With respect to internal fruit morphology, both pla centa and pericarp rapidly expanded from 416 dpp. The rate and amount of expansion was very similar for both tissues. The mesocarp was initially green at 0 and 4 dpp, but became progressively lighter with age. Increase in mesocarp cell size is accompanied bv increased vacuolization between 4 and 12 dpp. The placenta tissue became gelatinous between 8 and 12 dpp and hardening of seed coats occurred between 12 and 16 dpp. 454 pyrosequencing data 454 pyrosequencing analysis of cDNA libraries prepared from pericarp RNA samples of fruit harvested 0, 4, 8, 12, and 16 days post pollination provided 1. 13 million reads. The resulting data were assembled into 27,859 contigs with a mean length of 834 base pairs.
All transcripts were mapped to the assembled cucumber genome of Huang et al. although in some cases more than one transcript mapped to the same location. The number of the reads per contig ranged from 2 to more than order OSI-027 14,000 with a mean of 67 reads per contig and median of 7 readscon tig. Assembed contig length increased steadily with the number of ESTscontig, until approximately 30 reads contig where it leveled off with an average length of ap proximately 1400 bp. Simi larly, frequency of identification of homologs in Arabidopsis increased with number of ESTscontig, leveling off at approximately 90% with approximately 30 readscontig. Gene ontology assignment to those contigs with putative homologs in Arabidopsis showed a similar dis tribution of gene functions as are present in the full Ara bidopsis genome, suggesting broad represen tation of the genome.
Ap proximately half of the contigs with 30 reads but without homologs in Arabidopsis had putative homologs in other species. The final portion, approximately 5% of the Nutlin-3b ic50 total, either did not have any identified homologs in the current NCBI nr database, or only had putative homologs in cucurbit species, suggesting that these transcripts may be unique to cucumber or cucur bits relative to the plant species sequenced to date. These potentially cucurbit unique transcripts included 91 very highly expressed contigs, represented by at least 100 ESTs. Eighteen had putative functional assignments, eight of which were known cu curbit specific phloem related proteins, such as phloem lectins and phloem proteins. Changes in transcript abundance during early fruit growth Based on the observed relationship between ESTscontig, contig length, and putative homologs in Arabidopsis. subsequent bioinformatic analyses were performed on contigs represented by at least 30 ESTs. The distribution of contigs represented by at least 30 ESTs that did not have putative homologs outside of cucurbit species was not evenly distributed across fruit age.