Phytochrome Interacting Factors (PIFs) in Solanum lycopersicum: Diversity, Evolutionary History and Expression Profiling during Different Developmental Processes.
Although the importance of light for tomato plant yield and edible fruit quality is well known, the PHYTOCHROME INTERACTING FACTORS (PIFs), main components of phytochrome-mediated light signal transduction, have been studied almost exclusively in Arabidopsis thaliana. Here, the diversity, evolution and expression profile of PIF gene subfamily in Solanum lycopersicum was characterized. Eight tomato PIF loci were identified, named SlPIF1a, SlPIF1b, SlPIF3, SlPIF4, SlPIF7a, SlPIF7b, SlPIF8a and SlPIF8b. The duplication of SlPIF1, SlPIF7 and SlPIF8 genes were dated and temporally coincided with the whole-genome triplication event that preceded tomato and potato divergence. Different patterns of mRNA accumulation in response to light treatments were observed during seedling deetiolation, dark-induced senescence, diel cycle and fruit ripening. SlPIF4 showed similar expression profile as that reported for A. thaliana homologs, indicating an evolutionary conserved function of PIF4 clade. A comprehensive analysis of the evolutionary and transcriptional data allowed proposing that duplicated SlPIFs have undergone sub- and neofunctionalization at mRNA level, pinpointing the importance of transcriptional regulation for the maintenance of duplicated genes. Altogether, the results indicate that genome polyploidization and functional divergence have played a major role in diversification of the Solanum PIF gene subfamily.
Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
Daniele
D
Rosado
Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
Giovanna
G
Gramegna
Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
Aline
A
Cruz
Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
Bruno Silvestre
BS
Lira
Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
Luciano
L
Freschi
Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil.
Nathalia
N
de Setta
Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
Magdalena
http://orcid.org/0000-0003-3650-772X
M
Rossi
D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics*; D003624:Darkness; D019143:Evolution, Molecular; D005638:Fruit / Q000254:growth & development / Q000528:radiation effects; D018507:Gene Expression Regulation, Developmental / Q000528:radiation effects; D056426:Genetic Loci / Q000235:genetics; D014644:Genetic Variation; D018551:Solanum lycopersicum / Q000235:genetics* / Q000254:growth & development* / Q000528:radiation effects; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*
D051792:Basic Helix-Loop-Helix Proteins; D010940:Plant Proteins