From The Polyploidy Portal

Contents

Approaches

We are using several approaches to understand the effects of polyploidy on plant function. These approaches are directed toward understanding how polyploidy affects gene expression and genome structure.

Statistical methods

We use methods developed in the Rebecca Doerge laboratory. You can download statistical software from Rebecca's Page.

Gene Expression

We have used custom made DNA microarrays to survey thousands of known genes in single experiments. We have converted to RNA-seq on Illumina platforms. Chromatin regulation is also being studied by parallel sequencing through the ChIP-seq approach.

Genome Structure

Polyploidy may be associated with changes in genome structure that could affect gene expression. We analyze polyploids for DNA rearrangements and for changes in DNA methylation.

The Arabidopsis arenosa genome project

We have received supplemental funding from NSF to sequence the A. arenosa genome. We use Illumina-Solexa sequencing of accession Care-1. In April 2009 we have achieved 20X coverage. We have assembled the genome de novo obtaining contigs whose N50 is 1,100 bases.

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