Genome-Wide Analysis of the TIFY Gene Family in Litchi (Litchi chinensis Sonn.): Identification and Expression Profiling

The TIFY family, known as a novel group of transcription factors unique to the plant, plays a number of roles and has been functionally characterized in numerous plant species. However, TIFY proteins remain unexplored in litchi. Here, we identified 14 <i>TIFY</i> genes in litchi, which were unevenly located on 8 of 15 chromosomes. All of the LcTIFY proteins were predicted to be nuclear-localized and were phylogenetically categorized into four subfamilies (TIFY, PPD, ZML, and JAZ). Duplication analysis detected no tandem duplications but identified one segmental duplication event with <i>LcTIFY</i> genes, suggesting that segmental duplication served as the primary driving force for the expansion of <i>LcTIFY</i> genes. Comparative collinear analysis revealed 12, 5, and 27 collinear gene pairs between litchi and <i>Arabidopsis</i>, rice, and apple, respectively, providing valuable clues for understanding the evolution of the <i>LcTIFY</i> genes. RNA-Seq and qRT-PCR analyses indicated tissue-preferential expression patterns among <i>LcTIFY</i> genes. Notably, <i>LcPPD1</i> and <i>LcJAZ5</i> expressions were negatively correlated with anthocyanin accumulation in the 'Feizixiao' variety, except that <i>LcJAZ5</i> displayed a positive correlation under CPPU treatment. In contrast, <i>LcJAZ7</i> expression showed a positive correlation across all treatments, implicating these genes in the regulation of pericarp pigmentation. Collectively, these findings lay the groundwork for future investigations into the functional roles of <i>TIFY</i> genes in litchi and offer valuable genetic resources for elucidating the mechanisms underlying litchi pigmentation, thereby providing fresh perspectives for subsequent research into the molecular mechanisms of color formation in plants.