks were located in regions enriched in retrotransposable elements, particularly L1Tc and VIPER, near strand switch regions, areas of high GC content, and in 51% of the cases at the transitional regions between conserved genes and virulence-factor multigene families. Notably, Hi-C analysis shows that candidate centromeric regions are frequently positioned between genomic domains with distinct 3D interaction profiles suggesting that they may contribute to genome compartmentalization, and frequently engage in 3D spatial clustering, suggesting a role in higher-order nuclear architecture. Conclusion Overall, our study provides a high-quality reference genome for the Dm28c strain, presents the first genome-wide centromere map in T. cruzi, and offers novel insights into centromere-mediated 3D genome organization.

• Isaksen, Anders; Nachtigall, Pedro Gabriel; Araya, Robin Aasegg; Beh, Jia Hao; Robinson, Samuel D. & Hansen, Thomas Fredrik [Show all 7 contributors for this article] (2025). Genome of the green-head ant, Rhytidoponera metallica, reveals mechanisms of toxin evolution in a genetically hyper-diverse eusocial species. Genome Biology. ISSN 1474-7596. 26(1). doi: 10.1186/s13059-025-03777-2. Full text in Research Archive Show summary

  Background While ants are textbook examples of eusocial animals in which altruistic behavior is maintained through kin selection, several ants form genetically diverse colonies that challenge this concept. One example is the Australian green-head ant (Rhytidoponera metallica) whose colonies harbor such extreme genetic variation that they have been speculated to represent an unstable form of eusociality. Yet, R. metallica is among the most successful ants on the Australian subcontinent. This success has been hypothesized to be partly due to the diverse venoms harbored within each colony. However, the genomic basis and evolutionary scenarios that maintain this toxin diversity remain unknown. Results To examine toxin genomic architecture, quantify individual-level genetic variation, and identify both proximate and ultimate mechanisms that have facilitated the toxin diversity in R. metallica, we generate a high-quality draft genome from a single worker. Most ectatotoxin genes are in clusters that contain evidence of multiple, complex gene-family expansions, some of which are likely explained by the presence of transposable elements. We also show that toxin regions of the genome exhibit elevated genetic variation despite being under strong selection and that this variation can translate to phenotypic diversity through toxin alleles with different functional properties. Conclusions Taken together, our results point to classical gene duplication and diversification as the main evolutionary mechanism by which the main toxin family in ant venoms evolves, suggest toxin-gene functional diversification under frequency-dependent selection maintains colony-level venom hypervariability in R. metallica, and provide new insight into the role of multi-level selection in eusocial animals.

• Maurstad, Marius Filomeno; Ramiro, Iris Bea; Øyen, Jan Philip; Sombke, Andy; Büsse, Sebastian & Nachtigall, Pedro Gabriel [Show all 8 contributors for this article] (2025). The green lacewing venom system and the complex mechanisms underlying its evolution. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 43. doi: 10.1093/molbev/msaf326. Full text in Research Archive Show summary

  Abstract Venom has independently evolved across many lineages, yet relatively few have been studied in detail, particularly among insects. Of these, Neuroptera (lacewings, antlions and relatives) remain largely unexplored, despite being widespread with agriculturally important groups such as green lacewings. While adults are non-venomous, neuropteran larvae are ferocious predators that use pincer-like mouthparts to inject paralysing and liquefying venom to subdue and consume their prey. Here, we provide a comprehensive investigation of the venom system in Neuroptera by integrating a high-quality genome, long-read transcriptomes spanning all life stages, microCT-reconstruction of venom glands, tissue-specific expression analyses, venom proteomics, and functional assays of the common green lacewing Chrysoperla carnea. We provide a re-description of the neuropteran venom system, demonstrate the venom’s insecticidal and cytotoxic activity, and show the venom comprises diverse toxin gene families and is richer and more similar to the venom of antlions than previously proposed. We show that this toxin arsenal is the result of a multitude of evolutionary events that include co-option, recruitment following gene duplication, diversification of toxin-paralogs by gene duplication, and functional innovation of new paralogs through both small structural and large architectural changes. In addition, we find that alternative splicing of toxin genes is an important contributor to the biochemical arsenal, which is a mechanism rarely documented among venomous animals. Our results demonstrate how multiple genomic and evolutionary mechanisms together contribute to the emergence and evolution of a complex molecular trait, and provide new insights into the evolution of venom in insects.

• Nachtigall, Pedro Gabriel; Hamilton, Brett R.; Kazandjian, Taline D.; Stincone, Paolo; Petras, Daniel & Casewell, Nicholas R. [Show all 7 contributors for this article] (2025). The gene regulatory mechanisms shaping the heterogeneity of venom production in the Cape coral snake. Genome Biology. ISSN 1474-7596. 26(1). doi: 10.1186/s13059-025-03602-w. Full text in Research Archive Show summary

  Background Venoms and their associated glands and delivery structures have evolved numerous times among animals. Within these venom systems, the molecular, cellular, and morphological components interact and co-evolve to generate distinct, venom phenotypes that are increasingly recognized as models for studying adaptive evolution. However, toxins are often unevenly distributed across venom-producing tissues in patterns that are not necessarily adaptive but instead likely result from constraints associated with protein secretion. Results We generate a high-quality draft genome of the Cape coral snake (Aspidelaps lubricus) and combine analyses of venom gland single-cell RNA-seq data with spatial venom gland in situ toxin distributions. Our results reveal that while different toxin families are produced by distinct populations of cells, toxin expression is fine-tuned by regulatory modules that result in further specialization of toxin production within each cell population. We also find that the evolution of regulatory elements closely mirrors the evolution of their associated toxin genes, resulting in spatial association of closely related and functionally similar toxins in the venom gland. While this compartmentalization is non-adaptive, the modularity of the underlying regulatory network likely facilitated the repeated evolution of defensive venom in spitting cobras. Conclusions Our results provide new insight into the variability of toxin regulation across snakes, reveal the molecular mechanisms underlying the heterogeneous toxin production in snake venom glands, and provide an example of how constraints can result in non-adaptive character states that appear to be adaptive, which may nevertheless facilitate evolutionary innovation and novelty.

• Barbosa, Denilson Fagundes; Oliveira, Liliane Santana; Nachtigall, Pedro Gabriel; Junior, Rodolpho Valentini; Souza, Nayane de & Paschoal, Alexandre Rossi [Show all 7 contributors for this article] (2024). cirCodAn: A GHMM-based tool for accurate prediction of coding regions in circRNA. In Prajapati, Vijay Kumar (Eds.), Advances in Protein Chemistry and Structural Biology: Translational Bioinformatics. Academic Press. ISSN 9780443193484. p. 289–334. doi: 10.1016/bs.apcsb.2023.11.012. Full text in Research Archive

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