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We developed a novel method of barcoding amplicon mixtures from polyploid individuals for 454 sequencing.
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De novo genome assemblies of A. halleri and A. lyrata were used for assigning sequencing reads from polyploid individuals to their parental origins (see Supplementary Methods for genome assembly information).
To gain additional insights into the evolution of tumorigenic subpopulations among polyploid cells, we isolated and cultured cells from soft agar colonies derived from polyploid cells [see Figure 7A below].
Was tetraploidy induced by some aspect of the regeneration system, or did the polyploids arise from polyploid cells pre-existing in the explant material?
Freebayes is also able to call variants from polyploid pooled samples.
They originated from polyploid (likely octoploid) North American ancestors and diversified from a single introduction to the Hawaiian Islands [ 13, 14].
Our study provides an optimized analytical pipeline for other researchers attempting to assemble transcriptome data from polyploid plant species.
This can happen when amplifying members of multigene families or any locus from polyploid genomes [ 23, 24].
In addition, PCR-recombination can also be a problem when sequencing nuclear genes, especially from polyploid genomes.
One striking result concerning polyploids is that despite unstable genomes and rapid re-patterning, the addition to the genome of a complete set of chromosomes is remarkably well-tolerated in eukaryotes (and many current species descend from polyploid ancestors).
It has even been proposed that the diploid vertebrate genomes were derived by reduction from polyploids [1].
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