Homoeologous Exchanges, Segmental Allopolyploidy, and Polyploid Genome Evolution

Abstract

Polyploidy is a major force in plant evolution and speciation. In newly formed allopolyploids, pairing between related chromosomes from different subgenomes (homoeologous chromosomes) during meiosis is common. The initial stages of allopolyploid formation are characterized by a spectrum of saltational genomic and regulatory alterations that are responsible for evolutionary novelty. Here we highlight the possible effects and roles of recombination between homoeologous chromosomes during the early stages of allopolyploid stabilization. Homoeologous exchanges (HEs) have been reported in young allopolyploids from across the angiosperms. Although all lineages undergo karyotype change via chromosome rearrangements over time, the early generations after allopolyploid formation are predicted to show an accelerated rate of genomic change. HEs can also cause changes in allele dosage, genome-wide methylation patterns, and downstream phenotypes, and can hence be responsible for speciation and genome stabilization events. Additionally, we propose that fixation of duplication-deletion events resulting from HEs could lead to the production of genomes which appear to be a mix of autopolyploid and allopolyploid segments, sometimes termed "segmental allopolyploids." We discuss the implications of these findings for our understanding of the relationship between genome instability in novel polyploids and genome evolution.

Climate Vulnerability Assessment of the Espeletia Complex on Páramo Sky Islands in the Northern Andes

“…Besides range shifts (Chen et al, 2011;Feeley et al, 2011;Donoghue and Edwards, 2014;Kolar et al, 2016;Freeman et al, 2020) and adaptive responses (Hoffmann and Sgro, 2011;Franks and Hoffmann, 2012;Donoghue, 2019;Ørsted et al, 2019), introgression, hybridization (Lafon-Placette et al, 2016), and polyploidization (Han et al, 2019;Mason and Wendel, 2020;Nieto Feliner et al, 2020) which have not been explicitly explored in this study, may also provide innovative (Donoghue and Sanderson, 2015) adaptive sources in plants (Abbott et al, 2013;Marques et al, 2019). The Espeletia complex is known for a high incidence of natural hybrids as told by phenotypic and genetic markers (Rauscher, 2002;Pouchon et al, 2018).…”

A duplicated copy of the meiotic geneZIP4preserves up to 50% pollen viability and grain number in polyploid wheat

“…Plant polyploidisation is often associated with extensive chromosomal rearrangements and changes in gene content and expression (Osborn et al, 2003;Adams & Wendel, 2005;Pelé et al, 2018;Mason & Wendel, 2020). Yet analysis of the recently sequenced hexaploid wheat (Triticum aestivum L.) genome and wheat RNA seq datasets from over 1000 tissues (including meiocytes), did not reveal extensive gene loss or changes in expression between related (homoeologous) chromosomes following polyploidisation (Ramírez-González et al, 2018).…”

The Impact of Polyploidization on the Evolution of Weed Species: Historical Understanding and Current Limitations

“…On a gene level, the multiple copies of genes or chromosomes in allopolyploids are referred to as homoeologs. Not to be confused with homologs, homoeologs are related genes that lie in the different subgenomes of an allopolyploid (Mason and Wendel, 2020). Homologous genes share a common ancestor, while homoeologous genes have the same parental origin (Mable, 2003).…”