| Summary: | NAC transcription factors play an important regulatory role in tomato fruit ripening. We chose a novel perspective to explore the traces left by two paleopolyploidizations in the NAC family using a bioinformatics approach. We found that 85 (<i>S. lycopersicum</i>) and 88 (<i>S. pennellii</i>) members of the NAC family were present in two tomatoes, and most of them were amplified from two paleohexaploidizations. We differentiated NAC family members from the different paleohexaploidizations and found that the SWGT-derived <i>NAC</i> genes had more rearrangement events, so it was different from the DWGT-derived <i>NAC</i> genes in terms of physicochemical properties, phylogeny, and gene location. The results of selection pressure show that DWGT-derived <i>NAC</i> genes tended to be positively selected in <i>S. lycopersicum</i> and negatively selected in <i>S. pennellii</i>. A comprehensive analysis of paleopolyploidization and expression reveals that DWGT-derived <i>NAC</i> genes tend to promote fruit ripening, and are expressed at the early and middle stages, whereas SWGT-derived <i>NAC</i> genes tend to terminate fruit growth and are expressed at the late stages of fruit ripening. This study obtained <i>NAC</i> genes from different sources that can be used as materials for tomato fruit development, and the method in the study can be extended to the study of other plants.
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