Almeida-Silva, FabricioProst-Boxoen, LucasVan de Peer, Yves2024-08-212024-07Almeida-Silva, F., Prost-Boxoen, L. & Van de Peer, Y. 2024, 'HYBRIDEXPRESS : an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors', New Phytologist, vol. 243, no. 2, pp. 811-819, doi : 10.1111/nph.19862.0028-646X (print)1469-8137 (online)10.1111/nph.19862http://hdl.handle.net/2263/97762DATA AVAILABILITY : To ensure full reproducibility, all code and data used in this manuscript are available in a GitHub repository at https://github.com/almeidasilvaf/HybridExpress_paper, and an online Quarto book with executed code chunks and output are available at https://almeidasilvaf.github.io/HybridExpress_paper/.SUPPLEMENTARY MATERIAL : TABLE S1. Overrepresented functional terms in each expression-based class in the cotton data set. TABLE S2. Overrepresented functional terms in each expression-based class in the rice data set.Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce HYBRIDEXPRESS, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). HYBRIDEXPRESS provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of HYBRIDEXPRESS through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. HYBRIDEXPRESS is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. HYBRIDEXPRESS is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).en© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation. This is the pre-peer reviewed version of the following article : 'HYBRIDEXPRESS: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors', New Phytologist, vol. 243, no. 2, pp. 811-819, 2024, doi : 10.1111/nph.19862. The definite version is available at : http://www.newphytologist.com.AllopolyploidyExpression-level dominanceGene expressionHybrid vigorTranscriptomic shockSDG-15: Life on landPostprint Article