Fig. 2

Differentially expressed genes in response to wild alleles of LNK2 and EID1 in each photoperiod separately. A Horizontal bars represent the number of differentially expressed transcripts in each genotype and condition. Vertical bars represent the number of differentially expressed genes in each set, with a set being a combination of comparisons. Only sets with more than 20 genes are shown. B and C Phylogenetic tree with protein sequences from Arabidopsis and tomato for the RVE family (B) and the PRR family (C) of circadian clock genes. Arabidopsis and tomato protein names are highlighted in gray and red respectively. Tomato proteins whose transcripts oscillate during the diel cycle are marked with an orange dot. D Log2 fold change in expression (± standard error) between S. lycopersicum var MoneyMaker (MM) and each of the near isogenic lines in this work. SD and LD stand for short days and long days. Color of the bars indicate the significance of each log2 fold change, with non-significant values in gray, q < 0.05 in blue and q < 0.01 in black