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SRX3746796: Genome duplication in Caryophyllales
1 ILLUMINA (Illumina HiSeq 2000) run: 28M spots, 5.7G bases, 3.3Gb downloads

Design: 6/11/2014 YY TruSeq mRNA stranded
Submitted by: University of Michigan, Ann Arbor
Study: Stranded transcriptome sequencing from 43 species across the plant order Caryophyllales
show Abstracthide Abstract
• Studies of the macroevolutionary legacy of paleopolyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications.• We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 44 were newly generated for this study, representing one of the densest sampled genomic-scale datasets yet available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped phylogenetic distribution of paleopolyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for paleo-allopolyploidy.• We identified twenty-six paleopolyploidy events distributed throughout Caryophyllales, and using novel techniques inferred two to be paleo-allopolyploidy.• Through dense phylogenomic sampling, we show the propensity of paleo-polyploidy in the clade Caryophyllales. We also provide the first method for utilizing transcriptome data to detect paleo-allopolyploidy, which is important as it may have different macro-evolutionary implications compared to paleo-autopolyploidy.
SAMN07527217 • SRS3003210 • All experiments • All runs
Name: MJM2585
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Selection: unspecified
Layout: PAIRED
Runs: 1 run, 28M spots, 5.7G bases, 3.3Gb
Run# of Spots# of BasesSizePublished


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