Divergent gene expression levels between diploid and autotetraploid Tolmiea (Saxifragaceae) relative to the total transcriptome, the cell, and biomass

Abstract

O_LIStudies of gene expression and polyploidy are typically restricted to characterizing differences in transcript concentration. Integrating multiple methods of transcript analysis, we document a difference in transcriptome size, and make multiple comparisons of transcript abundance in diploid and autotetraploid Tolmiea.\nC_LIO_LIWe use RNA spike-in standards to identify and correct for differences in transcriptome size, and compare levels of gene expression across multiple scales: per transcriptome, per cell, and per biomass.\nC_LIO_LIIn total, ~17% of all loci were identified as differentially expressed (DEGs) between the diploid and autopolyploid species. A shift in total transcriptome size resulted in only ~58% of the total DEGs being identified as differentially expressed following a per transcriptome normalization. When transcript abundance was normalized per cell, ~82% of the total DEGs were recovered. The discrepancy between per-transcriptome and per-cell recovery of DEGs occurs because per-transcriptome normalizations are concentration-based and therefore blind to differences in transcriptome size.\nC_LIO_LIWhile each normalization enables valid comparisons at biologically relevant scales, a holistic comparison of multiple normalizations provides additional explanatory power not available from any single approach. Notably, autotetraploid loci tend to conserve diploid-like transcript abundance per biomass through increased gene expression per cell, and these loci are enriched for photosynthesis-related functions.\nC_LI