Mary Akinyuwa

SUMMARY: Genome expansion in angiosperms is largely driven by transposable element (TE) proliferation, counteracted by epigenetic silencing. To investigate how TE amplification reshapes silencing landscapes, we compared two closely related, clonally propagating duckweeds, the TE‐rich Wolffia brasiliensis , for which we report a draft genome assembly, and the TE‐poor Spirodela polyrhiza , that share a broadly conserved silencing and methylation machinery. W. brasiliensis displays extensive and recent TE amplification with pervasive TE‐gene interspersion, elevated genome‐wide CG methylation, and high levels of both 22‐ and 24‐nt siRNAs. Systematic cross‐species comparison reveals that per‐element silencing rules are conserved between the two duckweeds: TE length predicting siRNA‐producing capacity, inverted‐repeat‐forming TEs as productive PTGS‐associated loci, 24‐nt siRNA production predicting non‐CG methylation, and intragenic constraint on RdDM‐associated methylation. What differs is the genome‐wide deployment of these rules across dramatically different TE loads and genome architectures: some divergent outcomes, including elevated 24‐nt siRNA abundance and pervasive TE‐wide CG methylation, scale directly with TE content, whereas others: near‐exclusive 22‐nt processing of PTGS substrates, gene proximity‐dependent RdDM at intergenic TEs, and a strong correlation between gene body CG methylation and intragenic TE content that is not detectable in S. polyrhiza ; require additional W. brasiliensis ‐specific contributions. These findings position TEs as central determinants of the epigenetic architecture that emerges from plant genome expansion, and reveal previously underappreciated plasticity in conserved silencing pathways.

Genome expansion in angiosperms is mainly determined by proliferation of transposable elements (TEs) whose activity is counteracted by epigenetic silencing mechanisms. However, the diversity in genome size as well as different composition and specificity of silencing components among species suggest a complex interplay during genome evolution. To investigate this relationship, we compare two closely related, clonally propagating duckweed species: Wolffia brasiliensis with a TE-rich genome and TE-poor Spirodela polyrhiza . Despite a similar and conserved epigenetic toolbox, W. brasiliensis is characterized by extensive TE amplification, pervasive TE-gene interspersion, elevated global CG methylation, and high levels of both 22- and 24-nt siRNAs. Pattern, abundance, and origin of small RNAs reveal plasticity in conserved post-transcriptional silencing (PTGS) pathways as well as selective RNA-directed DNA methylation engagement. Strikingly, intragenic TEs frequently produce siRNAs yet fail to acquire stable non-CG methylation, while their presence correlates strongly with the emergence of gene body CG methylation extending beyond TE sequences. These results indicate that structural consequences of TE expansion - length, configuration, and genomic context - can reshape small RNA deployment and methylation landscapes without major alteration of core silencing pathways composition and expression. These findings in duckweeds highlight the central role of TEs in structuring plant (epi-)genomes and illustrate their role for evolution of genome architecture even in predominantly clonally reproducing plants.

The cotton leafroll dwarf virus (CLDV), an important viral pathogen responsible for substantial losses in cotton crops, has recently emerged in the United States (US). Although CLDV shares similarities with other members of the genus Polerovirus in terms of encoded proteins, their functional characteristics remain largely unexplored. In this study, we expressed and analyzed each protein encoded by CLDV to determine its intracellular localization using fluorescence protein fusion. We also evaluated their potential to induce plant responses, such as the induction of hypersensitive response-like necrosis and the generation of reactive oxygen species. Our findings show that the proteins encoded by CLDV exhibit comparable localization patterns and elicit similar robust plant responses as observed with cognate proteins from other viruses within the genus Polerovirus. This study contributes to our understanding of the functional repertoire of genes carried by Polerovirus members, particularly to CLDV that has recently emerged as a widespread viral pathogen infecting cotton in the US.

The P0 proteins encoded by Cotton leafroll dwarf virus (CLRDV) serve as viral suppressors of RNA silencing (VSR). CLRDV P0 proteins share a VSR-associated F-box-like motif. This study investigated the role of specific amino acid (aa) residues within the F-box-like motif, elucidating their implications for VSR potency, pathogenicity, and intracellular localization. Analysis of various single aa substitution mutants within the F-box-like motif to understand their effect on P0 proteins’ VSR potency revealed that specific mutations significantly affect P0’s ability to suppress RNA silencing, emphasizing the crucial role of the F-box-like motif. Subcellular localization examinations indicated that the P0 proteins associate with the nucleus and endoplasmic reticulum, which may be linked to their VSR function. Also, the induction of hypersensitive response (HR)-like symptoms and the accumulation of reactive oxygen species by P0 proteins was observed, suggesting their role as pathogenicity factors. These results indicated that specific mutations significantly affect the functions of multifaceted P0 proteins, highlighting the F-box-like motif’s crucial role. Our study highlights the importance of further molecular investigations to elucidate how different CLRDV strains manifest various disease symptoms and severity. This is crucial considering the global economic importance of cotton and the potential emergence of more threatening CLRDV isolates.

Cultivated pear consists of several Pyrus species with P. communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully-phased chromosome-scale genome assembly of P. communis cv. ‘d’Anjou’. Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totalling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other, and to the Malus domestica ‘Honeycrisp’ apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of d’Anjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.

Earth’s life may have originated as self-replicating RNA. Some of the simplest current RNA replicators are RNA viruses, defined by linear RNA genomes encoding an RNA-dependent RNA polymerase (RdRP), and subviral agents with single-stranded, circular RNA genomes, such as viroids encoding paired self-cleaving ribozymes. Amongst a massive expansion of candidate viroid and viroid-like elements, we report that fungal pathogens, ambiviruses, are viroid-like elements which undergo rolling circle replication and encode their own viral RdRP, thus they are a distinct hybrid infectious agent. These findings point to a deep evolutionary history between modern RNA viruses and sub-viral elements and offer new perspectives on the evolution of primordial infectious agents, and RNA life. One-Sentence Summary Novel infectious agents resembling self-cleaving viroid-like RNAs whilst encoding a viral RNA-dependent RNA polymerase.