Journal of Molecular Evolution

, Volume 83, Issue 1–2, pp 26–37 | Cite as

Diversification of R2R3-MYB Transcription Factors in the Tomato Family Solanaceae

  • Daniel J. Gates
  • Susan R. Strickler
  • Lukas A. Mueller
  • Bradley J. S. C. Olson
  • Stacey D. Smith
Original Article


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.


Genome Size Gene Subfamily Diversification Rate R2R3 MYBs Mate Pair Library 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors would like to thank E. Braun for advice regarding alignments and using HMMer and J. Storz for providing useful references. We would also like to thank two anonymous reviewers for providing helpful feedback.

Supplementary material

239_2016_9750_MOESM1_ESM.jpg (4.8 mb)
Fig S1 Phylogeny of R2R3 MYB genes from Solanaceae with Arabidopsis sequences. ML tree based upon a DNA alignment with all Solanaceae sequences and bootstrap scores of > 70% represented by filled in circles. Subgroups are identified to the right of delimited clades. Sequences beginning with “Solyc” are from Solanum lycopersicum, those from S. tuberosum begin with “DMT”, sequences from Nicotiana benthamiana begin with “Nb”, sequences from Iochroma cyaneum begin with “g”, and sequences from Arabidopsis thaliana begin with “At”. For Nicotiana and Solanum the numbers follow the unique identifier given by Supplementary material 1 (JPEG 4916 kb)
239_2016_9750_MOESM2_ESM.jpg (4.8 mb)
Fig S2 Amino acid phylogeny of R2R3 MYB genes from Solanaceae with Arabidopsis sequences. ML tree based upon amino acid alignment with bootstrap scores of > 70% represented by filled in circles. Subgroup identifiers and naming scheme for the different species follows that of S1 Fig. Supplementary material 2 (JPEG 4916 kb)
239_2016_9750_MOESM3_ESM.docx (45 kb)
Table S1 Subgroup names of Solanaceae sequences. Genes with prior functional information are marked by a superscript designation and relevant citations are listed in the footnote. Sequence naming follows S1 Fig. Supplementary material 3 (DOCX 44 kb)


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Daniel J. Gates
    • 1
    • 2
  • Susan R. Strickler
    • 3
  • Lukas A. Mueller
    • 3
  • Bradley J. S. C. Olson
    • 4
  • Stacey D. Smith
    • 2
  1. 1.School of Biological SciencesUniversity of NebraskaLincolnUSA
  2. 2.Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderUSA
  3. 3.Boyce Thompson Institute for Plant ResearchIthacaUSA
  4. 4.Division of MolecularCellular and Developmental Biology, Kansas State UniversityManhattan,USA

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