Inference of polyploid origin and inheritance mode from population genomic data

Abstract

Summary/AbstractWhole-genome duplications yield varied chromosomal pairing patterns, ranging from strictly bivalent to multivalent, resulting in disomic and polysomic inheritance modes. In the bivalent case, homeologous chromosomes form pairs, where in a multivalent pattern all copies are homologous and are therefore free to pair and recombine. As sufficient sequencing data is more readily available than high-quality cytological assessments of meiotic behavior or population genetic assessment of allelic segregation, especially for non-model organisms, here we describe two bioinformatics approaches to infer origins and inheritance modes of polyploids using short-read sequencing data. The first approach is based on distributions of allelic read depth at the heterozygous sites within an individual, as the expectations of such distributions are different for disomic and polysomic inheritance modes. The second approach is more laborious and based on a phylogenetic assessment of partially phased haplotypes of a polyploid in comparison to the closest diploid relatives. We discuss the sources of deviations from expected inheritance patterns, advantages and pitfalls of both methods, effects of mating types on the performance of the methods, and possible future developments.

Different Chromosome Segregation Patterns Coexist in the Tetraploid Adriatic Sturgeon Acipenser naccarii

“…We also observed the presence of two loci with a marked tendency to disomy with a few unexpected allele combinations, pointing to a possible imperfect preferential pairing expected at intermediate stages of functional diploidization [10,11]; this coexistence of different ploidy levels was previously described in other organisms. In plants, for example, the co-existence of different segregation patterns (e.g., tetrasomic and disomic) with different intermediate degrees of preferential pairing among chromosomes provides evidence of a process of functional reduction of ploidy which reasonably cannot occur simultaneously throughout the genome, but which is the result of a progressive differentiation [11,25].…”