EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6000 genes from a basal eudicot

Abstract

The Floral Genome Project (FGP) selected California poppy (Eschscholzia californica Cham. ssp. Californica) to help identify new florally-expressed genes related to floral diversity in basal eudicots. A large, non-normalized cDNA library was constructed from premeiotic and meiotic floral buds and sequenced to generate a database of 9,079 high quality Expressed Sequence Tags (ESTs). These sequences clustered into 5,713 unigenes, including 1,414 contigs and 4,299 singletons. Homologs of genes regulating many aspects of flower development were identified, including those for organ identity and development, cell and tissue differentiation, cell cycle control, and secondary metabolism. Over 5% of the transcriptome consisted of homologs to known floral gene families. Most are the first representatives of their respective gene families in basal eudicots and their conservation suggests they are important for floral development and/or function. App. 10% of the transcripts encoded transcription factors and other regulatory genes, including nine genes from the seven major lineages of the important MADS-box family of developmental regulators. Homologs of alkaloid pathway genes were also recovered, providing opportunities to explore adaptive evolution in secondary products. Furthermore, comparison of the poppy ESTs with the Arabidopsis genome provided support for putative Arabidopsis genes that previously lacked annotation. Finally, over 1,800 unique sequences had no observable homology in the public databases. The California poppy EST database and library will help bridge our understanding of flower initiation and development among higher eudicot and monocot model plants and provide new opportunities for comparative analysis of gene families across angiosperm species.

Opium poppy and Madagascar periwinkle: model non‐model systems to investigate alkaloid biosynthesis in plants

“…Further efforts with this plant have yielded a total of 25 000 ESTs from seedlings, stems, roots and elicitor-treated cell cultures (Ziegler et al, 2005(Ziegler et al, , 2006Zulak et al, 2007). A recent floral genome project contributed 11 000 ESTs from Eschscholzia californica (Carlson et al, 2006), and the release of a Coptis japonica database has also been reported Kato et al, 2007). NAPGEN (Natural Products Genomic Research), a consortium of Canadian investigators, has recently established a database of over 400 000 ESTs from a wide variety of plants that accumulate potentially health-related bioactive metabolites.…”

An EST database for Liriodendron tulipifera L. floral buds: the first EST resource for functional and comparative genomics in Liriodendron

“…RNA was extracted from each of the three sets of buds separately, according to the manufacturer's protocol (http:// www.ambion.com/techlib/prot/bp_1911.pdf) for the RNAqueous®-Midi Kit (Ambion), with modifications as per Carlson et al (2006). RNA was precipitated using 0.1 volumes sodium acetate and three volumes of 100% ethanol.…”

“…The amount of mRNA obtained was 32.9 μg, a yield of approximately 12.4 μg of mRNA per gram of bud tissues. cDNA library construction A directional cDNA library, designated Ltu01, was constructed from approximately 7 μg of mRNA using the ZAP-cDNA® Synthesis Kit (Stratagene), according to manufacturer's instructions (http://www.stratagene.com/ manuals/200401.pdf), and following the modifications of Carlson et al (2006). The pBluescript II SK(+/−) phagemid vector form of the library was excised from an aliquot of the lambda vector (into SOLR host cells) before library manipulation for DNA sequencing.…”

“…The Plant Genome Network at Cornell University provided automated processing, quality control, data archiving, unigene assembly, and library statistics as described in Carlson et al (2006). The resulting EST database and unigene assemblies can be accessed at http://pgn.cornell.…”

Mining expressed sequence tags of rapeseed (Brassica napus L.) to predict the drought responsive regulatory network

“…The vector, repetitive, chloroplast, and mitochondrial sequences were removed and the trimmed sequences were excluded from further analysis when they were less than 100 bp or they had greater than 4 % ambiguous bases (Carlson et al 2006;Masoudi-Nejad et al 2006). The remaining high quality ESTs of each library were subsequently clustered and assembled into unigenes (contigs and singletons) using EGassembler with Overlap percent identity cutoff >80 %.…”