Expansion of antisense lncRNA transcriptomes since the loss of RNAi

Antisense long noncoding RNAs (ASlncRNAs) have been implicated in regulating gene expression in response to physiological cues. However, little is known about ASlncRNA evolutionary dynamics, and what underlies the evolution of their expression. Here, using budding yeast species Saccharomyces and Naumovozyma as models, we show that ASlncRNA repertoires have expanded since the loss of RNAi, in terms of their expression levels, their lengths, and their degree of overlap with coding genes. Furthermore, we show RNAi is inhibitory to ASlncRNA transcriptomes, and that elevation of ASlncRNAs in the presence of RNAi is deleterious to Naumovozyma castellii, a natural host of RNAi. Together, our work suggests that the loss of RNAi had a substantial impact on the genome-wide increase in expression of ASlncRNAs across budding yeast evolution.