De novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discovery

Bočaj, Valentina; Pongrac, Paula; Fischer, Sina; Likar, Matevž

Abstract

Hyperaccumulators are a group of plant species that accumulate high concentrations of one or more metal(loid)s in their above-ground tissues without showing any signs of toxicity. Several hyperaccumulating species belong to the Brassicaceae family, among them the Cd and Zn hyperaccumulator Noccaea praecox. In this paper, we present de novo transcriptome assembled from two naturally occurring N. praecox populations growing in (i) metal-enriched soil and (ii) soil non-contaminated with metals (control site). Total RNA was extracted from the leaves of both populations. We obtained 801,935,101 reads, which were successfully assembled and annotated. The resulting assembly contains 135,323 transcripts, with 103,396 transcripts (76.4%) annotated with at least one function and encoding 53,142 putative proteins. Due to its close relationship with the hyperaccumulating model species N. cearulescens, it will be possible to derive protein functions from sequence comparisons with this species. Comparisons will highlight common and differing pathways of metal acquisition, storage, and detoxification which will allow us to expand our knowledge of these processes.

Citation

Bočaj, V., Pongrac, P., Fischer, S., & Likar, M. (2023). De novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discovery. Scientific Data, 10, Article 856. https://doi.org/10.1038/s41597-023-02776-x

• Journal Article Type: Article
• Acceptance Date: Nov 23, 2023
• Online Publication Date: Dec 1, 2023
• Publication Date: Dec 1, 2023
• Deposit Date: Feb 9, 2024
• Publicly Available Date: Feb 12, 2024
• Journal: Scientific Data
• Electronic ISSN: 2052-4463
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 10
• Article Number: 856
• DOI: https://doi.org/10.1038/s41597-023-02776-x
• Public URL: https://nottingham-repository.worktribe.com/output/28133291
• Publisher URL: https://www.nature.com/articles/s41597-023-02776-x