Recursive Paleohexaploidization Shaped the Durian Genome

Abstract

The durian (Durio zibethinus) genome has recently become available, and analysis of this genome reveals two paleopolyploidization events previously inferred as shared with cotton (Gossypium spp.). Here, we reanalyzed the durian genome in comparison with other well-characterized genomes. We found that durian and cotton were actually affected by different polyploidization events: hexaploidization in durian ;19-21 million years ago (mya) and decaploidization in cotton ;13-14 mya. Previous interpretations of shared polyploidization events may have resulted from the elevated evolutionary rates in cotton genes due to the decaploidization and insufficient consideration of the complexity of plant genomes. The decaploidization elevated evolutionary rates of cotton genes by ;64% compared to durian and explained a previous ;4-fold over dating of the event. In contrast, the hexaploidization in durian did not prominently elevate gene evolutionary rates, likely due to its long generation time. Moreover, divergent evolutionary rates probably explain 98.4% of reconstructed phylogenetic trees of homologous genes being incongruent with expected topology. The findings provide further insight into the roles played by polypoidization in the evolution of genomes and genes, and they suggest revisiting existing reconstructed phylogenetic trees. and led the research. J.W. implemented and coordinated the analysis.

Deciphering the high‐quality genome sequence of coriander that causes controversial feelings

“…Ks were estimated using the Nei–Gojobori approach implemented by BioPerl Statistical module (Nei and Gojobori, ). We adopted a kernel function analysis of Ks distribution of colinear homologs within or between different genomes according to our previous reports (Wang et al, ; Wang et al, ). Ks distribution was viewed as a mix of multiple normal distributions.…”

“…We estimated the evolutionary rates of ECH‐produced duplicated genes, corrected according to our report (Wang et al, ). The maximum likelihood estimate µ from inferred Ks means of ECH‐produced duplicated genes was aligned to have the same value of those of grape.…”

Genome-wide identification, phylogenetic and expressional analysis of the UXS gene family in cotton

“…These duplicated genes provide enormous opportunities for biological innovation [37][38][39]. It has been more and more evident that whole-genome duplications have contributed to the origination, fast divergence [40], establishment of major plant taxa [41,42], such as seed and flowering plants [43], and furthermore the subsets of the latter monocots and dicots [44][45][46][47].…”

Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology

“…(Jaillon et al, 2007;Jiao et al, 2011;Wang et al, 2017). Cotton was affected by a decaploidization event, likely shared with the other Gossypium relatives, but not the non-Gossypium Malvaceae plants, such as durian and cacao (Wang et al, 2016(Wang et al, , 2019. This means that, if no gene loss had occurred, a grape gene would have one cacao ortholog and five orthologs in collinear positions in Gossypium raimondii (DD).…”

“…Using grape orthologs as a reference, the comparison of cacao and cotton genes showed that cotton genes evolved 19 and 15% faster at synonymous and non-synonymous substitution sites than their cacao homologs, respectively. Cacao was used to assess the difference in evolutionary rates between durian and cotton, indicating that after division from cacao, cotton evolves about 64% faster than durian (Wang et al, 2019). The difference between cotton paralogs is greater than the difference between them and cacao orthologs due to the increased rate of cotton evolution.…”