Genome-Wide Identification and Analysis of the MYB Transcription Factor Superfamily in Solanum lycopersicum.
MYB proteins constitute one of the largest transcription factor families in the plant kingdom, members of which perform a variety of functions in plant biological processes. However, there are only very limited reports on the characterization of MYB transcription factors in tomato (Solanum lycopersicum). In our study, a total of 127 MYB genes have been identified in the tomato genome. A complete overview of these MYB genes is presented, including the phylogeny, gene structures, protein motifs, chromosome locations and expression patterns. The 127 SlMYB proteins could be classified into 18 subgroups based on domain similarity and phylogenetic topology. Phylogenetic analysis of SlMYBs along with MYBs from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) indicated 14 subfamilies. Conserved motifs outside the MYB domain may reflect their functional conservation. The identified tomato MYB genes were distributed on 12 chromosomes at various densities but mainly in chromosomes 6 and 10 (12.6% and 11.8%, respectively). Genome-wide segmental and tandem duplications were also found, which may contribute to the expansion of SlMYB genes. RNA-sequencing and microarray data revealed tissue-specific and stress-responsive expression patterns of SlMYB genes. The expression profiles of SlMYB genes in response to salicylic acid (SA) and jasmonic acid methyl ester (MeJA) were also investigated by real-time PCR. Moreover, ethylene-responsive element-binding factor-associated amphiphilic repression (EAR) motifs were found in 24 SlMYB proteins. Collectively, our comprehensive analysis of SlMYB genes will facilitate future functional studies of the tomato MYB gene family and probably other Solanaceae plants.
Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China.
Zhenjun
Z
Li
Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China.
Rihe
R
Peng
Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China.
Yongsheng
Y
Tian
Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China.
Hongjuan
H
Han
Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China.
Jing
J
Xu
Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai 201106, PR China qhyao_saas@163.com.
Quanhong
Q
Yao
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017930:Genes, Reporter; D018745:Genome, Plant / Q000235:genetics*; D018551:Solanum lycopersicum / Q000166:cytology / Q000235:genetics* / Q000378:metabolism; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D014157:Transcription Factors / Q000235:genetics*; D015533:Transcriptional Activation
D010940:Plant Proteins; D014157:Transcription Factors
Duplication; EAR; MYB; Phylogenetic analysis; Tomato; Transcription factor