🧬 PubMed RNA Editing Daily Digest

Whole-genome duplication (polyploidy) is a primary driver of plant evolution, yet its impact on the co-evolving mitochondrial genome remains poorly understood. The genus Camellia, with its diverse ploidy levels, offers an ideal system to investigate the resulting structural and molecular evolution of the mitogenome. Comparative mitogenomic analysis across a ploidy gradient (2×, 4×, 6×) revealed that mitochondrial genome size (900 kb) and core gene content remained highly conserved despite significant nuclear genome expansion. However, polyploid species exhibited extensive genomic rearrangements compared to their diploid relatives, indicating substantial structural evolution. Lineage-specific selection was identified in metabolic genes, such as sdh3, suggesting molecular diversification of energy-related pathways. RNA editing patterns were independent of ploidy, maintaining a stable frequency and distribution of editing sites across all species, with Leucine being the most frequent conversion product. Additionally, we identified 17-22 chloroplast-to-mitochondrion DNA transfers (MTPTs), including 3-7 tRNA genes with intact structures. The retention of these fragments varied between lineages, reflecting neutral genomic flux rather than ploidy-dependent functional selection. Our findings demonstrate that while core mitogenomic features are robust to polyploidization, structural flux and lineage-specific molecular shifts are prominent. This study highlights the role of neutral processes and structural turnover in mitogenome evolution following whole-genome duplication, providing insights into cytonuclear coordination in polyploid Camellia.

Phoebe chekiangensis, a nationally protected tree endemic to southeastern China, is of high ecological and economic value but lacks genomic resources for conservation and evolutionary studies. In this study, we assembled its complete organelle genomes, including a circular mitogenome of 864,971 bp and a plastome of 154,460 bp. The mitogenome is enriched in dispersed and simple sequence repeats, consistent with extensive structural rearrangements across Lauraceae, whereas coding regions (over 80 % similarity) remain largely collinear under strong functional constraints. We identified 31 mitochondrial plastid DNA sequences (26,890 bp; 3.11 % of the mitogenome), including five intact plastid protein-coding genes (PCGs) and 14 tRNAs, reflecting frequent plastid-to-mitochondrion transfers that may restore missing tRNAs and enhance genome variability. RNA editing analysis revealed 71 mitochondrial and 13 plastid sites, with cox1 harboring the most, suggesting post-transcriptional modification of respiratory genes that could contribute to stress tolerance. Comparative analyses showed that plastid PCGs evolve faster than mitochondrial PCGs, and atp6 displayed a signal of positive selection, potentially linked to adaptive adjustments in ATP synthase function and respiratory efficiency. Phylogenetic analyses based on organelle genomes confirmed the monophyly of Lauraceae but revealed little topological conflicts, likely reflecting lineage-specific substitution-rate heterogeneity. In conclusion, our results provide new insights into the dynamics of organelle genome evolution and establish valuable genomic resources for the conservation and molecular systematics of P. chekiangensis and Lauraceae.

Genome editing has revolutionized plant biology research

Genome wide CRISPR-based perturbation screens are powerful discovery tools enabling the identification of novel gene dependencies through either gain or loss of function. While genome wide guide RNA (gRNA) libraries have advantages when using enAsCas12a, such as multiplex single gRNAs per gene, they may be subject to similar confounding factors that can affect the interpretation of large genome-wide datasets. Here, we examine the impact of these variables in over twenty enAsCas12a multiple gRNA based perturbation screens performed using Humagne C, Humagne D and Inzolia libraries in human cells, as well as external datasets containing Cas9-based CRISPR library screens, including from DepMap. We demonstrate that the choice of CRISPR library is often the most significant factor that influences genetic perturbation results, outweighing other variables such as either target cell lines or culture media conditions. A potential contributor to this effect is gRNA representation within a given CRISPR library, where lower gRNA representation can lead to variable and more pronounced gene effect scores using either log fold change or Chronos analysis. These effects may be mitigated by using either multiple gRNA constructs per gene, by optimisation of CRISPR library production processes or by targeting with multiple independent gRNA libraries. Importantly, we also propose strategies for addressing gRNA representation bias during CRISPR screen hit prioritisation. CRISPR library gRNA representation dependent bias remains a major challenge in the interpretation of gene essentiality in perturbation screens.

Plastid genomes (plastomes) of land plants are characterized by their architectural and genic content stability. However, fern plastomes exhibit unexpected dynamism, characterized by the presence of mobile protein-coding genes (CDS) - Mobile Open Reading Frames in Fern Organelles (MORFFOs). We investigate the evolutionary dynamics of MORFFOs in 30 species of Anemiaceae (Schizaeales), an ancient lineage of ferns, focusing on their transposition, substitution patterns, codon usages, and RNA editing patterns. MORFFOs expand plastome size and occur in diverse intergenic regions, exhibiting dynamic locations, genealogies, and exceptionally high substitution rates compared with canonical plastid CDS. Sliding window and codon usage analyses demonstrate that MORFFOs are under purifying selection but exhibit distinct codon preferences that deviate from those of other plastid CDS, suggesting functional constraints. Phylogenetic incongruence between MORFFOs and other plastid CDS, along with their extraordinary substitution rates and mobility, implies their replication outside plastids. Our findings highlight that MORFFOs are dynamic, potentially selfish genetic elements capable of transcription, translation, and replication independently from plastomes, and fern plastomes might acquire these mobile CDS through frequent horizontal gene transfer and possibly intracellular gene transfer. Los genomas de los plastidios (plastomas) de las plantas terrestres se caracterizan por la estabilidad de su arquitectura y de su contenido génico. Sin embargo, los plastomas de los helechos muestran un dinamismo inesperado, caracterizado por la presencia de genes móviles que codifican proteínas (MORFFOs, por sus siglas en inglés). Nosotros investigamos la dinámica evolutiva de los MORFFOs en 30 especies de Anemia (Anemiaceae), un linaje antiguo de helechos. Centrándonos en su transposición, patrones de sustitución, uso de codones y patrones de edición de ARN. Los MORFFOs aumentan el tamaño del plastoma y se presentan en diversas regiones intergénicas, exhibiendo ubicaciones dinámicas, genealogías y tasas de sustitución excepcionalmente altas en comparación con los genes codificantes de proteínas (CDS) plastídicos canónicos. Los análisis de ‘sliding windows’ y de uso de codones demuestran que los MORFFOs están bajo selección purificadora, pero presentan preferencias de codones distintas, que se desvían de las de otros CDS plastídicos, lo que sugiere restricciones funcionales. La incongruencia filogenética entre los MORFFOs y otros CDS plastídicos, junto con sus extraordinarias tasas de sustitución y movilidad, sugiere su replicación fuera de los plastidios. Nuestros resultados destacan que los MORFFOs son elementos genéticos dinámicos, potencialmente egoístas, capaces de transcripción, traducción y replicación de forma independiente a los plastomas; además, los plastomas de los helechos podrían adquirir estos CDS móviles a través de transferencias horizontales de genes (HGT) frecuentes y, posiblemente, transferencias intracelulares de genes (IGT).