Functional annotation of expressed sequence tags as a tool to understand the molecular mechanism controlling flower bud development in tree peony

Abstract

Tree peony (Paeonia suffruticosaAndrews) is an important medicinal and ornamental plant. In China, its root bark is an important ingredient for traditional Chinese medicine. It is valued as an ornamental plant because its flower shows a wide variation in shape and color. We used flower buds at different developmental stages to construct the first cDNA library for this organism. A total of 2241 raw expressed sequence tags (ESTs) were obtained after unidirectional sequencing. After processing and assembly, they resulted in a total of 1300 unigenes [363 contigs with an average size of 3.5 ESTs (ranging from 2 up to 36) and 937 singletons]. Gene Ontology categories were assigned and further summarized into 13 broad families with biological roles according to similar functional characteristics or cellular roles. A total of 185 single nucleotide polymorphisms were detected for all contigs. We were able to detect open reading frames in the consensus sequences of 1268 unigenes. 97.5% of the ESTs showed significant similarity to sequences present in public databases. One hundred and sixty-seven short sequence repeats were obtained in the whole data set. All the analysis and information will be valuable resources for a better understanding of this important plant and also can be used for functional study in Paeoniaceae.

Transcriptome analysis of tree peony during chilling requirement fulfillment: Assembling, annotation and markers discovering

“…Di-nucleotide repeats were by far the most common SSRs in our ESTs, with tri-nucleotide repeats being present at much smaller frequencies. Only 14 tetra-nucleotide repeats could be detected with a percentage of 0.62% (Table 3), which was coincide with the one reported by Shu in tree peony (Shu et al, 2009). The most frequent SSR motif was TC (340), followed by AG (323), GA (310), and CT (269) in di-nucleotide repeats, and GAA (36) was the most in tri-nucleotide repeats, followed by AGA, CCA and CAT (32).…”

“…3). Our results differed from a recent study of tree peony (Shu et al, 2009). The most abundant category in the analysis of Shu et al was protein synthesis, including ribosomal proteins, translation factors and RNAbinding proteins (Shu et al, 2009).…”

“…Our results differed from a recent study of tree peony (Shu et al, 2009). The most abundant category in the analysis of Shu et al was protein synthesis, including ribosomal proteins, translation factors and RNAbinding proteins (Shu et al, 2009). The most possible reason for the difference was that we did not collect our samples at the same developing stages as in Shu et al The second explanation was that we obtained more raw ESTs (625,342) than they did (2241 raw ESTs).…”

“…Huang et al reported 31 unique genes that might be associated with dormancy release during chilling treatments in a subtractive cDNA library, but most of them were related to structural function (Huang et al, 2008a(Huang et al, , 2008b. Currently only 2204 pieces of EST are found in National Center for Biotechnology Information (NCBI) database, and most of them were recently submitted with a purpose for bud differentiation in tree peony (Shu et al, 2009).…”

Rapid microsatellite development for tree peony and its implications

“…Little genomic information is currently available for this species. In a previous study, we constructed a cDNA library from flower buds and obtained 2,241 ESTs, from which 167 SSRs were derived and a dataset of 185 putative SNPs obtained for breeding based on their high availability and stability [15]. Although more than 200 SSRs have been submitted to public databases [16], the number is inadequate with respect to the 1,500 cultivars of tree peony.…”