POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes

Abstract

We describe POInTbrowse, a web portal that gives access to the orthology inferences made for polyploid genomes with POInT, the Polyploidy Orthology Inference Tool. Ancient, or paleo-, polyploidy events are widely distributed across the eukaryotic phylogeny, and the combination of duplicated and lost duplicated genes that these polyploidies produce can confound the identification of orthologous genes between genomes. POInT uses conserved synteny and phylogenetic models to infer orthologous genes between genomes with a shared polyploidy. It also gives confidence estimates for those orthology inferences. POInTbrowse gives both graphical and query-based access to these inferences from 12 different polyploidy events, allowing users to visualize genomic regions produced by polyploidies and perform batch queries for each polyploidy event, downloading genes trees and coding sequences for orthologous genes meeting user-specified criteria. POInTbrowse and the associated data are online at https://wgd.statgen.ncsu.edu.

Species Tree Topology Impacts the Inference of Ancient Whole-Genome Duplications Across the Angiosperm Phylogeny

“…Our syntenic analyses often supported both alternative hypotheses for a given WGD, as observed for the ARTHβ WGD in the A1 analysis under the TimeTree topology (Kumar et al, 2017, 2022). Many tools already exist for analyzing complex syntenic data, however they also require a priori knowledge of the shared WGD history among species (Tang et al, 2011; Parey et al, 2020; Siddiqui and Conant, 2023). Given the added power syntenic analysis can give to disentangling complex WGD histories, our analyses and other WGD focused syntenic tools highlight the need for formal tests to infer the shared polyploid ancestry of species using synteny.…”

“…In the case of WGD, entire chromosomes are duplicated and often rearranged, forming groups of collinear genes commonly referred to as syntenic blocks (Renwick, 1971; Passarge et al, 1999; Kellis et al, 2004; Byrne and Wolfe, 2005; Jiao et al, 2014). Other processes can create syntenic blocks and plant species often experienced more than one WGD, sometimes making it difficult to ascertain if two species share the same WGD history (Tang et al, 2008a, 2011; One Thousand Plant Transcriptomes Initiative, 2019; Siddiqui and Conant, 2023). Despite these limitations, the availability of data and the accessibility of tools that can quickly generate K s and syntenic inferences have made both approaches popular (Haas et al, 2004; Barker et al, 2010; Tang et al, 2011; Wang et al, 2012; Zwaenepoel and Van de Peer, 2019b; Henry et al, 2022; Sun et al, 2022).…”