The effect of methodological considerations on the construction of gene-based plant pan-genomes

Pan-genomics is an emerging approach for studying the genetic diversity within plant populations. In contrast to common resequencing studies that compare whole genome sequencing data to a single reference genome, the construction of a pan-genome involves the direct comparison of multiple genomes to one another, thereby enabling the detection of genomic sequences and genes not present in the reference, as well as the analysis of gene content diversity. While multiple studies describing pan-genomes of various plant species have been published in recent years, our understanding regarding the effect of the computational procedures used for pan-genome construction is still limited.
Here we examine the effect of several key methodological factors on the obtained gene pool and on gene presence-absence detections by constructing and comparing multiple pan-genomes of Arabidopsis thaliana and cultivated soybean, as well as conducting a meta-analysis on published pan-genomes. These factors include..., , Please see the DRYAD_README.txt file for details.