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

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 one kbp 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 non-coding 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.

Intron losses and gains in the nematodes

“…S1) and obtained the value of 10.22 introns/kbp for the last common nematode ancestor. It was slightly higher than animal ancestor (8.8 introns/kbp) [ 21 ] and close to modern intron-rich nematode species. The model species in Caenorhabditis (from 3.31 to 3.65) have evolved to nearly 1/3 of the ancestral intron density, while intron-poor species in Strongyloididae have less than 1/10 of ancestral intron density.…”

“…The previous studies have shown that the model fit was significantly impacted by variations in loss rate across intron sites [ 5 ]. Moreover, inaccurate prediction of intron loss rate could lead to underestimating intron density of eukaryotic ancestors [ 12 , 21 ]. In this study, intron loss and gain rates were optimized in MALIN using maximum likelihood with constant rate model and rate-variation model and starting from the standard null model, running 1000 optimization rounds (likelihood convergence threshold = 0.001).…”

“…A large-scale comparative analysis showed that the ancestors of all major eukaryotic groups and the last eukaryotic common ancestor all have intron-rich genomes, with the intron densities ranging from 53 to 74% of that in the human genome [ 5 ]. Together with this one, many studies indicate that recurrent intron losses dominated the evolution of eukaryotic genes, with a few episodes of substantial gains [ 6 – 21 ].…”

The International Space Station Environment Triggers Molecular Responses in Aspergillus niger

“…Future studies should be warranted to investigate whether A. niger JSC-093350089 strain’s response to the ISS environment changes with consecutive exposures to the ISS environment when compared to the original ISS isolate. Finally, it has been previously reported that in Aspergillus genome intragenic regions contain high-level developmental and metabolic transcriptional regulators ( Noble and Andrianopoulos, 2013 ; Lim et al, 2021 ). Therefore, the high occurrence of SNPs and INDELS in the intergenic regions may contribute to developing the space environment-induced phenotype in A. niger JSC-093350089.…”

Molecular Mechanisms of Fungal Signaling

“…After the latter dissociates, all snRNPs can be recycled for additional rounds of splicing [102] Even though AS is widely accepted for increasing transcriptome and proteome diversity in higher eukaryotes, a comprehensive understanding of the molecular mechanisms in fungi and its putative downstream functional effects in signaling is mainly unexplored [110] [111]. The fungal kingdom is a species-rich group of organisms with genome sizes ranging from 10 to 90 Mb [112] [113] [114]. According to the most recent studies, Ascomycota, Basidiomycota, and Deuteromycota have a higher incidence of AS than previously thought [115] Interestingly, most genes encoding proteins of nonpathogenic fungi, such as Saccharomyces cerevisiae and Candida albicans, have a simple gene structure with only one intron, whereas genes of pathogenic fungi, such as Cryptococcus neoformans, contain multiple introns [127] [119] [128] [129].…”