Allopolyploid subgenome identification and implications for evolutionary analysis.

Allopolyploids are individuals that have two or more complete sets of chromosomes derived from different species. The number of chromosome-scaled allopolyploid genomes assembled has increased as genome sequencing has become cheaper, longer, and more accurate. Several computational tools have been developed to leverage differences in biology between progenitor species to identify subgenomes of allopolyploids. Whole-genome duplications (WGDs) are widespread genomic events in eukaryotes that are hypothesized to contribute to the evolutionary success of many lineages, including flowering plants, Saccharomyces yeast, and vertebrates. WGDs generally can be classified into autopolyploids (ploidy increase descended from one species) or allopolyploids (ploidy increase descended from multiple species). Assignment of allopolyploid progenitor species (called subgenomes in the polyploid) is important to understanding the biology and evolution of polyploids, including the asymmetric subgenome evolution following hybridization (biased fractionation). Here, I review the different methodologies used to identify the ancestors of allopolyploid subgenomes, discuss the advantages and disadvantages of these methods, and outline the implications of how these methods affect the subsequent evolutionary analysis of these genomes. [ABSTRACT FROM AUTHOR]