Convergent and/or parallel evolution of RNA-binding proteins in angiosperms after polyploidization

Increasing studies suggest that the biased retention of stress-related transcription factors (TFs) after whole-genome duplications (WGDs) could rewire gene transcriptional networks, facilitating plant adaptation to challenging environments. However, the role of posttranscriptional factors (e.g. RNA-binding proteins, RBPs) following WGDs has been largely ignored. Uncovering thousands of RBPs in 21 representative angiosperm species, we integrate genomic, transcriptomic, regulatomic, and paleotemperature datasets to unravel their evolutionary trajectories and roles in adapting to challenging environments. We reveal functional enrichments of RBP genes in stress responses and identify their convergent retention across diverse angiosperms from independent WGDs, coinciding with global cooling periods. Numerous RBP duplicates derived from WGDs are then identified as cold-induced. A significant overlap of 29 orthogroups between WGD-derived and cold-induced RBP genes across diverse angiosperms highlights a correlation between WGD and cold stress. Notably, we unveil an orthogroup (Glycine-rich RNA-binding Proteins 7/8, GRP7/8) and relevant TF duplicates (CCA1/LHY, RVE4/8, CBF2/4, etc.), co-retained in different angiosperms post-WGDs. Finally, we illustrate their roles in rewiring circadian and cold-regulatory networks at both transcriptional and posttranscriptional levels during global cooling. Altogether, we underline the adaptive evolution of RBPs in angiosperms after WGDs during global cooling, improving our understanding of plants surviving periods of environmental turmoil.

Chromosome-level genome of putative autohexaploid Actinidia deliciosa provides insights into polyploidisation and evolution

Actinidia ('Mihoutao' in Chinese) includes species with complex ploidy, among which diploid Actinidia chinensis and hexaploid Actinidia deliciosa are economically and nutritionally important fruit crops. Actinidia deliciosa has been proposed to be an autohexaploid (2n = 174) with diploid A. chinensis (2n = 58) as the putative parent. A CCS-based assembly anchored to a high-resolution linkage map provided a chromosome-resolved genome for hexaploid A. deliciosa yielded a 3.91-Gb assembly of 174 pseudochromosomes comprising 29 homologous groups with 6 members each, which contain 39 854 genes with an average of 4.57 alleles per gene. Here we provide evidence that much of the hexaploid genome matches diploid A. chinensis; 95.5% of homologous gene pairs exhibited >90% similarity. However, intragenome and intergenome comparisons of synteny indicate chromosomal changes. Our data, therefore, indicate that if A. deliciosa is an autoploid, chromosomal rearrangement occurred following autohexaploidy. A highly diversified pattern of gene expression and a history of rapid population expansion after polyploidisation likely facilitated the adaptation and niche differentiation of A. deliciosa in nature. The allele-defined hexaploid genome of A. deliciosa provides new genomic resources to accelerate crop improvement and to understand polyploid genome evolution.

Help or hindrance? The evolutionary impact of whole-genome duplication on immunogenetic diversity and parasite load

Whole-genome duplication (WGD) events occur in all kingdoms and have been hypothesized to promote adaptability. WGDs identified in the early history of vertebrates, teleosts, and angiosperms have been linked to the large-scale diversification of these lineages. However, the mechanics and full outcomes of WGD regarding potential evolutionary impacts remain a topic of debate. The Corydoradinae are a diverse subfamily of Neotropical catfishes with over 170 species described and a history of WGDs. They are divided into nine mtDNA lineages, with species coexisting in sympatric-and often mimetic-communities containing representatives of two or more of the nine lineages. Given their similar life histories, coexisting species of Corydoras might be exposed to similar parasite loads and because of their different histories of WGD and genome size they provide a powerful system for investigating the impacts of WGD on immune diversity and function in an animal system. Here, we compared parasite counts and the diversity of the immune-related toll-like receptors (TLR) in two coexisting species of Corydoras catfish (C. maculifer and C. araguaiaensis), one diploid and one putative tetraploid. In the putative tetraploid C. araguaiaensis, we found significantly lower numbers of parasites and significantly higher diversity (measured by both synonymous and nonsynonymous SNP counts) in two TLR genes than in the diploid C. maculifer. These results provide insight into how WGD may impact evolution, in this case by providing greater immunogenetic diversity.