Plant Polyploidy: Origin, Evolution, and Its Influence on Crop Domestication

The prevalence and recurrence of polyploidization in plant species make it one of the most important evolutionary events in plants, and as a result, polyploidization is an extensively investigated research field. Due to the rapid development of sequencing technologies, there is increased evidence to support that polyploidization plays an important role in the diversification of plant species, evolution of genes, and the domestication of crops. Here, we reviewed the influence of polyploidization on various aspects of plant evolution, mainly focused on polyploid origin, characteristics, subsequent genome divergence, and its impact on gene function innovation and crop domestication. The occurrence of many independent polyploidization events in plants was found to be tightly associated with the timing of extreme climate events or natural disasters on earth, leading to mass extinction while possibly facilitating increased polyploidization. Following allo-polyploidization, a distinct phenomenon known as sub-genome dominance occurred during sub-genome evolution, which was found to be associated with the methylation of transposons. Extensive gene fractionations(lost) following polyploidization were reported in almost all paleo-polyploids, and the evolutionary fates of multi-copy genes, such as sub-/neo-functionalization, were further proposed to illustrate their underlying mechanisms. Moreover,polyploidization was found to significantly impact species diversification, with subsequent effects on crop domestication and the development of traits with agronomic importance. Based on the progress of plant polyploidization studies, we discussed several main topics that might further improve our understanding of polyploid evolution and that are likely contribute to the application of polyploidization in crop breeding in the near future.

Cultivated hawthorn(Crataegus pinnatifida var.major)genome sheds light on the evolution of Maleae(apple tribe)

Cultivated hawthorn(Crataegus pinnatifida var.major)is an important medicinal and edible plant with a long history of use for health protection in China.Herein,we provide a de novo chromosomelevel genome sequence of the hawthorn cultivar“Qiu Jinxing.”We assembled an 823.41 Mb genome encoding 40571 genes and further anchored the779.24 Mb sequence into 17 pseudo-chromosomes,which account for 94.64%of the assembled genome.Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae(apple tribe)at approximately 35.4 Mya.Notably,genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome.In addition,our results indicated that the Maleae share a unique ancient tetraploidization event;however,no recent independent whole-genome duplication event was specifically detected in hawthorn.The amplification of non-specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome.Furthermore,we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms.We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleopolyploid origin patterns(autopolyploidization or allopolyploidization)of Maleae.Overall,our study provides an improved context for understanding the evolution of Maleae species,and this new highquality reference genome provides a useful resource for the horticultural improvement of hawthorn.