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Am J Bot. 2019 Feb;106(2):280-291. doi: 10.1002/ajb2.1239. Epub 2019 Feb 19.

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

Visger CJ1, Wong GK2,3,4, Zhang Y4,5, Soltis PS6,7,8, Soltis DE6,7,8,9.

Author information

1
Department of Biological Sciences, California State University Sacramento, Sacramento, CA, 95819, USA.
2
Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
3
Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
4
Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
5
Shenzhen Hua Han Gene Co. Ltd., 7F Jian An Shan Hai Building, No. 8000, Shennan Road, Futian District, Shenzhen, 518040, China.
6
Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
7
Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
8
Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.
9
Department of Biology, University of Florida, Gainesville, FL, 32611, USA.

Abstract

PREMISE OF THE STUDY:

Studies of gene expression and polyploidy are typically restricted to characterizing differences in transcript concentration. Using diploid and autotetraploid Tolmiea, we present an integrated approach for cross-ploidy comparisons that account for differences in transcriptome size and cell density and make multiple comparisons of transcript abundance.

METHODS:

We use RNA spike-in standards in concert with cell size and density 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.

KEY RESULTS:

In total, ~17% of all loci were identified as differentially expressed (DEGs) between the diploid and autopolyploid species. The per-transcriptome normalization, the method researchers typically use, captured the fewest DEGs (58% of total DEGs) and failed to detect any DEGs not found by the alternative normalizations. When transcript abundance was normalized per biomass and per cell, ~66% and ~82% of the total DEGs were recovered, respectively. 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.

CONCLUSIONS:

While 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.

KEYWORDS:

Tolmiea ; RNA standards; RNAseq; Saxifragaceae; autopolyploidy; gene expression; polyploidy; transcriptome size

PMID:
30779448
DOI:
10.1002/ajb2.1239

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