De novo assembled transcriptome and predicted proteins of Vanilla planifolia during the flower-to-fruit transition

This dataset contains the de novo assembled transcriptome of Vanilla planifolia Andrews and the predicted protein sequences derived from the assembly. The RNA-seq data represent four key developmental stages during the flower-to-fruit transition:

1. Pre-pollination (Pre-pol): floral bud before anthesis

2. Pollination (Pol): flower at anthesis with pollen deposited on the stigma

3. Post-pollination (Post-pol): ovary sampled 25 days after pollination

4. Fertilization (Fer): ovary containing fertilized ovules sampled 60 days after pollination

Raw RNA-seq reads were evaluated using FastQC v0.11.9, including assessment of Phred quality scores, sequence length distribution, GC content, duplicated sequences, and adapter contamination.

Reads were trimmed and filtered using Trimmomatic v0.39 to remove adapter sequences, allowing a maximum error rate of 2 bp per 30 bases, applying a minimum Phred score of 15, and retaining reads with a minimum length of 30 bp.

A de novo transcriptome assembly was generated using Trinity v2.4. Assembly quality was evaluated using several metrics including total number of genes, GC content, median contig length, mean contig length, total assembled bases, and ExN50 statistics, including the E95N50 value.

Protein-coding regions were predicted from the assembled transcripts using TransDecoder, generating translated amino acid sequences corresponding to candidate open reading frames (ORFs).

The files included in this dataset are:

• Trinity.fasta – nucleotide sequences of the assembled transcripts

• Predicted protein sequences (FASTA) derived from the transcriptome assembly using TransDecoder

These resources provide a transcriptomic and proteomic sequence dataset for studying reproductive development, pollination-induced responses, fertilization processes, and the molecular regulation of the flower-to-fruit transition in V. planifolia.

The transcriptome assembly and associated analyses are described in:

Hernandez-Miranda et al. (2025). Transcriptomic dynamics during the flower-to-fruit transition in Vanilla planifolia. BMC Plant Biology.
https://doi.org/10.1186/s12870-025-06476-z