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SRX1705418: Transcriptome of A. spathulata
1 LS454 (454 GS FLX) run: 1.2M spots, 397.8M bases, 267.6Mb downloads

Design: RNA was extracted from leaves, flower buds, and mature flowers. We isolated RNA using either Trizol reagent, RNeasy kits, or a combination of the two methods. In the combined approach, the standard Trizol protocol was followed through the chloroform extraction step at which point 0.53X volumes of 100% ethanol was added to the aqueous phase and the entire RNA/ethanol mixture then applied to an RNeasy column and the Qiagen protocol followed thereafter. Approximately equal amounts of total RNA isolated from each tissue type were pooled prior to EST library preparation. For 454 sequencing , we used modified oligo-dT primers during cDNA synthesis to reduce the length of mononucleotide runs associated with the polyA tail of mRNA. Mononucleotide runs reduce sequence quality and quantity due to excessive light production and crosstalk between neighboring cells. For cDNA synthesis of the 454 libraries, we either used a broken chain short oligo-dT primer or two different modified oligo-dT primers: one to prime the polyA tail of mRNA during first strand cDNA synthesis and another to further break down the stretches of polyA sequence during second strand cDNA synthesis. We then normalized and amplified the cDNA using the TRIMMER-DIRECT cDNA Normalization Kit as above. After normalization, cDNA was sonicated to 500 to 800bp fragments and size-selected to remove small fragments. Then the fragmented ends were polished and ligated with adaptors. The optimal ligation products were selectively amplified and subjected to two rounds of size selection including gel electrophoresis and AMpure SPRI bead purification. Raw reads for each newly sequenced transcriptome were cleaned and assembled into contigs. We used the SnoWhite cleaning pipeline to remove adapters, chimeras, and other possible contaminating sequences from raw reads. The cleaned reads were assembled using MIRA with the recommended settings for Sanger or 454 assemblies. Following MIRA, we finished the transcriptome assemblies with CAP3 using a percent overlap of 94%.
Submitted by: University of Arizona
Study: Paleoploidy in Compositae
show Abstracthide Abstract
Like many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses have found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature. We sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy. We found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia. Our analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from recent linkage maps, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.
SAMN04633243 • SRS1397721 • All experiments • All runs
Name: Acicarpha spathulata
Instrument: 454 GS FLX
Strategy: EST
Selection: size fractionation
Layout: PAIRED
Runs: 1 run, 1.2M spots, 397.8M bases, 267.6Mb
Run# of Spots# of BasesSizePublished


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