This observation is consistent with the high level of DNA replication occurring in young, dividing cells. Similarly, ribosomal protein genes were among the most highly represented transcripts at 04 dpp but minimally present in the 8 or 1216 dpp ages. The 1216 dpp group was marked by numerous abiotic stress related genes. Strikingly, genes with unknown function or without Arabidopsis homologs, dominated the group at 8 dpp, accounting for more than half of the contigs. The exponential growth stage of tomato also was asso ciated with a larger proportion of ESTs with unknown function relative to other ages. Fewer genes with un known function or without Arabidopsis homologs oc curred in the 1216 dpp group and only 1 member of the 0 4dpp group had no assigned putative function or was without a homolog in Arabidopsis.
To identify less highly represented genes that were strongly enriched at a specific age group, contigs were normalized for portion of reads observed at different time points. If transcription pop over to this website levels were constant during development, 20% of the transcript reads would be observed at each of the five sample ages. Overall distribution of portion of transcripts observed at a given age followed this expectation for the transcriptome set, with a mean value of 41. 05%, 19. 77%, and 39. 18%, re spectively for 04, 8, and 1216dpp age groups. The tails of the distribution were examined for genes for which transcript levels were strongly enriched in a specific age group. This resulted in three non overlapping sets of genes. There also was minimal overlap with the genes listed in Table 2.
The genes listed in Table 2 had an average of 862 ESTscontig whereas the mean number of ESTscon tig for the genes identified in this manner was 166. As was seen for the most highly represented group of genes, there was uneven distribution a fantastic read of genes without homo logs in Arabidopsis or with unknown function. those accounted for 18. 3% for 04 dpp enriched transcripts, but for 34. 1% and 33. 8% for 8dpp and 1216 dpp enriched transcripts, respectively. Fruit setpre exponential growth Functional enrichment analysis of those transcripts with age group enriched transcript levels indicated that the 04 dpp age group had significantly increased representation of genes associated with cell organization and biogenesis, and DNA or RNA metabolism, that subsided with age.
In addition to histone genes, which were also among the most highly abundant transcripts for this age group, numerous putative cell cycle genes, cyclin and cyclin dependent kinase related gene family members, exhibited greater than 90% of transcript reads at 04 dpp. Extensive protein interaction and gene expression data from Arabi dopsis have allowed for the development of a picture of the cyclin interactome, including characterization of com plexes associated with different cell phases.