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bioRxiv · 10.1101/2025.11.24.690262

AmarylOmicBase: A unified transcriptome database to accelerate gene discovery in Amaryllidoideae species

Goncalves dos Santos, K. C.·Merindol, N.·Desgagne-Penix, I.
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Abstract

Amaryllidoideae plants produce structurally diverse and unique alkaloids with potent anti-cholinesterase, antiviral, and antitumor activities, making this subfamily a rich source of pharmaceutical leads. Despite the absence of reference genomes for any Amaryllidoideae species, many enzyme characterization and pathway reconstruction efforts to date have been made possible through transcriptome mining, often requiring bioinformatic expertise and data preprocessing. To facilitate new studies in this subfamily, here we present AmarylOmicBase, a unified transcriptomic dataset that integrates assemblies, annotations, and expression profiles from 39 studies, covering 27 species and four hybrid cultivars across 13 genera of Amaryllidoideae. The AmarylOmicBase includes both published and de novo assemblies generated from published raw data using Trinity or IsoSeq workflows and provides standardized functional annotation and quantitative expression datasets. AmarylOmicBase provides ready-to-use datasets that support gene discovery, comparative transcriptomics, and pathway-level investigations for specialized metabolism, including Amaryllidaceae alkaloid biosynthesis. By providing ready-to-use datasets and fully reproducible analysis scripts, this resource reduces computational barriers and expands access to transcriptomic information for researchers working on non-model plant species. AmarylOmicBase provides a centralized resource for transcriptomic data that can be reused in studies of enzyme function, pathway evolution, and regulatory processes in Amaryllidoideae.

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Goncalves dos Santos, K. C., Merindol, N., Desgagne-Penix, I.. 2025-11-27. AmarylOmicBase: A unified transcriptome database to accelerate gene discovery in Amaryllidoideae species. https://doi.org/10.1101/2025.11.24.690262

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