De novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discovery
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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-12-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-023-02776-x |
| _version_ | 1827604446298767360 |
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| author | Valentina Bočaj Paula Pongrac Sina Fischer Matevž Likar |
| author_facet | Valentina Bočaj Paula Pongrac Sina Fischer Matevž Likar |
| author_sort | Valentina Bočaj |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T05:59:38Z |
| format | Article |
| id | doaj.art-56fc63a13a28460eb47d59cc1cf676a1 |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-03-09T05:59:38Z |
| publishDate | 2023-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj.art-56fc63a13a28460eb47d59cc1cf676a12023-12-03T12:10:12ZengNature PortfolioScientific Data2052-44632023-12-011011710.1038/s41597-023-02776-xDe novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discoveryValentina Bočaj0Paula Pongrac1Sina Fischer2Matevž Likar3University of Ljubljana, Biotechnical FacultyUniversity of Ljubljana, Biotechnical FacultyUniversity of Nottingham, Future Food Beacon of Excellence and School of BiosciencesUniversity of Ljubljana, Biotechnical FacultyAbstract 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.https://doi.org/10.1038/s41597-023-02776-x |
| spellingShingle | Valentina Bočaj Paula Pongrac Sina Fischer Matevž Likar De novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discovery Scientific Data |
| title | De novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discovery |
| title_full | De novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discovery |
| title_fullStr | De novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discovery |
| title_full_unstemmed | De novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discovery |
| title_short | De novo transcriptome assembly of hyperaccumulating Noccaea praecox for gene discovery |
| title_sort | de novo transcriptome assembly of hyperaccumulating noccaea praecox for gene discovery |
| url | https://doi.org/10.1038/s41597-023-02776-x |
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