Differential gene expression in Lavandula angustifolia Mill. under adaptation ex vitro
Bibliographic record
Abstract
Propagation of commercial lavender (Lavandula angustifolia Mill.) cultivars in vitro has a number of advantages over seed or vegetative (cuttings) propagation: obtaining a uniform, genetically stable and healthy planting material. At the same time, the effectiveness of this process depends on the subsequent adaptation of the obtained plants to the open-field conditions. The research was carried out on the 'Prima' cultivar in the collection of the Nikita Botanical Gardens. Leaves were collected from plants grown in vitro before transferring them to in vivo conditions and from plants after 7 days adaptation in a Conviron multilevel plant growth chamber (Canada). Lavender plants were cultured in vitro on MS culture medium supplemented with 0.5 mg/L BAP or 0.5 mg/L kinetin and 0.025 mg/L NAA at a temperature of 22-25 C, 14-16-hour photoperiod, light intensity -25.0-37.5 mol m -2 s -1 . To induct rhizogenesis (after third passage). MS medium with different content of auxins, IBA or NAA (0.5-1.0 mg/L), was used. To analyze possible molecular mechanisms, which are the base of the adaptive processes in plants, at the time of transition from in vitro growth to in vivo growth the sampels of total RNA were isolated from leaves by the NucleoSpin RNA Plant protocol (NucleoSpin, Germany) and 24 barcoded RNA-Seq libraries were created using Illumna TruSeq Stranded mRNA Library Prep Kit. Sequencing was made on a high-performance sequencer Illumina NextSeq 550 using the NextSeq 500 HighOutputv2 Kit with an estimated capacity of at least 90 million reads. As a result of sequencing, 3 libraries of transcriptomic data were obtained for each of the states (in vitro and in vivo). For the obtained data, pre-preparation, de novo transcriptome assembly, transcript-level expression analysis, search for protein-coding regions and their annotation using the SwissProt Viridiplantae database, and evaluation of differential expression were made. The transcripts of up-regulation and down-regulation have been identified. The following software packages were used: FastP v. 0.19.5, Trinityv.2.11.0, Kallistov.0.46.1, TransDecoder v.5.5.0, BLASTv.2.11.0, edgeRv.3.32.1.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".