Genome-wide identification and expression analysis of transcription factors in Solanum lycopersicum

•A silico genomic analysis of TF prediction was performed through the tomato genome•2026 TF genes in the tomato genome totally identified•298 TFs showed that many of these TFs played the roles in the plant's growth and the responses to various stresses.•8 TF genes further analyzed by RT-PCR analysis in different tissues.

Transcription factors (TFs) are essential regulators during gene expression. To better understand TF genes in tomato (Solanum lycopersicum L.), a silico genomic analysis of TF prediction was performed through the tomato genome. A total of 2026 TF genes were identified in the tomato genome, and they account for approximately 5.83% of its estimated total number of genes. These genes can be also classified into 57 families. The largest family is famous for the MYB superfamily and comprises 220 MYB TF genes. Predicted TFs were distributed across all 12 chromosomes with different densities. Chromosome 01 possesses 241 TFs, accounting for the largest number of TFs. According to microarray and expressed sequence tag data, expression patterns of 298 TFs showed that many of these TFs play roles in growth, development, diverse biological processes and responses to various stresses of S. lycopersicum L. Eight TF genes were further analyzed by reverse transcription polymerase chain reaction analysis in different tissues (root, stem, leaf, flower, and fruit). To the best of our knowledge, this study is the first to report genome-wide analysis of tomato TF gene families. This study provides valuable information regarding classification and putative functions of TFs in Solanaceae.