We also found that some phototransduction genes co-duplicate with developmental genes.
Determination of sTREM-1 was performed in duplicate by a developmental enzyme-linked immunoabsorbent assay according to the instructions of the manufacturer (R&D Inc, Minneapolis, USA).
Variation in anthocyanin profile and in transcriptional level of duplicate genes among developmental stages and cultivars was studied using a complete randomized design, and tested for significance using ANOVA run by COSTAT statistical package (CoHort Software, Monterey, CA, USA).
Although a few studies observe distinct expression profiles of duplicates during the developmental time scale (Bassham et al, 2008; Kleinjan et al, 2008), the role of duplicated genes in the temporal organization of the cell remains unclear (Gu et al, 2002; Wagner, 2002).
If the mechanisms for symbiotic partnerships were present early during the diversification of the rosid I clade, perhaps through a modification of the infection thread symbioses of the ancient plant-arbuscular mycorrhizal symbiosis [as suggested by 20], then polyploidy early in the legumes may have provided the gene duplicates for further developmental specializations leading to the nodule.
To better visualize the reciprocal expression patterns of gene duplicates across different developmental stages, organ types, and cell types, we also generated graphs that contain the expression profiles between duplicated gene pairs (supplementary figs. S1 and S2, Supplementary Material online).
Similar patterns of heterogeneity in amino acid substitutions or differential selection were also observed by Dermitzakis and Clark [ 83] between duplicates of several developmental gene families (e.g., Notch, Bmp and Hox9) in mouse and human.
Full-genome zebrafish expression microarrays representing 37,157 unique zebrafish genes were used to measure global transcript levels under control and hypoxia exposure (0.3% oxygen for 2 hr) in duplicate at the two developmental stages.
In fact, among the 15,979 CpGi regions annotated in UCSC mm8 freeze, a total of 5,523 (34.6%) were partially or entirely methylated in one or more of the 24 samples analyzed in this study (4 tissues each with duplicated samples for 3 developmental stages; data not shown).
