Likelihood-based Modeling of Brassiceae Ancient Whole-genome Triplication with POInT

Background

Ancient polyploidy events are prevalent throughout the evolutionary history of flowering plants (One Thousand Plant Transcriptomes Initiative, 2019) and have contributed to the diversity of complexity of present-day species (van de Peer et al., 2009). When the sub genomes were derived from genetically distant parents, such events are termed as allopolyploidy. Post-polyploidy gene loss in allopolyploids are often unbalanced across different sub genomes (Cheng et al., 2012). The biased fractionation reshaped genomic landscape, and the gene retention/loss pattern has important implications in crop development (Qi et al., 2021). However, sub genome assignment in allopolyploids is still challenging (Edger et al., 2018).

POInT (the Polyploid Orthology Inference Tool) is a likelihood-based tool for modeling ancient polyploidy events (Conant and Wolfe, 2008; Emery et al., 2018; Hao and Conant, 2022; Conant, 2023). POInT supports user-defined ploidy levels, namely whole-genome duplication (Conant and Wolfe, 2008; Emery et al., 2018; Conant, 2020), triplication (Schoonmaker et al., 2020; Hao et al., 2021), or quadruplication (Hao et al., 2022). Using POInT, we have modeled the whole-genome triplication (WGT) events shared by the members of the tribe Brassiceae (Hao et al., 2021). The synteny-based and phylogenetically aware analysis of gene loss across different sub genomes provides statistical support for the two-step hypothesis of hexaploidy and biased fractionation across the LF, MF1, and MF2 sub genomes after the ancient WGT (Cheng et al., 2012; Tang et al., 2012). Here, we present a step-by-step guide to recreate the WGT model comparisons in Hao et al. (2021).