Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species. However, the molecular mechanisms that govern HEs are not well understood. Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence analyses. In total, 37 HEs were identified and HE junctions were mapped precisely. HEs exhibit typical patterns of homologous recombination hotspots, being biased toward low-copy, subtelomeric regions of chromosome arms and showing association with known recombination hotspot motifs. But, strikingly, while homologous recombination preferentially takes place upstream and downstream of coding regions, HEs are highly enriched within gene bodies, giving rise to novel recombinant transcripts, which in turn are predicted to generate new protein fusion variants. To test whether this is a widespread phenomenon, a dataset of high-resolution HE junctions was analyzed for allopolyploid Brassica , rice, Arabidopsis suecica , banana, and peanut. Intragenic recombination and formation of chimeric genes was detected in HEs of all species and was prominent in most of them. HE thus provides a mechanism for evolutionary novelty in transcript and protein sequences in nascent allopolyploids.

Introduction: The 90-kDa heat shock protein (HSP90) acts as an essential molecular chaperone, involving plantresilience against diverse abiotic and biotic stresses. Although HSP90 genes have been studied in various plant species,they have not yet been characterized in sweetpotato. Methods: In this study, we performed genome-wide identification, chromosomal localization, phylogenetic analysis, collinearity analysis, and promoter analysis of HSP90 genes in I. batatas and three closely related Ipomoea species. We also investigated gene expression patterns under cold, salt, and PEG-induced drought stresses, constructed protein-protein interaction networks, and determined the subcellular localization and functional role of IbHSP90-2 via heterologous expression in yeast. Results: We identified 10 HSP90 genes in I. batatas , 11 in I. trifida , and 10 each in I.triloba and I.cordatotriloba . Chromosomal localization analysis showed an uneven distribution of HSP90 genes across 15 chromosomes. Phylogenetic and collinearity analyses grouped these genes into four subfamilies,with segmental duplication being the main factor for gene family expansion. Promoter analysis revealed multiple stress-responsive cis-acting elements, indicating that IbHSP90 genes may play a role in stress regulation. Expression analysis revealed that most IbHSP90s were downregulated under cold, salt, and PEG-induced drought stresses. Additionally, we developed a protein -protein interaction network that identified connections with heat shock factors. Experiments on subcellular localization revealed that IbHSP90-2 is present in both the cytoplasm and nucleus. Finally, heterologous expression of IbHSP90-2 in yeast compromised cold resistance. Discussion: This study offers a significant resource for comprehending the evolution of plant HSP90 proteins and supports the genetic enhancement of cold tolerance in sweetpotato.

Pathogenesis‐related Protein 1 (PR1) is a core component of plant innate immunity and plays crucial roles in plant growth, development, and stress response, especially biological stress. However, limited information is available on the PR1 genes in sweet potato and other Ipomoea species. In this study, 33, 50, and 36 PR1 or PR1‐like genes were identified from sweet potato ( I. batatas ), I. trifida, and I. triloba , respectively. Phylogenetic analysis categorized these genes into five groups, reflecting their evolutionary divergence. Cis‐regulatory elements associated with light, hormone, and stress responses. Tissue‐specific expression profiling of I. trifida and I. triloba revealed high expression levels in the flowers and flower‐buds, indicating potential roles in reproductive developmental processes. Stress response analysis showed that most PR1 genes in sweet potato were downregulated under biotic and abiotic treatments, whereas IbPR1‐5 was consistently upregulated across all three stress conditions. Our study provides novel insights into the evolutionary dynamics of PR1 genes across the three Ipomoea genomes and contributes to the future molecular breeding of sweet potato cultivars.