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1. Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species

   https://doi.org/10.1093/molbev/msab094  

   Lim, Chun Shen; Weinstein, Brooke N; Roy, Scott W; Brown, Chris M (March 2021, Molecular Biology and Evolution)

   Ouangraoua, Aida (Ed.)

   Abstract Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron–exon structures, and raising the question as to why these few introns are retained. Here, we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per 1 kb of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome-associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and noncoding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression. 

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2. Genomic analysis in Entamoeba reveals intron gain and unbiased intron loss, transformed splicing signals, and a coevolved snRNA.

   https://doi.org/10.1101/2022.06.08.495308  

   Roy, Scottt William; Bowser, Bradley A (July 2022, bioRxiv)
3. An Alternative Self-Splicing Intron Lifecycle Revealed by Dynamic Intron Turnover in Epichloë Endophyte Mitochondrial Genomes

   https://doi.org/10.1093/molbev/msaf076  

   Chan, Jennie; Truglio, Mauro; Schardl, Christopher L; Cox, Murray P; Young, Carolyn A; Ganley, Austen_R D (April 2025, Molecular Biology and Evolution)

   Townsend, Jeffrey (Ed.)

   Abstract Self-splicing group I and II introns are selfish genetic elements that are widely yet patchily distributed across the tree of life. Their selfish behavior comes from super-Mendelian inheritance behaviors, collectively called “homing”, which allow them to rapidly spread within populations to the specific genomic sites they home into. Observations of self-splicing intron evolutionary dynamics have led to the formulation of an intron “lifecycle” model where, once fixed in a population, the introns lose selection for homing and undergo an extensive period of degradation until their eventual loss. Here, we find that self-splicing introns are common in the mitochondrial genomes of Epichloë species, endophytic fungi that live in symbioses with grasses. However, these introns show substantial intron presence–absence polymorphism, with our analyses suggesting that these result from a combination of vertical intron inheritance coupled with multiple invasion and loss events over the course of Epichloë evolution. Surprisingly, we find little evidence for the extensive intron degradation expected under the existing intron lifecycle model. Instead, these introns in Epichloë appear to be lost soon after fixation, suggesting that Epichloë self-splicing introns have a different lifecycle. However, rapid intron loss alone cannot explain our results, indicating that additional factors, such as the evolution of homing suppressors, also contribute to Epichloë self-splicing intron dynamics. This work shows that self-splicing introns have more diverse evolutionary dynamics than previously appreciated. 

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4. Transposable elements drive intron gain in diverse eukaryotes

   https://doi.org/10.1101/2022.06.06.494994  

   Gozashti, Landen; Roy, Scott William; Thornlow, Bryan; Kramer, Alexander; Ares, Manuel Jr.; Corbett-Detig, Russell (July 2022, bioRxiv)
5. Intron-Based Single Transcript Unit CRISPR Systems for Plant Genome Editing

   https://doi.org/10.1186/s12284-020-0369-8  

   Zhong, Zhaohui; Liu, Shishi; Liu, Xiaopei; Liu, Binglin; Tang, Xu; Ren, Qiurong; Zhou, Jianping; Zheng, Xuelian; Qi, Yiping; Zhang, Yong (December 2020, Rice)