10.5061/DRYAD.D63T5
Gates, Daniel J.
University of Nebraska - Lincoln
University of Colorado Boulder
Strickler, Susan R.
Boyce Thompson Institute for Plant Research, Ithaca, USA
Mueller, Lukas A.
Boyce Thompson Institute for Plant Research, Ithaca, USA
Olson, Bradley J. S. C.
Kansas State University
Smith, Stacey D.
University of Colorado Boulder
Data from: Diversification of R2R3-MYB transcription factors in the tomato
family Solanaceae
Dryad
dataset
2016
Iochroma cyaneum
Nicotiana benthamiana
R2R3 MYB
Solanum tuberosum
gene family evolution
2016-07-03T16:26:11Z
2016-07-03T16:26:11Z
en
https://doi.org/10.1007/s00239-016-9750-z
625013 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
MYB transcription factors play an important role in regulating key plant
developmental processes involving defense, cell shape, pigmentation, and
root formation. Within this gene family, sequences containing an R2R3 MYB
domain are the most abundant type and exhibit a wide diversity of
functions. In this study, we identify 559 R2R3 MYB genes using whole
genome data from four species of Solanaceae and reconstruct their
evolutionary relationships. We compare the Solanaceae R2R3 MYBs to the
well-characterized Arabidopsis thaliana sequences to estimate functional
diversity and to identify gains and losses of MYB clades in the
Solanaceae. We identify numerous R2R3 MYBs that do not appear closely
related to Arabidopsis MYBs, and thus may represent clades of genes that
have been lost along the Arabidopsis lineage or gained after the
divergence of Rosid and Asterid lineages. Despite differences in the
distribution of R2R3 MYBs across functional subgroups and species, the
overall size of the R2R3 subfamily has changed relatively little over the
roughly 50 million-year history of Solanaceae. We added our information
regarding R2R3 MYBs in Solanaceae to other data and performed a
meta-analysis to trace the evolution of subfamily size across land plants.
The results reveal many shifts in the number of R2R3 genes, including a 54
% increase along the angiosperm stem lineage. The variation in R2R3
subfamily size across land plants is weakly positively correlated with
genome size and strongly positively correlated with total number of genes.
The retention of such a large number of R2R3 copies over long evolutionary
time periods suggests that they have acquired new functions and been
maintained by selection. Discovering the nature of this functional
diversity will require integrating forward and reverse genetic approaches
on an -omics scale.
DryadTwo amino acid alignments (ClustaX and Mafft), a PAL2NAL translated
nucleotide alignment based upon the ClustalX amino acid alignment and a
nucleotide tree and amino acid (ClustalX alignment) tree.