Characterization of YABBY genes and the correlation between their transcript levels and histone modifications in strawberry

YABBY (YAB) is a class of plant-specific transcription factors playing important roles in the growth and development of leaves and leaf-derived organs/tissues. The fleshy fruit of strawberry is developed from the expanded receptacle, a leaf-derived organ. In this study, we have identified six and 25 YAB proteins in the woodland strawberry (Fragaria vesca, 2n=2x=14) and the cultivated strawberry (Fragaria x ananassa, 2n=8x=56), respectively, and performed phylogenetic and structural analyses to characterize the YAB proteins. Transcriptome data demonstrate that FveYAB and FaYAB genes have temporal- and spatial-expression patterns in fruit development and ripening. Particularly, the transcript levels of FveYAB5 and its orthologous genes, FaYAB16 and FaYAB18, are up-regulated during ripening. Chromatin immunoprecipitation (ChIP) experiment reveals that FveYAB5, FaYAB16 and FaYAB18 are enriched in the active mark histone 3 lysine 9/lysine 14 acetylation (H3K9/K14ac) in the mature red fruits. Further, ChIP-seq profiles from the small white stage to the red stage reveal that FveYAB5 is positively correlated with H3K9/K14ac while negatively correlated with histone 3 lysine 27 trimethylation, indicating a role of histone modifications in its transcriptional regulation. On the other hand, our transcriptome data reveal that the transcript levels of some FveYAB genes are responsive to temperature stress, in that FveYAB1, FveYAB2 and FveYAB5 are down-regulated after heat shock, while FveYAB1 and FveYAB5 are up-regulated after cold shock. In general, our work characterizes the YAB family proteins in terms of transcription patterns, association with histone modifications and responsiveness to temperature stress, which provides information for further functional studies.