Genome-wide identification and characterization of R2R3MYB family in Solanum lycopersicum

Liu

et al. 2015

IJMS

Plant homeodomain (PHD)-finger proteins were found universally in eukaryotes and known as key players in regulating transcription and chromatin structure. Many PHD-finger proteins have been well studied on structure and function in animals. Whereas, only a few of plant PHD-finger factors had been characterized, and majority of PHD-finger proteins were functionally unclear. In this study, a complete comprehensive analysis of maize PHD family is presented. Sixty-seven PHD-finger genes in maize were identified and further divided into ten groups according to phylogenetic analysis that was supported by motif and intron/exon analysis. These genes were unevenly distributed on ten chromosomes and contained 12 segmental duplication events, suggesting that segmental duplications were the major contributors in expansion of the maize PHD family. The paralogous genes mainly experienced purifying selection with restrictive functional divergence after the duplication events on the basis of the Ka/Ks ratio. Gene digital expression analysis showed that the PHD family had a wide expression profile in maize development. In addition, 15 potential stress response genes were detected by promoter cis-element and expression analysis. Two proteins ZmPHD14 and ZmPHD19 were located in the nucleus. These results provided a solid base for future functional genome study of the PHD-finger family in maize and afforded important clues for characterizing and cloning potentially important candidates in response to abiotic stresses.

Section: Methodsmentioning

confidence: 99%

Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response

Liu

et al. 2015

IJMS

Bioscience, Biotechnology, and Biochemistry

“…In Arabidopsis, three R2R3-MYB genes, AtMYB21, AtMYB24, and AtMYB57, regulate flower opening and stamen elongation downstream of the JA signaling pathway [22,23,39]. To identify the orthologs of these genes in tomato, we performed a similarity analysis of a subset of tomato and Arabidopsis R2R3-MYB genes [40]. We found that only SlMYB21 (Solyc02g067760) belonged to the same clade as AtMYB21/24/57, suggesting that SlMYB21 is a unique ortholog of AtMYB21/24/57 (Figure 3(D)).…”

Section: Expression Of Ja-related Genes During Flower Bud Developmentmentioning

confidence: 99%

Jasmonic acid facilitates flower opening and floral organ development through the upregulated expression of SlMYB21 transcription factor in tomato

Niwa

Suzuki

Takebayashi

et al. 2018

Plants coordinate the timing of flower opening with pollen and gynoecium maturation to achieve successful pollination. However, little is known about how the coordination is executed. We found that flower bud development was paused immediately before flower opening in a jasmonic acid (JA)-insensitive tomato mutant, jai1-1. Phytohormone measurement and RNA analysis in flower buds revealed that newly synthesised JA peaked at two days before flower opening and the expression of a transcription factor gene SlMYB21 delayed in jai1-1. Buds of transgenic tomato plants expressing an artificial repressor, AtMYB24-SRDX, which was expected to impede the function of SlMYB21, aborted flower opening and resembled those of jai1-1. Furthermore, the AtMYB24-SRDX plants produced abnormal pollen grains deficient in germination and pistils that did not support pollen tube elongation. We concluded that JA facilitates the expression of SlMYB21, which coordinates flower opening, pollen maturation, and gynoecium function in tomato.

“…In spite of this knowledge about genome evolution, there are no analyses which explain the physiological and biochemical differences among these genera. In recent years, studies in grape [12] , maize [13] , soybean [14] and tomato [15] have attempted to identify the physiological effects of acquisition, duplication, conservation and deletions of the R2R3MYB family of transcription factors. This family has been associated with the control of secondary metabolites [16] , [17] , [18] , [19] , development of structures [20] , opening and closing of stomata [21] , cold tolerance [22] phosphorous capture [23] , hormone synthesis and cell signaling biotic [24] , [25] and abiotic stress [22] , among others.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and characterization of R2R3MYB family in Rosaceae

2016

Transcription factors R2R3MYB family have been associated with the control of secondary metabolites, development of structures, cold tolerance and response to biotic and abiotic stress, among others. In recent years, genomes of Rosaceae botanical family are available. Although this information has been used to study the karyotype evolution of these species from an ancestral genome, there are no studies that treat the evolution and diversity of gene families present in these species or in the botanical family. Here we present the first comparative study of the R2R3MYB subfamily of transcription factors in three species of Rosaceae family (Malus domestica, Prunus persica and Fragaria vesca). We described 186, 98 and 86 non-redundant gene models for apple, peach and strawberry, respectively. In this research, we analyzed the intron–exon structure and genomic distribution of R2R3MYB families mentioned above. The phylogenetic comparisons revealed putative functions of some R2R3MYB transcription factors. This analysis found 44 functional subgroups, seven of which were unique for Rosaceae. In addition, our results showed a highly collinearity among some genes revealing the existence of conserved gene models between the three species studied. Although some gene models in these species have been validated under several approaches, more research in the Rosaceae family is necessary to determine gene expression patterns in specific tissues and development stages to facilitate understanding of the regulatory and biochemical mechanism in this botanical family.