Comparison between the Gametophyte and the Sporophyte Transcriptomes of the Endangered Fern Vandenboschia speciosa Martín-Blázquez, Rubén Bakkali, Mohammed Ruiz-Estévez, Mercedes Garrido Ramos, Manuel Ángel Ferns Vandenboschia speciosa De novo transcriptome assembly Gene expression profile Data Availability Statement: The resulting database was deposited in FigShare, https://figshare. com/; https://doi.org/10.6084/m9.figshare.21502005, accessed on 4 November 2022. Acknowledgments: The Dirección General de Gestión del Medio Natural y Espacios Protegidos of the Consejería de Medio Ambiente y Ordenación del Territorio de la Junta de Andalucía (now Consejería de Agricultura, Ganadería, Pesca y Desarrollo Sostenible) authorized and facilitated the sampling of the material. We are highly indebted to Carmen Rodríguez Hiraldo and Jaime Pereña Ortiz who, together with the team of Agentes de Medio Ambiente of the Consejería, helped us with the sampling procedure. Supplementary Materials: The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/genes14010166/s1. Figure S1: Contig coverage distribution per transcriptome; Table S1: Transcripts expressed only in the gametophyte; Table S2: Transcripts expressed only in the sporophyte; Table S3: Top 1000 most expressed transcripts in the gametophyte; Table S4: Biological process GO term enrichment analysis for the gametophyte; Table S5: Molecular function GO term enrichment analysis for the gametophyte; Table S6: Cellular component GO term enrichment analysis for the gametophyte; Table S7: Top 1000 most expressed transcripts in the sporophyte; Table S8: Biological process GO term enrichment analysis for the sporophyte; Table S9: Molecular function GO term enrichment analysis for the sporophyte; Table S10: Cellular component GO term enrichment analysis for the sporophyte. Genomic resources are essential to understanding the evolution and functional biology of organisms. Nevertheless, generating genomic resources from endangered species may be challenging due to the scarcity of available specimens and sampling difficulties. In this study, we compare the transcriptomes of the sporophyte and the gametophyte of the endangered fern Vandenboschia speciosa. After Illumina sequencing and de novo transcriptome assembly of the gametophyte, annotation proved the existence of cross-species contamination in the gametophyte sample. Thus, we developed an in silico decontamination step for the gametophyte sequences. Once the quality check of the decontaminated reads passed, we produced a de novo assembly with the decontaminated gametophyte reads (with 43,139 contigs) and another combining the sporophyte and in silico decontaminated gametophyte reads (with 42,918 contigs). A comparison of the enriched GO terms from the top 1000 most expressed transcripts from both tissues showed that the gametophyte GO term set was enriched in sequences involved in development, response to stress, and plastid organization, while the sporophyte GO term set had a larger representation of more general metabolic functions. This study complements the available genomic resources on the life cycle of the endangered fern Vandenboschia speciosa. 2023-02-24T10:43:47Z 2023-02-24T10:43:47Z 2023-01-07 journal article Martín-Blázquez, R.; Bakkali, M.; Ruiz-Estévez, M.; Garrido-Ramos, M.A. Comparison between the Gametophyte and the Sporophyte Transcriptomes of the Endangered Fern Vandenboschia speciosa. Genes 2023, 14, 166. [https://doi.org/10.3390/genes14010166] https://hdl.handle.net/10481/80210 https://doi.org/10.3390/genes14010166 eng http://creativecommons.org/licenses/by/4.0/ open access Atribución 4.0 Internacional MDPI