Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication.

Publisher: BioMed Central Country of Publication: England NLM ID: 100966975 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2148 (Electronic) Linking ISSN: 14712148 NLM ISO Abbreviation: BMC Evol Biol Subsets: MEDLINE

Original Publication: London : BioMed Central, [2001-

Gene Duplication* ; Genome, Plant*; Arabidopsis/*genetics ; Arabidopsis Proteins/*genetics ; Transcription Factors/*genetics; Evolution, Molecular ; Gene Expression Regulation, Plant ; Genes, Duplicate ; Linear Models ; Odds Ratio

Background: Transcription factors (TFs) play a key role in regulating plant development and response to environmental stimuli. While most genes revert to single copy after whole genome duplication (WGD) event, transcription factors are retained at a significantly higher rate. Little is known about how TF duplicates have diverged in their expression and regulation, the answer to which may contribute to a better understanding of the elevated retention rate among TFs.
Results: Here we assessed what features may explain differences in the retention of TF duplicates and other genes using Arabidopsis thaliana as a model. We integrated 34 expression, sequence, and conservation features to build a linear model for predicting the extent of duplicate retention following WGD events among TFs and 19 groups of genes with other functions. We found that TFs was the least well predicted, demonstrating the features of TFs are substantially deviated from duplicate genes in other function groups. Consistent with this, the evolution of TF expression patterns and cis-regulatory cites favors the partitioning of ancestral states among the resulting duplicates: one "ancestral" TF duplicate retains most ancestral expression and cis-regulatory sites, while the "non-ancestral" duplicate is enriched for novel regulatory sites. By modeling the retention of ancestral expression and cis-regulatory states in duplicate pairs using a system of differential equations, we found that TF duplicate pairs in a partitioned state are preferentially maintained.
Conclusions: These TF duplicates with asymmetrically partitioned ancestral states are likely maintained because one copy retains ancestral functions while the other, at least in some cases, acquires novel cis-regulatory sites that may be important for novel, adaptive traits.

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Keywords: Duplicate retention; Expression divergence; cis-regulatory evolution

0 (Arabidopsis Proteins)
0 (Transcription Factors)

Date Created: 20190315 Date Completed: 20190705 Latest Revision: 20200309

20250114

PMC6416927

10.1186/s12862-019-1398-z

30866803