Epigenetic insights into extreme longevity in the world’s oldest terrestrial animal, Jonathan

Benjamin Vaisvil, Daniel P. Schmitt, Angela Jones, Vinayak Kapatral, James M. Ford, Madison L. Taylor, Mathia Colwell, Jonathan Hollins, Sam Pascucci, Konstantin Weissenow, Burkhard Rost, Pascal Notin , Justin Gerlach, Thomas C. Terwilliger, Li-Wei Hung, Lars Juhl Jensen, Kathlyn Reed, Todd R. Robeck, Steve Horvath, Christopher Faulk, Yanjun Ma, and Stephen W. Clark

Abstract

Aldabra giant tortoises (Aldabrachelys gigantea) are exceptionally long-lived. We sequenced the genome and methylome of Jonathan, a 194-year-old Aldabra, to explore the molecular basis of his longevity. Relative to other giant tortoises (A. gigantea and Chelonoidis abingdonii), Jonathan has unique gene variants in most aging pathways. Moreover, Jonathan has substantial DNA methylation and methylation entropy changes compared to four other Aldabras ranging in age from a 5-year-old juvenile to older adults. Notably, we found that lower-entropy regions in Jonathan’s methylome were enriched for the promoters of genes involved in the mitochondrial electron transport chain, and RNA metabolism. This suggests that high-fidelity transcription of the genes in these pathways may be crucial for long-lived species. Our findings support a model for aging wherein the maintenance of low methylation entropy in gene promoters is coupled to efficient mitochondrial energy production, efficient RNA processing, and efficient genomic repair.

Genome and functional annotation of Nerium oleander reveal environmental stress-associated and metabolic pathways

Naira Ibrahim, Ananda Nanjundaswamy, Daniel P. Schmitt & Vinayak Kapatral

Abstract

We generated a high-quality draft genome assembly for Nerium oleander of approximately 447 Mb, comprising 269 contigs with a GC content of 33%. Genome annotation identified 33,243 protein-coding genes and 3,078 RNA features. Predicted functional annotation revealed identification of gene families associated with stress response and metal homeostasis, including pathways related to amino acid metabolism, glutathione metabolism, ABC transporters, and NRAMP transporter families. In addition, genes putatively involved in secondary metabolism and phytohormone biosynthesis were identified, including those associated with salicylic acid, gibberellic acid, brassinosteroids, auxins, cytokinin, abscisic acid, and jasmonic acid pathways, as well as metal-binding and detoxification-related compounds such as phytochelatins and metallothioneins. These results provide genomic evidence for a broad repertoire of stress-associated and metal-responsive pathways in N. oleander. The genome blueprint establishes a foundation for future transcriptomic and functional studies to validate gene expression and regulatory mechanisms under heavy metal and other abiotic stress conditions and supports its potential application in phytoremediation and stress tolerance research.