Horizontal transfer and homologous recombination shaping the landscape of mitochondrial introns
Up to 25% of yeast mitochondrial genome is composed of introns, and most mitochondrial introns are group I introns. The group I introns distribute sporadically within and between species, which have been thought to be derived by homing endonuclease genes (HEGs). Our results suggest that recurrent gene conversion following horizontal transfer could serve as an excellent mechanism facilitate intron gain and loss independent of HEG function. This is exciting data that changes common views on group I intron mobility and dynamics. (Wu et al 2014)
Spliceosomal introns are a key feature of eukaryote genome architecture. However, how the spliceosomal introns spreading across eukaryotic genomes have been obscure. In our study, we demonstrated three crucial stages in the lifecycle of spliceosomal introns, where intron elements can proliferate within the genome, spread horizontally among conspecific strains, and introgress between related species. These processes are very similar to those involving mobile introns and transposable elements, and also consistent with the hypothesis that spliceosomal introns are of a transposon origin. IIHE: intergenic intron homolog elements; ILE: Genic intron homolog. (Wu et al 2017)
Understanding the mechanisms that allow fungi to grow on particular substrates is important for both fungal ecology and applied uses of different feedstocks in industrial processes. We grew the wood-decaying polypore Fomitopsis pinicola on three different wood under various culture conditions. We found that F. pinicola is able to modify both gene expression and RNA editing profiles across different substrate species and culture conditions. Many of the genes involved encode enzymes with known or predicted functions in wood decay. This work provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates. (Wu et al 2018)
Emergence of de novo genes has occurred in many lineages during evolution, but the birth, spread, and function of these genes remains unresolved. Here we have searched for de novo genes from Saccharomyces cerevisiae S288C using rigorous methods, which reduced the effects of bad annotation and genomic gaps on the identification of de novo genes. Through this analysis, we have found 84 new genes originating de novo from previously non-coding regions, and 87% of which are very likely involved in various biological processes. We noticed that 10% and 33% of de novo genes were only expressed and translated under specific conditions, therefore, verification of de novo genes through transcriptome and ribosome profiling, especially from limited expression data, may underestimate the number of bona fide new genes. We further show that SNP/indel mutation, high GC content and DNA shuffling could be involved in the birth of de novo genes, while domestication and natural selection drive the spread and fixation of these genes. Finally, we provide evidence suggesting the possible parallel origin of a new gene. (Wu et al 2018)
Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has
an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). We sequenced the genomes of one
agaricoid (Aga) strain and one secotioid (Sec) strain and performed bulked segregant and RNAseq analysis. On the basis of BSA and RNAseq analysis, the top candidate genes related to fruiting body development spanning 1.5 Mb (4% of the genome) were found, possibly on a single chromosome, although the precise locus that controls the secotioid phenotype is unresolved (Wu et al 2018).