Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium.
New Phytol. 2024 Jul;243(2):811-819. doi: 10.1111/nph.19862. Epub 2024 May 27.
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).
杂交是指来自不同遗传背景的个体杂交的过程，它在进化、生物入侵和作物育种中起着关键作用。在转录水平上，杂交通常会导致复杂的非加性效应，这给理解其后果带来了挑战。虽然有标准的转录组分析方法可以比较杂种与其亲本，但这些方法尚未在软件包中实现，这阻碍了其可重复性。我们引入了 hybridexpress，这是一个 R/Bioconductor 包，旨在促进杂种三亲体（杂种及其亲本）中基因表达模式的分析、可视化和比较。hybridexpress 为用户提供了一个用户友好且全面的工作流程，其中包括所有标准的比较分析步骤，包括数据归一化、中亲表达值的计算、样本聚类、基于表达的基因分类为类别和类，以及功能术语的过度表达分析。我们通过对棉花异源多倍体化和水稻根系性状杂种优势的比较转录组分析说明了 hybridexpress 的实用性。hybridexpress 旨在简化杂种三亲体的比较转录组研究，推进我们对异源多倍体进化动态的理解，并增强植物育种策略。hybridexpress 可从 Bioconductor（https://bioconductor.org/packages/HybridExpress）免费获得，其源代码可在 GitHub（https://github.com/almeidasilvaf/HybridExpress）上获得。
