A simple and accurate method for inferring missing ploidy information from sequence data

Abstract

Polyploidy can be a critical factor for explaining plant trait variation, niche diversification, or speciation. However, inferring ploidy from silica-dried or historical samples using chromosome counts or flow cytometry is not possible, and scaling up ploidy estimation to population-level fresh contemporary samples can be challenging as well. Thus, we present a new method for estimating ploidy levels directly from sequencing data using machine learning; the Polyploid Population Genomics Tool Kit (PPGTK). The machine-learning approach is advantageous as it relaxes the assumptions of previous probabilistic methods and provides per-sample probabilities, allowing investigators to evaluate uncertainty in their system of interest.. We demonstrate performance and accuracy of the method on simulated and empirical data. Simulations showed above 99% accuracy, even for low coverage data, as long reads were mappable to the reference genome. For empirical analyses, we used target enrichment data from blueberry wild relatives (Vaccinium sect. Cyanococcus) and whole-genome data from sweetpotato wild relatives (Ipomoea ser. Batatas). Ploidy was recovered with 99% accuracy across 70 Vaccinium individuals and 97% across 82 Ipomoea individuals. Analysis of many individuals is fast and requires only a multisample VCF, which is presumably generated for the research anyway, and some samples of known ploidy for training the classifier. The approach implemented in PPGTK is promising for collections-based research as well, enabling ploidy classification of historical specimens based on present-day observations. The method is implemented in a new Python package as a single command that can run on a conventional laptop.