Genome-wide annotation, tissue specific expression, and temporal expression profiling of transcription factors revealed candidate components of circadian clock in pineapple genome

Circadian clocks provide fitness advantage by coordinating internal metabolic processes and fine-tuning physiological events to external cyclic environments. Core clock components exhibit rhythmic changes in gene expression over a 24 hour period, and many of them are transcription factors (TFs) and transcription coregulators (TCs). In this study, we annotated TF/TCs in pineapple genome, and analyzed their tissue-specific and temporal expression pattern. We identified 1,398 TFs from 67 TF families and 80 TCs from 20 TC families. Nine TF families and two TC families were most abundant, accounting for approximately 50% of TF/TCs. Grouping of TF/TCs based on their combinatorial expression in leaf, flower, root, and fruit identified 581 TF/TCs upregulated in only one tissue, and 193 TF/TCs co-upregulated in more than one tissue. Majority of the genes in the latter group were co-upregulated in both leaf and flower, or in the root and fruit. Members 14 TF families and 1 TC family were significantly upregulated in only one tissue, and only one TF family was significantly upregulated in two tissues. Temporal expression profiles of pineapple TF/TCs in the green leaf tip and white leaf base tissues revealed diel peak in the expression of 547 TFs and 36 TCs. A total of 158 TF/TCs were cycling only in the white leaf base, 251 were cycling only in the green leaf tip, and 174 were cycling in both tissues. We identified a set of 66 TF/TCs whose expression was phase-locked between the green and white tissue, and this set was enriched in homologs of known Arabidopsis circadian system components. Our results suggest that phase-locked TF/TCs are prospective circadian system components, and their functional characterization may be instrumental in understanding the regulation of CAM photosynthesis in pineapple.