Background Polyploidy, especially allopolyploidy, which entails merging divergent genomes via hybridization and whole-genome duplication (WGD), is a major route to speciation in plants. The duplication among the parental genomes (subgenomes) often leads to one subgenome becoming dominant over the other(s), resulting in subgenome asymmetry in gene content and expression. Polyploid wheats are allopolyploids with most genes present in two (tetraploid) or three (hexaploid) functional copies, which commonly show subgenome expression asymmetry. It is unknown whether a similar subgenome asymmetry exists during translation. We aim to address this key biological question and explore the major contributing factors to subgenome translation asymmetry. Results Here, we obtain the first tetraploid wheat translatome and reveal that subgenome expression asymmetry exists at the translational level. We further perform in vivo RNA structure profiling to obtain the wheat RNA structure landscape and find that mRNA structure has a strong impact on translation, independent of GC content. We discover a previously uncharacterized contribution of RNA structure in subgenome translation asymmetry. We identify 3564 single-nucleotide variations (SNVs) across the transcriptomes between the two tetraploid wheat subgenomes, which induce large RNA structure disparities. These SNVs are highly conserved within durum wheat cultivars but are divergent in both domesticated and wild emmer wheat. Conclusions We successfully determine both the translatome and in vivo RNA structurome in tetraploid wheat. We reveal that RNA structure serves as an important modulator of translational subgenome expression asymmetry in polyploids. Our work provides a new perspective for molecular breeding of major polyploid crops.

Cytonuclear coordination between biparental nuclear genomes and uniparental cytoplasmic organellar genomes in plants is often resolved by genetic and transcriptional cytonuclear responses. Whether this mechanism also acts in allopolyploid members of other kingdoms is not clear. Additionally, cytonuclear coordination of interleaved allopolyploid cells/individuals within the same population is underexplored. The yeast Saccharomyces pastorianus provides the opportunity to explore cytonuclear coevolution during different growth stages and from novel dimensions. Using S. pastorianus cells from multiple growth stages in the same environment, we show that nuclear mitochondria-targeted (NMT) genes have undergone both asymmetric gene conversion and growth stage-specific biased expression favoring genes from the mitochondrial genome donor (S. eubayanus). Our results suggest that cytonuclear coordination in allopolyploid lager yeast species entails an orchestrated and compensatory genetic and transcriptional evolutionary regulatory shift. The common as well as unique properties of cytonuclear coordination underlying allopolyploidy between unicellular yeasts and higher plants offers novel insights into mechanisms of cytonuclear evolution associated with allopolyploid speciation.

Prophages are temperate phages integrated into the host bacterial genome. They play an important role in the adaptation and the pathogenicity of bacteria, especially pathogenic bacteria. In this review, we described the distribution of prophages in different hosts and different environments, and focused on the significance of prophages. At the singlecell level, prophages can help the host adapt to harsh external environments by directly carrying virulence genes, encoding regulatory factors and activating lysogeny. At the population level, prophages can influence the overall evolutionary direction and ecological function of the host bacterial community. This review will help us understand the important role of prophages as unique organisms in individual bacteria and microbial populations.

The continually growing human population creates a concomitantly increasing demand for nutritious crops with high yields. Advances in high throughput sequencing technologies have revealed the genetic architecture of major crops. This includes extensive information enabling comprehensive genetic markers for breeding selection, new gene discoveries, and novel gene regulatory strategies for crop editing. RNA structure is an important type of genetic feature, essential for post-transcriptional regulation of gene expression. Here, we summarize recent advances in genome-wide RNA structure studies in crops and review the associated RNA structure-mediated regulation of gene expression. We also discuss the functional importance of those single nucleotide variations that induce large RNA structure disparities. Lastly, we discuss the potential role of RNA structure in crop molecular breeding.